Fluorophores - Integrated DNA Technologies

1 General Information
Phone: 03-5248-3066
Fax: 03-5248-2930
e-mail: oligo@mbl.co.jp

About Integrated DNA Technologies
The Source for Custom DNA and RNA Synthesis
1 General Information
Innovation, Ongoing Research and Development
IDT's Commitment
1

Table of Contents
1 General Information
General Information
1
IDT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Inside Front Cover
How to Order . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Inside Front Cover
Shipping Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Inside Front Cover
About IDT . . . . 1
IDT Advantage 4
2DNA Synthesis and Purification
Custom Oligonucleotide Synthesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Yield Guarantees . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Oligonucleotide Purification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Custom DNA Synthesis in Plates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Preparative and Analytical Services . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
3RNA Synthesis and Purification
Custom RNA Oligonucleotide Synthesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Purification & Yield Guarantees . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
RNA Modifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
RNase Substrates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
4Functional Genomics/Gene Knockdown
Antisense Oligonucleotides . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
RNA Interference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
DNA-Directed RNAi . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
miRNA . . . . . 77
5DNA & RNA Probes for Fluorescence-Based Applications
Dual-Labeled DNA Probes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Dual-Labeled LNA Probes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
Dual-Labeled RNA Probes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
Molecular Beacons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
Phone: 03-5248-3066
Fax: 03-5248-2930
e-mail: oligo@mbl.co.jp
2

Table of Contents
6 Modifications
Phosphorylation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
Attachment Chemistry / Linkers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
Fluorophores . 45
Dark Quenchers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Spacers . . . . . 62
Modified Bases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Phosphorothioate Bonds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
1 General Information
7Molecular Biology Products
RNaseAlert Substrate and Nuclease Detection System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
DNaseAlert Substrate and Nuclease Detection System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
Nuclease-free Buffers and Reagents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
StarFire® Nucleic Acid Labeling System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
ReadyMade Primers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
miRNA Cloning Linker . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
Oligo Length Standards . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
Microarray Products . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
SpotQC . . . . . 80
Oligo Spotting Buffer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
8Custom Services
SciTools (PrimerQuest , mFold & OligoAnalyzer) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
Packaging and Formulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Mass Spectrometry and CE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
Preparative and Analytical Services . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
9Usage, Warranty and Licenses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
10
3

The IDT Advantage
1 General Information
Expanded Quality Control:
Quality Guarantee:
Specifications:
Experienced Technical Support:
Technical Bulletins:
SciTools:
Phone: 03-5248-3066
Fax: 03-5248-2930
e-mail: oligo@mbl.co.jp
4

DNA Synthesis
and Purification
2 DNA Synthesis and Purification
5

Custom DNA Synthesis
Synthesis Scale
Price
2 DNA Synthesis and Purification
25 nmole / Base
100 nmole / Base
250 nmole / Base
1 µmole / Base
10 µmole
Yield Guarantees for Standard Desalted DNA Oligos
Yields (listed for unmodified oligos and will vary with length):
Synthesis Scale Available Lengths Guaranteed Yield
25 nmole 15-60 Bases 3 ODs
100 nmole 10-80 Bases 6 ODs
250 nmole 5-100 Bases 15 ODs
1 µmole 5-100 Bases 45 ODs
µ
Phone: 03-5248-3066
Fax: 03-5248-2930
e-mail: oligo@mbl.co.jp
6

Oligonucleotide Purification
Product PAGE HPLC IE HPLC RNase-Free Dual HPLC Dual PAGE
Pricing HPLC & HPLC
100 nmole
250 nmole
1 µmole
10 µmole
2 DNA Synthesis and Purification
PAGE Purification
HPLC Purification
RNase-Free HPLC Purification
Guaranteed yields for purified, unmodified oligos 20 to 50 bases in length
100 nmole 250 nmole 1 µmole
PAGE Purification 1 OD 2 ODs 10 ODs
HPLC Purification 1 OD 4 ODs 20 ODs
IE-HPLC Purification 1 OD 4 ODs 20 ODs
RNase-Free HPLC Purification 1 OD 4 ODs 20 ODs
Dual HPLC Purification 1 OD 2 ODs 10 ODs
Dual PAGE & HPLC 0.5 OD 1 OD 5 ODs
7

Custom DNA Synthesis in Plates
2 DNA Synthesis and Purification
Synthesis Scale
25-nmole Plate Oligo
100-nmole Plate Oligo
250-nmole Plate Oligo
1-µmole Plate Oligo
Plate Oligo Price
/ Base
/ Base
/ Base
/ Base
Standard Plate Oligo Modifications
Plate Modification Pricing 25nmole 100nmole 250nmole 1µmole
5' Phosphorylation
5' Amino Modifier C6
5' Acrydite
5' I-Linker N/A
5' Biotin
5' 6-FAM N/A
Phone: 03-5248-3066
Fax: 03-5248-2930
e-mail: oligo@mbl.co.jp
8

3 RNA Synthesis and Purification
RNA Synthesis
and Purification
Phone: 03-5248-3066
Fax: 03-5248-2930
e-mail: oligo@mbl.co.jp
10

Custom RNA Synthesis and Purification
Product Pricing 100 nmole 250 nmole 1 µmole
RNA
/ Base / Base / Base
2'-O-Methyl RNA
/ Base / Base / Base
DNA (in Chimeric Oligos) / Base / Base / Base
Locked Nucleic Acids (LNAs)
/ Base / Base / Base
RNase-Free HPLC Purification (See page 7)
3 RNA Synthesis and Purification
Annealing of Complementary Oligos
Length Restrictions:
NO SETUP FEES!
Guaranteed Yields
Yields (listed for unmodified RNA oligos 20-45 bases in length):
Synthesis Standard Desalting RNase-Free HPLC
Scale Guaranteed Yield Guaranteed Yields
100 nmole 6 ODs 1 OD
250 nmole 15 ODs 4 ODs
1 µmole 45 ODs 20 ODs
2'-O-Methyl RNA
11

Custom RNA Synthesis and Purification
Standard RNA Modifications (for other modifications, please inquire.)
Product 5' INTERNAL
3 RNA Synthesis and Purification
2-Aminopurine X X
5-Methyl dC X X
5-Nitroindole X X
Spacer 9 X X
Phosphorylation
X
Amino Modifier C6
X
Biotin
X
C3 Spacer X X
deoxyInosine X X
deoxyUridine X X
dSpacer X X
Acrydite
X
Spacer 18 X X
Amino Modifier C6 dT X X
Uni-Link Amino Modifier X X
Large-Scale RNA Synthesis
RNase Substrates
References:
1. Hypersensitive substrate for
ribonucleases. Kelemen, B.R.,
Klink, T.A., Behlke, M.A., Eubanks,
S.R., Leland, P.A., and Raines, R.T.
Nucleic Acids Res. 27:3696-3701
(1999).
2. Fast, facile, hypersensitive assays
for ribonucleolytic activity. Park, C.,
Kelemen, B.R., Klink, T.A., Sweeney,
R.Y., Behlke, M.A., Eubanks, S.R.,
and Raines, R.T. Methods Enzymol.
341:81-94 (2001).
Phone: 03-5248-3066
Fax: 03-5248-2930
e-mail: oligo@mbl.co.jp
12
Product Pricing Sequences 10 nmoles
rU RNase Substrate 5' 6-FAM -ArUAA-3' TAMRA
rC RNase Substrate 5' 6-FAM -ArCAA-3' TAMRA
rA RNase Substrate 5' 6-FAM -ArAAA-3' TAMRA
rG RNase Substrate 5' 6-FAM -ArGAA-3' TAMRA

Functional Genomics
Antisense
4 Functional Genomincs
RNA Interference
ddRNAi
miRNAs
13

Antisense Oligonucleotides
4 Functional Genomincs
Phone: 03-5248-3066
Fax: 03-5248-2930
e-mail: oligo@mbl.co.jp
14

A n t i s e n s e O l i g o n u c l e o t i d e s
Phosphorothioates and Chimeric Oligos
LNA, 2'-O-Methyl RNA, and 5-Methyl dC
References:
1. Role of RNase H in hybridarrested
translation by antisense
oligonucleotides. Walder, R.Y. and
Walder, J.A. Proc. Natl. Acad. Sci.
USA, 85:5011 (1988).
2. Targeted degradation of
mRNA in Xenopus oocytes and
embryos directed by modified
oligonucleotides: studies of An2 and
cyclin in embryogenesis.
Dagle, J.M., Walder, J.A.and Weeks,
D.L. Nucleic Acids Res., 18:4751
(1990).
3. Antisense inhibition of
gene expression in cells by
oligonucleotides incorporating
locked nucleic acids: effect fo
mRNA target sequence and chimera
design. Braasch, D.A., Liu, Y.,
and Corey, D.R. Nucleic Acids
Research, 30:5160-5167 (2002).
4. Design of antisense oligos
stabilized by locked nucleic acids.
Kurreck, J., Wyszko, E., Clemens,
G., and Erdmann, V.A. Nucleic Acids
Research, 30:1911-1918 (2002).
5. Comparison of different antisense
strategies in mammalian cells using
locked nucleic acids, 2'-O-methyl
RNA, phosphorothioates and small
interfering RNA. Grunweller, A.,
Wyszko, E., Bieber, B., Jahnel, R.,
Erdmann, V.A., and Kurreck, J.
Nucleic Acids Research, 31:3185-
3193(2003).
4 Functional Genomincs
15

Examples of RNase H Active Antisense Oligos:
5' T*C*C*T*G*C*G*A*A*A*T*G*T*C*C*A*T*C*G*T 3' DNA, All PS
5' T*C*C*TGCGAAATGTCCAT*C*G*T 3' DNA, PS/PO chimera
5' mU*mC*mC*mU*mG*C*G*A*A*A*T*G*T*C*C*mA*mU*mC*mG*mU 3' 2'-O-Me/DNA chimera, All PS
5' +T+C+C+T+GC*G*A*A*A*T*G*T*C*C+A+T+C+G+T/3Phos/3' LNA/DNA chimera, PS/PO
chimera, 3'-phos
4 Functional Genomics
* = Phosphorothioate Bonds
mN = 2'-O-Me RNA base
+N = LNA base
Product Pricing 100 nmole 250 nmole 1 µmole
Phosphorothioate Bond / Bond / Bond / Bond
DNA / Base / Base / Base
2'-O-Methyl RNA / Base / Base / Base
5'-Locked Nucleic Acids (LNAs)
Locked Nucleic Acids (LNAs)
5-Methyl dC
5-Methyl dC
5' 6-FAM
3' 6-FAM
HPLC Purification
Na + Salt Exchange
Phosphorothioate Linkage
O
N
NH
5'
N
N
NH2
O
O
NH 2
N
O
OMe
O
P
S -
N
O
O
O
O
O
N
NH
O
P
S -
N
N
NH 2
O
O
Phone: 03-5248-3066
Fax: 03-5248-2930
e-mail: oligo@mbl.co.jp
16
O
O P S -
O
3'

4 Functional Genomincs
17

4 Functional Genomics
Phone: 03-5248-3066
Fax: 03-5248-2930
e-mail: oligo@mbl.co.jp
18

RNA Interference
4 Functional Genomincs
Pathway for RNAi
19

RNA Interference
4 Functional Genomics
References:
1. Gene silencing in mammals by
small interfering RNAs. McManus,
M.T., and Sharp, P.A. Nature
Reviews Genetics, 3:737 (2002).
2. Potent and specific genetic
interference by double-stranded RNA
in Caenorhabditis elegans. Fire, A.,
Xu, S., Montgomery, M.K., Kostas,
S.A., Driver, S.E., and Mello, C.C.
Nature, 391:806-11 (1998).
3. Duplexes of 21-nucleotide RNAs
meditate RNA interference in
cultured mammalian cells. Elbashir,
S.M., Harborth, J., Lendeckel, W.,
Yalcin, A., Weber, K., and Tuschl, T.
Nature, 411:494-98 (2001).
4. Inhibition of SV40 gene
expression by microinjected small
antisense RNA and DNA molecules.
Graessmann, G., Michaels, G., Berg,
B., and Graessmann, A. Nucleic
Acids Res., 19:53 (1991).
5. Functional anatomy of RNAis
for mediating efficient RNAi in
Drosophila melanogaster embryo
lysate. Elbashir, S.M., Martinez,
J., Patkaniowska, A., Lendeckel,
W., and Tuschl, T. EMBO Journal,
20:6877-88 (2001).
6. Structural variations and
stabilizing modifications of synthetic
RNAis in mammalian cells.
Czauderna, F., Fechtner, M., Dames,
S., Aygun, H., Klippel, A., Pronk,
G.J., Giese, K., and Kaufmann,
J. Nucleic Acids Res., 31:2705-16
(2003).
7. RNAi function in RNAi: a
chemical modification analysis.
Chiu, Y.-L., and Rana, T.M. RNA,
9:1034-48 (2003).
8. Synthetic dsRNA dicer substrates
enhance RNAi potency and efficacy.
Kim, D.-H., Behlke, M.A., Rose,
S.D., Chang, M.-S., Choi, S., and
Rossi, J.J. Nature Biotechnology,
Vol 23 (2005).
Chemical Modifications
Phone: 03-5248-3066
Fax: 03-5248-2930
e-mail: oligo@mbl.co.jp
20

Purity and QC
Duplex Yield
Price
10 nmole / Duplex
25 nmole 45,000 / Duplex
100 nmole / Duplex
4 Functional Genomincs
Length Restrictions:
RNAi Modifications
Duplex Yield 5' Phosphorylation 5' 6-FAM 5' Biotin 5' Cy3
10 nmole
25 nmole
100 nmole
IDT is the only company to guarantee purity
with a FREE CE trace on every RNAi oligo!
21

4 Functional Genomics
Phone: 03-5248-3066
Fax: 03-5248-2930
e-mail: oligo@mbl.co.jp
22

4 Functional Genomincs
23

DNA-Directed RNAi
4 Functional Genomics
Phone: 03-5248-3066
Fax: 03-5248-2930
e-mail: oligo@mbl.co.jp
24

DNA-Directed RNA Interference (ddRNAi)
Product Yield Tube Plate
10-nmole ddRNAi Oligo 1 OD / Base / Base
100-nmole ddRNAi Oligo 5 ODs / Base / Base
* Minimum 24 oligos per plate
References:
1. RNA interference in mammalian
cells using siRNAs synthesized with
T7 RNA polymerase. Donze, O., and
Picard, D. Nucleic Acids Res., 30:
e46 (2002).
2. Interferon induction by siRNAs
and ssRNAs synthesized by phage
polymerase. Kim, D.-H., Longo, M.,
Han, Y., Lundberg, P., Cantin, E.,
and Rossi, J.J. Nature Biotechnology,
22:321-325 (2003).
3. Expression of small interfering
RNAs targeted against HIV-1 rev
transcripts in human cells. Lee, N.S.,
Dohjima, T., Bauer, G., Li, H., Li,
M.-J., Ehsani, A., Salvaterra, P.,
and Rossi, J. Nature Biotechnology,
19:500-505 (2002)
4. An approach to genomewide
screens of expressed small
interfering RNAs in mammalian
cells. Zheng, L., Liu, J., Batalov, S.,
Zhou, D., Orth, A., Ding, S., and
Schultz, P.G. Proc. Natl. Acad. Sci.,
USA, 101:135-140(2004).
5. A resource for large-scale
RNA-interference-based screen in
mammals. Paddison, P.J., Silva,
J.M., Conklin, D.S., Schlabach,
M., Li, M., Aruleba, S., Balija, V.,
O'Shaughnessy, A., Gnoj, L., Scobie,
K., Chang, K., Westbrook, T., Cleary,
M., Sachidanandam, R., McCombie,
W.R., Elledge, S.J., and Hannon, G.J.
Nature, 428:427-431(2004).
6. A large-scale RNAi screen
in human cells identifies new
components of the p53 pathway.
Berns, K., Hijmans, E.M.,
Mullenders, J., Brummelkamp,
T.R., Velds, A., Heimerikx, M.,
Kerkhoven, R.M., Madiredjo, M.,
Nijkamp, W., Weigelt, B., Agami,
R., Ge, W., Cavet, G., Linsley, P.S.,
Beigersbergen, R.L., and Bernards,
R. Nature, 428:431-7(2004).
4 Functional Genomincs
25

4 Functional Genomics
DNA for in vitro RNA expression
DNA oligos for cloning into an in vivo
expression vector
Phone: 03-5248-3066
Fax: 03-5248-2930
e-mail: oligo@mbl.co.jp
26

4 Functional Genomincs
27

Phone: 03-5248-3066
Fax: 03-5248-2930
e-mail: oligo@mbl.co.jp
28

Fluorescent DNA and RNA
Probes
5 DNA & RNA Probes for Fluorescence-Based Applications
Hybridization of a Molecular Beacon to its target DNA sequence
29

Donor
Fluorescence
Acceptor
Absorption
Fluorescent DNA and RNA Probes
Wavelengths
5 DNA & RNA Probes for Fluorescence-Based Applications
See pages 40-69 for more
information on fluorescent
dyes.
Technical Note!
ö
Dark Quenchers Provide Superior Performance
Absorbance Range of Dark Quenchers
Absorbance and Emission
maxima may vary slightly with
oligo composition. Listed Ab/
Em Max were measured on a
standardized oligo sequence in
10 mM Tris, 50 mM KCl, 5 mM
MgCl 2 , pH 8.3.
Phone: 03-5248-3066
Fax: 03-5248-2930
e-mail: oligo@mbl.co.jp
30
Emission Maxima for Reporter Dyes
®®®

Dual-Labeled DNA Probes
Reporter: 5' 6-FAM
Quencher Scale Guarantee Price
3' TAMRA 100 nmole 10 nmoles
250 nmole 20 nmoles
1 µmole 40 nmoles
3' Iowa Black FQ 100 nmole 10 nmoles
250 nmole 25 nmoles
1 µmole 50 nmoles
3' Black Hole 100 nmole 10 nmoles
Quencher ® -1 250 nmole 25 nmoles
1 µmole 50 nmoles
3' Black Hole 100 nmole 10 nmoles
Quencher ® -2 250 nmole 25 nmoles
1 µmole 50 nmoles
3' TAMRA NHS Ester 250 nmole 20 nmoles
1 µmole 40 nmoles
Reporter: 5' HEX
Quencher Scale Guarantee Price
3' Iowa Black FQ 100 nmole 10 nmoles
250 nmole 25 nmoles
1 µmole 50 nmoles
5 DNA & RNA Probes for Fluorescence-Based Applications
3' Black Hole 100 nmole 10 nmoles
Quencher ® -1 250 nmole 25 nmoles
1 µmole 50 nmoles
3' Black Hole 100 nmole 10 nmoles
Quencher ® -2 250 nmole 25 nmoles
1 µmole 50 nmoles
3' TAMRA NHS Ester 250 nmole 20 nmoles
1 µmole 40 nmoles
® ®
31

Dual-Labeled DNA Probes
Reporter: 5' TET
Quencher Scale Guarantee Price
3' Iowa Black FQ 100 nmole 10 nmoles
250 nmole 25 nmoles
1 µmole 50 nmoles
3' Black Hole 100 nmole 10 nmoles
Quencher ® -2 250 nmole 25 nmoles
1 µmole 50 nmoles
5 DNA & RNA Probes for Fluorescence-Based Applications
3' TAMRA 100 nmole 10 nmoles
250 nmole 20 nmoles
1 µmole 40 nmoles
3' TAMRA NHS Ester 250 nmole 20 nmoles
1 µmole 40 nmoles
Reporter: 5' Cy3
Quencher Scale Guarantee Price
3' Iowa Black RQ 100 nmole 2 nmoles
250 nmole 8 nmoles
1 µmole 20 nmoles
3' Black Hole 100 nmole 2 nmoles
Quencher ® -2 250 nmole 8 nmoles
1 µmole 20 nmoles
Reporter: 5' Cy5
Quencher Scale Guarantee Price
3' Iowa Black RQ 100 nmole 2 nmoles
250 nmole 8 nmoles
1 µmole 20 nmoles
3' Black Hole 100 nmole 2 nmoles
Quencher ® -2 250 nmole 8 nmoles
1 µmole 20 nmoles
Reporter: 5' CAL Fluor ® Orange 560
Quencher Scale Guarantee Price
3' Iowa Black FQ 100 nmole 10 nmoles
250 nmole 20 nmoles
1 µmole 40 nmoles
Phone: 03-5248-3066
Fax: 03-5248-2930
e-mail: oligo@mbl.co.jp
32
3' Black Hole 100 nmole 10 nmoles
Quencher ® -2 250 nmole 20 nmoles
1 µmole 40 nmoles

Reporter: 5' CAL Fluor ® Red 610
Quencher Scale Guarantee Price
3' Iowa Black RQ 100 nmole 10 nmoles
250 nmole 20 nmoles
1 µmole 40 nmoles
3' Black Hole 100 nmole 10 nmoles
Quencher ® -2 250 nmole 20 nmoles
1 µmole 40 nmoles
Reporter: 5' JOE NHS Ester
Quencher Scale Guarantee Price
3' Iowa Black FQ 250 nmole 8 nmoles
1 µmole 20 nmoles
3' Black Hole 250 nmole 8 nmoles
Quencher ® -1 1 µmole 20 nmoles
3' Black Hole 250 nmole 8 nmoles
Quencher ® -2 1 µmole 20 nmoles
3' TAMRA 250 nmole 8 nmoles
1 µmole 20 nmoles
Reporter: 5' Oregon Green® 488-X NHS Ester
Quencher Scale Guarantee Price
3' Iowa Black FQ 250 nmole 8 nmoles
1 µmole 20 nmoles
5 DNA & RNA Probes for Fluorescence-Based Applications
3' Black Hole 250 nmole 8 nmoles
Quencher ® -1 1 µmole 20 nmoles
3' Black Hole 250 nmole 8 nmoles
Quencher ® -2 1 µmole 20 nmoles
3' TAMRA 250 nmole 8 nmoles
1 µmole 20 nmoles
33

Dual-Labeled DNA Probes
Reporter: 5' Oregon Green® 514 NHS Ester
Quencher Scale Guarantee Price
3' Iowa Black FQ 250 nmole 8 nmoles
1 µmole 20 nmoles
3' Black Hole 250 nmole 8 nmoles
Quencher ® -1 1 µmole 20 nmoles
5 DNA & RNA Probes for Fluorescence-Based Applications
3' Black Hole 250 nmole 8 nmoles
Quencher ® -2 1 µmole 20 nmoles
3' TAMRA 250 nmole 8 nmoles
1 µmole 20 nmoles
Reporter: 5' ROX NHS Ester
Quencher Scale Guarantee Price
3' Iowa Black RQ 250 nmole 8 nmoles
1 µmole 20 nmoles
3' Black Hole 250 nmole 8 nmoles
Quencher ® -2 1 µmole 20 nmoles
Reporter: 5' TAMRA NHS Ester
Quencher Scale Guarantee Price
3' Iowa Black RQ 250 nmole 8 nmoles
1 µmole 20 nmoles
3' Black Hole 250 nmole 8 nmoles
Quencher ® -2 1 µmole 20 nmoles
Reporter: 5' Texas Red®-X NHS Ester
Quencher Scale Guarantee Price
3' Iowa Black RQ 250 nmole 8 nmoles
1 µmole 20 nmoles
3' Black Hole 250 nmole 8 nmoles
Quencher ® -2 1 µmole 20 nmoles
Phone: 03-5248-3066
Fax: 03-5248-2930
e-mail: oligo@mbl.co.jp
34

Quencher: 5' Iowa Black RQ
Reporter Scale Guarantee Price
3' Cy3 100 nmole 2 nmoles
250 nmole 8 nmoles
1 µmole 20 nmoles
3' TAMRA NHS Ester 250 nmole 8 nmoles
1 µmole 20 nmoles
3' Texas Red ® -X 250 nmole 8 nmoles
NHS Ester 1 µmole 20 nmoles
Quencher: 5' Iowa Black FQ
Reporter Scale Guarantee Price
3' 6-FAM 100 nmole 10 nmoles
250 nmole 20 nmoles
1 µmole 40 nmoles
3' Oregon Green ® 250 nmole 8 nmoles
488-X NHS Ester 1 µmole 20 nmoles
3' Oregon Green ® 250 nmole 8 nmoles
514 NHS Ester 1 µmole 20 nmoles
5 DNA & RNA Probes for Fluorescence-Based Applications
35

Dual-Labeled LNA Probes
5 DNA & RNA Probes for Fluorescence-Based Applications
References:
1. Evaluation of the performance of
LNA and MGB probes in 5'-nuclease
assays. Letertre, C., Perelle, S.,
Dilasser, F., Arar, K., and Fach,
P. Molecular and Cellular Probes,
17:307-311 (2003).
2. Real-time genotyping with
oligonucleotide probes containing
locked nucleic acids. Ugozzoli,
L.A., Latorra. D., Pucket, R., Arar,
K., and Hamby, K. Analytical
Biochemistry, 324:143-152 (2004).
3. Locked nucleic acid (LNA) single
nucleotide polymorphism (SNP)
genotype analysis and validation
using real-time PCR. Johnson, M.P.,
Haupt, L.M., and Griffiths, L.R.
Nucleic Acids Res., 32:e55 (2004).
Reporter: 5' 6-FAM
Quencher Scale Guarantee Price
3' Iowa Black FQ 250 nmole 8 nmoles
1 µmole 20 nmoles
3' Black Hole 250 nmole 8 nmoles
Quencher ® -1 1 µmole 20 nmoles
Reporter: 5' Cy3
Quencher Scale Guarantee Price
3' Iowa Black FQ 250 nmole 4 nmoles
1 µmole 10 nmoles
3' Black Hole 250 nmole 4 nmoles
Quencher ® -2 1 µmole 10 nmoles
Reporter: 5' CAL Fluor® 610
Quencher Scale Guarantee Price
3' Iowa Black RQ 250 nmole 8 nmoles
1 µmole 20 nmoles
3' Black Hole 250 nmole 8 nmoles
Quencher ® -2 1 µmole 20 nmoles
Locked Nucleic Acids are
licensed from Exiqon, http://
www.exiqon.com/.
Reporter: 5' Cy5
Quencher Scale Guarantee Price
Phone: 03-5248-3066
Fax: 03-5248-2930
e-mail: oligo@mbl.co.jp
36
3' Iowa Black RQ 250 nmole 4 nmoles
1 µmole 10 nmoles
3' Black Hole 250 nmole 4 nmoles
Quencher ® -2 1 µmole 10 nmoles

Dual-Labeled RNA Probes - Only at IDT!
Reporter: 5' 6-FAM
Quencher Scale Guarantee Price
3' TAMRA 250 nmole 2.5 nmoles
1 µmole 10 nmoles
3' Black Hole 250 nmole 5 nmoles
Quencher ® -1 1 µmole 20 nmoles
Reporter: 5' TET
Quencher Scale Guarantee Price
3' Black Hole 250 nmole 5 nmoles
Quencher ® -1 1 µmole 20 nmoles
Reporter: 5' HEX
Quencher Scale Guarantee Price
3' Black Hole 250 nmole 5 nmoles
Quencher ® -1 1 µmole 20 nmoles
5 DNA & RNA Probes for Fluorescence-Based Applications
Reporter: 5' Cy5
Quencher Scale Guarantee Price
3' Black Hole 250 nmole 1.25 nmoles
Quencher ® -2 1 µmole 5 nmoles
37

Molecular Beacons
Please see our website
at www.idtdna.com for
more possible reporter /
quencher combinations.
5 DNA & RNA Probes for Fluorescence-Based Applications
Technical Note!
The signal-to-noise ratio (STNR)
for each Molecular Beacon is
determined by hybridizing it to
its complementary sequence and
comparing fluorescence to to
background. For FAM -labeled
Molecular Beacons, guaranteed
STNR is >15. For all other dyes,
a STNR of >10 is required to
pass quality control.
References:
1. Thermodynamic basis of the enhanced
specificity of structured DNA probes.
Bonnet et al. Proc Natl Acad Sci USA
96: 6171–6176 (1999).
Reporter: 5' 6-FAM
Quencher Scale Guarantee Price
3' Dabcyl 250 nmole 10 nmoles
1 µmole 40 nmoles
3' Black Hole 250 nmole 10 nmoles
Quencher ® -1 1 µmole 40 nmoles
Reporter: 5' TET
Quencher Scale Guarantee Price
3' Dabcyl 250 nmole 10 nmoles
1 µmole 40 nmoles
3' Black Hole 250 nmole 10 nmoles
Quencher 1 1 µmole 40 nmoles
Reporter: 5' HEX
Quencher Scale Guarantee Price
3' Dabcyl 250 nmole 10 nmoles
1 µmole 40 nmoles
3' Black Hole 250 nmole 10 nmoles
Quencher ® -2 1 µmole 40 nmoles
Reporter: 5' Cy3
Quencher Scale Guarantee Price
3' Black Hole 250 nmole 5 nmoles
Quencher ® -2 1 µmole 20 nmoles
Reporter: 5' Cy5
Quencher Scale Guarantee Price
Phone: 03-5248-3066
Fax: 03-5248-2930
e-mail: oligo@mbl.co.jp
38
3' Black Hole 250 nmole 5 nmoles
Quencher ® - 2 1 µmole 20 nmoles

Modifications
Technical Note!
5' 5' Amino Modifier C6 (phosphoramidite)
Int Internal amino-C6-dT (phosphoramidite)
3' 3' Amino Modifier (CPG)
6 Modifications
39

Phosphorylation
Phosphorylation
MW: 79.9
6 Modifications
SCALE 5' INT. 3'
25 nmole - -
100 nmole -
250 nmole -
1.0 µmole -
Attachment Chemistry / Linkers
Acrydite
MW: 247.2
OH
O P O -
O
3'
SCALE 5' INT. 3'
25 nmole - -
100 nmole - -
250 nmole - -
1.0 µmole - -
O
H
N
O
O P O -
O
3'
Amino Modifiers
Amino Modifier C6
SCALE 5' INT. 3'
25 nmole - -
100 nmole - -
250 nmole - -
1.0 µmole - -
H 2 N
MW: 179.2
O
O P O -
O
3'
e-mail: oligo@mbl.co.jp
40

Attachment Chemistry / Linkers
Amino Modifier C12
MW: 264.3
SCALE 5' INT. 3'
100 nmole - -
H 2 N
O
250 nmole - -
O P O -
1.0 µmole - -
Amino Modifier C6 dT
MW: 458.4
O
3'
6 Modifications
O
O
SCALE 5' INT. 3'
HN
N
H
NH2
100 nmole -
'5
O
O
O
N
250 nmole -
O
1.0 µmole -
O P O -
O
3'
Internal Amino Modifier C6 dT
Amino Modifier
MW: 179.2
SCALE 5' INT. 3'
100 nmole - -
250 nmole - -
'5
O
NH 2
1.0 µmole - -
41

Attachment Chemistry / Linkers
Uni-Link Amino Modifier
MW: 209.2
SCALE 5' INT. 3'
O
5'
100 nmole -
250 nmole -
H 2 N
O
O P O -
6 Modifications
1.0 µmole -
Biotinylation
O
3'
Biotin
3' MW: 437.5
5' MW: 405.4
SCALE 5' INT. 3'
O
25 nmole - -
HN
NH
100 nmole -
250 nmole -
S
H
N
O
Biotin dT *
1.0 µmole -
O
5' Biotin
MW: 684.7
O P O -
O
3'
SCALE 5' INT. 3'
O
HN
NH
100 nmole -
250 nmole -
1.0 µmole -
'5
O
O
O
HN
O
N
O
N
H
H
N
O
S
O
O P O -
O
3'
Internal Biotin dT
e-mail: oligo@mbl.co.jp
42

Attachment Chemistry / Linkers
Biotin-TEG *
MW: 569.6
SCALE 5' INT. 3'
HN
O
NH
100 nmole -
S
H
N
O
O
O
O
O
5'
250 nmole -
O
O
1.0 µmole -
5' Biotin-TEG
Additional purification is only required on 5' Biotin-TEG.
Dual Biotin *
MW: 871.0
O
O P O -
O
3'
6 Modifications
HN
NH
OH
SCALE 5' INT. 3'
S
H
N
100 nmole - -
O
O
O
250 nmole - -
HN
NH
O
P
O
O -
1.0 µmole - -
S
H
N
Reference:
1. Enhanced concatemer cloning-a modification to the SAGE (Serial Analysis of Gene Expression)
technique. Powell, J., Nucleic Acids Research, 26:3445-46 (1998).
O
O
O P O -
PC Biotin
MW: 597.6
O
3'
O
SCALE 5' INT. 3'
HN
NH
O
100 nmole - -
250 nmole - -
S
O
H
N
N
H
NO 2
1.0 µmole - -
O
O P O -
O
3'
* Additional purification required
43

Attachment Chemistry / Linkers
Digoxigenin NHS Ester *
5' MW: 722.9
3' MW: 722.9
O
O
SCALE 5' INT. 3'
OH
CH3
6 Modifications
100 nmole -
250 nmole -
1.0 µmole -
I-Linker
N
H
O
H
N
O
MW: 208.2
O
CH3
OH
SCALE 5' INT. 3'
100 nmole - -
250 nmole - -
1.0 µmole - -
Thiol Modifications
Thiol Modifier C3 S-S
MW: 244.3
SCALE 5' INT. 3'
100 nmole - -
O
250 nmole - -
1.0 µmole - -
'5
S
S
OH
e-mail: oligo@mbl.co.jp
44

Attachment Chemistry / Linkers
Thiol Modifier C6 S-S
MW: 328.4
SCALE 5' INT. 3'
100 nmole - -
HO
S
S
250 nmole - -
1.0 µmole - -
O
O P O -
Fluorophores
Alexa Fluor® Dyes
O
3'
6 Modifications
Alexa Fluor® 488 NHS Ester *
5' MW: 694.6
Int. MW: 973.9
Ab max 492 nm Em max 517 nm 3' MW: 694.6
SCALE 5' INT. 3'
100 nmole
SO 3
- SO 3
-
H 2 N O
NH + 2
250 nmole
1.0 µmole
O
Absorbance and Fluorescence Emission
492 nm 517 nm
400 450 500 550 600 650
Wavelength (nm)
* HPLC purification required
Absorbance
Fluorescence Emission
HN
O
O –
45

Fluorophores
Alexa Fluor® 532 NHS Ester * 5' MW: 787.8
Int. MW: 1067.1
Ab max 527 nm Em max 553 nm 3' MW: 787.8
SCALE 5' INT. 3'
100 nmole
250 nmole
1.0 µmole
H
N
SO 3 H SO 3
-
O H +
N
6 Modifications
Absorbance
Absorbance and Fluorescence Emission
527 nm 553 nm
Fluorescence Emission
HN
O
420 470 520 570 620 670
Wavelength (nm)
5' MW: 1120.5
Int. MW: 1399.7
Ab max 555 nm Em max 571 nm 3' MW: 1120.5
SCALE 5' INT. 3'
100 nmole
SO 3
- SO 3
-
250 nmole
H
N
O
H +
N
1.0 µmole
O
Cl
OH
Absorbance
Absorbance and Fluorescence Emission
555 nm 571 nm
Fluorescence Emission
N
H
H
N
O
S
Cl
Cl
O
435 485 535 585 635 685
Wavelength (nm)
* HPLC purification required
e-mail: oligo@mbl.co.jp
46

Fluorophores
5' MW: 883.9
Int. MW: 1163.2
Ab max 584 nm Em max 616 nm 3' MW: 883.9
SCALE 5' INT. 3'
100 nmole
N O
N +
250 nmole
1.0 µmole
Absorbance
Absorbance and Fluorescence Emission
584 nm 616 nm
Fluorescence Emission
CH 2 SO 3 H
HN
O
O
O –
CH 2 SO 3
-
6 Modifications
475 525 575 625 675 725
Wavelength (nm)
5' MW: 1020.2
Int. MW: 1299.4
Ab max 650 nm Em max 670 nm 3' MW: 1020.2
Absorbance and Fluorescence Emission
SCALE 5' INT. 3'
100 nmole
250 nmole
Absorbance
650 nm 670 nm
Fluorescence Emission
1.0 µmole
530 580 630 680 730 780
Wavelength (nm)
* HPLC purification required
47

Fluorophores
Alexa Fluor® 660 NHS Ester * 5' MW: 940.7
Int. MW: 1219.9
Ab max 661 nm Em max 691 nm 3' MW: 940.7
Absorbance and Fluorescence Emission
6 Modifications
SCALE 5' INT. 3'
100 nmole
250 nmole
1.0 µmole
Absorbance
661 nm 691 nm
500 550 600 650 700 750 800
Wavelength (nm)
Fluorescence Emission
Alexa Fluor® 750 NHS Ester * 5' MW: 1046.1
Int. MW: 1325.3
Ab max 753 nm Em max 775 nm 3' MW: 1046.1
SCALE 5' INT. 3'
100 nmole
250 nmole
1.0 µmole
Absorbance
Absorbance and Fluorescence Emission
753 nm 775 nm
600 650 700 750 800 850
Wavelength (nm)
Fluorescence Emission
* HPLC purification required
e-mail: oligo@mbl.co.jp
48

Fluorophores
Bodipy® Dyes
Bodipy® 630/650-X NHS Ester *
5' MW: 724.6
Int. MW: 1003.8
Ab max 638 nm Em max 653 nm 3' MW: 724.6
SCALE 5' INT. 3'
100 nmole
250 nmole
1.0 µmole
6 Modifications
Absorbance and Fluorescence Emission
638 nm 653 nm
Absorbance
Fluorescence Emission
S
N
F
B - N +
F
HC C
H
O HN
O
HN
O
525 575 625 675 725
Wavelength (nm)
Internal Bodipy® 630/650 NHS Ester
* HPLC purification required
49

Fluorophores
CAL Fluor Dyes
®
®
5' CAL Fluor® Orange 560 *
5' MW: 560.6
Ab max 539nm
Em max 562nm
6 Modifications
Absorbance and Fluorescence Emission
SCALE 5' INT. 3'
539 nm 562 nm
100 nmole - -
250 nmole - -
1.0 µmole - -
5' CAL Fluor® Red 610 *
5' MW: 636.7
Ab max 591nm Em max 611nm
SCALE 5' INT. 3'
591 nm 611 nm
100 nmole - -
250 nmole - -
1.0 µmole - -
Absorbance
Fluorescence Emission
490 510 530 550 570 590 610 630 650
Wavelength (nm)
Absorbance
Absorbance and Fluorescence Emission
540 560 580 600 620 640 660 680 700
Wavelength (nm)
Fluorescence Emission
e-mail: oligo@mbl.co.jp
50

Fluorophores
Cy Dyes
Cy3 * 5' MW: 506.6
Ab max 550 nm Em max 564 nm 3' MW: 644.6
SCALE 5' INT. 3'
100 nmole -
250 nmole -
1.0 µmole -
Absorbance and Fluorescence Emission
550 nm 564 nm
HO
N +
N
O
6 Modifications
Absorbance
Fluorescence Emission
5' Cy3
O P O -
O
3'
440 490 540 590 640
Wavelength (nm)
Cy5 * 5' MW: 532.6
Ab max 648 nm Em max 668 nm 3' MW: 670.7
SCALE 5' INT. 3'
100 nmole -
250 nmole -
1.0 µmole -
N +
N
Absorbance and Fluorescence Emission
648 nm 668 nm
HO
O
O P O -
Absorbance
Fluorescence Emission
5' Cy5
O
3'
525 575 625 675 725
Wavelength (nm)
* HPLC purification required
51

Fluorophores
Cy5.5 * 5' MW: 632.7
Ab max 685 nm Em max 706 nm 3' MW: 770.8
SCALE 5' INT. 3'
100 nmole -
250 nmole -
1.0 µmole -
N +
N
6 Modifications
Absorbance
Absorbance and Fluorescence Emission
685 nm 706 nm
Fluorescence Emission
HO
5' Cy5.5
O
O P O -
O
3'
575 625 675 725 775
Wavelength (nm)
6-FAM (Fluorescein)
5' MW: 537.5
Ab max 495 nm Em max 520 nm 3' MW: 569.5
SCALE 5' INT. 3'
-O
O
O
100 nmole -
250 nmole -
1.0 µmole -
O
O –
O
Absorbance and Fluorescence Emission
HN
495 nm 520 nm
Absorbance
Fluorescence Emission
O
400 450 500 550 600
Wavelength (nm)
O P O -
* HPLC purification required
5' 6-FAM
O
3'
e-mail: oligo@mbl.co.jp
52

Fluorophores
Fluorescein dT * MW: 816.7
Ab max 495 nm
Em max 520 nm
SCALE 5' INT. 3'
100 nmole -
-O
O
O
250 nmole -
1.0 µmole -
Absorbance
Absorbance and Fluorescence Emission
495 nm 520 nm
Fluorescence Emission
'5
O
O
O
O
HN
O P O -
O
3'
O
N
O
N
H
Internal Fluorescein dT
H
N
O
O –
O
6 Modifications
400 490 500 550 600 650
Wavelength (nm)
HEX MW: 744.1
Ab max 538 nm
Em max 555 nm
SCALE 5' INT. 3'
Cl
Cl
100 nmole - -
-O
O
O
250 nmole - -
1.0 µmole - -
Cl
Cl
O –
Cl
O
Absorbance and Fluorescence Emission
O
Cl
538 nm 555 nm
HN
Absorbance
Fluorescence Emission
O
450 500 550 600 650
Wavelength (nm)
O
P
O -
O
3'
* HPLC purification required
53

Fluorophores
JOE NHS Ester *
5' MW: 666.4
Int. MW: 945.7
Ab max 529 nm Em max 555 nm 3' MW: 666.4
SCALE 5' INT. 3'
Cl
Cl
100 nmole
-O
O
O
6 Modifications
250 nmole
1.0 µmole
Absorbance
Absorbance and Fluorescence Emission
529 nm 555 nm
Fluorescence Emission
H 3 CO
H
N
O
O –
O
OCH 3
400 450 500 550 600 650
Wavelength (nm)
Oregon Green Dyes
®®
Oregon Green® 488-X NHS Ester * 5' MW: 686.6
Int. MW: 965.9
Ab max 494 nm Em max 518 nm 3' MW: 686.6
SCALE 5' INT. 3'
100 nmole
-O
O
O
250 nmole
1.0 µmole
Absorbance and Fluorescence Emission
494 nm 518 nm
N
H
O
F
H
N
O –
O
F
Absorbance
Fluorescence Emission
O
400 450 500 550 600
Wavelength (nm)
* HPLC purification required
e-mail: oligo@mbl.co.jp
54

Fluorophores
5' MW: 673.5
Int. MW: 952.8
Ab max 508 nm Em max 528 nm 3' MW: 673.5
SCALE 5' INT. 3'
100 nmole
-O
O
O
250 nmole
F
F
1.0 µmole
F
O –
Absorbance
Absorbance and Fluorescence Emission
508 nm 528 nm
Fluorescence Emission
H
N
O
S
F
F
O
6 Modifications
400 450 500 550 600 650
Wavelength (nm)
Oyster ® Dyes
®
®
®
Oyster® 556 NHS Ester * 5' MW: 871.4
Int. MW: 1150.7
Ab max 561 nm Em max 572 nm 3' MW: 871.4
SCALE 5' INT. 3'
Absorbance and Fluorescence Emission
561 nm 572 nm
100 nmole
250 nmole
1.0 µmole
Absorbance
420 470 520 570 620 670 720
Wavelength (nm)
Fluorescence Emission
* HPLC purification required
55

Fluorophores
5' MW: 917.3
Int. MW: 1196.6
Ab max 647 nm Em max 663 nm 3' MW: 917.3
Absorbance and Fluorescence Emission
SCALE 5' INT. 3'
647 nm 663 nm
6 Modifications
100 nmole
250 nmole
1.0 µmole
Absorbance
500 550 600 650 700 750 800
Wavelength (nm)
Fluorescence Emission
Rhodamine Dyes
5' MW: 647.6
Int. MW: 926.9
Ab max 504 nm Em max 531 nm 3' MW: 647.6
H 2 N
O NH 2
+
SCALE 5' INT. 3'
100 nmole
250 nmole
1.0 µmole
HN
O –
O
Absorbance and Fluorescence Emission
504 nm 531 nm
O
O
Absorbance
Fluorescence Emission
NH
* HPLC purification required
400 450 500 550 600 650
Wavelength (nm)
e-mail: oligo@mbl.co.jp
56

Fluorophores
Rhodamine Red -X NHS Ester * 5' MW: 833.0
Int. MW: 1112.2
Ab max 573 nm Em max 592 nm 3' MW: 833.0
SCALE 5' INT. 3'
100 nmole
250 nmole
N
O N +
1.0 µmole
Absorbance
Absorbance and Fluorescence Emission
573 nm 592 nm
Fluorescence Emission
H
N
O
N
H
SO 2
SO 3
-
6 Modifications
500 540 580 620 660 700
Wavelength (nm)
ROX NHS Ester * 5' MW: 695.8
Int. MW: 975.0
Ab max 588 nm Em max 608 nm 3' MW: 695.8
®
SCALE 5' INT. 3'
100 nmole
250 nmole
1.0 µmole
Absorbance and Fluorescence Emission
N O
N +
H
N
O –
O
Absorbance
588 nm 608 nm
Fluorescence Emission
O
450 500 550 600 650 700
Wavelength (nm)
* HPLC purification required
57

Fluorophores
TAMRA Dyes
TAMRA -Sp * MW: 1008.9
Ab max 559 nm
Em max 583 nm
Absorbance and Fluorescence Emission
559 nm 583 nm
6 Modifications
SCALE 5' INT. 3'
100 nmole - -
250 nmole - -
1.0 µmole - -
Absorbance
455 515 565 615 665
Wavelength (nm)
Fluorescence Emission
5' MW: 591.6
Int. MW: 870.9
Ab max 559 nm Em max 583 nm 3' MW: 950.8
SCALE 5' INT. 3'
100 nmole
N
O N +
250 nmole
O –
1.0 µmole
H
N
O
Absorbance and Fluorescence Emission
559 nm 583 nm
455 515 565 615 665
* HPLC purification required Wavelength (nm)
Absorbance
Fluorescence Emission
O
e-mail: oligo@mbl.co.jp
58

Fluorophores
TET
Ab max 522 nm
Em max 539 nm
MW: 675.2
SCALE 5' INT. 3'
-O
O
O
100 nmole - -
Cl
Cl
250 nmole - -
Cl
O –
1.0 µmole - -
Absorbance
Absorbance and Fluorescence Emission
522 nm 539 nm
Fluorescence Emission
O
HN
Cl
O
O
O
P
O
6 Modifications
400 450 500 550 600
Wavelength (nm)
O -
3'
TEXAS RED®-X NHS Ester
5' MW: 881.0
Int. MW: 1160.3
Ab max 598 nm Em max 617 nm 3' MW: 881.0
®
SCALE 5' INT. 3'
100 nmole
250 nmole
1.0 µmole
Absorbance and Fluorescence Emission
N O
N +
SO 3
-
2
H
N
S
O
O
2
N
H
598 nm 617 nm
Absorbance
Fluorescence Emission
4
450 500 550 600 650 700
Wavelength (nm)
* HPLC purification required
59

Dark Quenchers
Iowa Black TM Quenchers
Iowa Black FQ
5' MW: 426.4
Ab max 531 nm 3' MW: 522.3
6 Modifications
SCALE 5' INT. 3'
100 nmole -
250 nmole -
1.0 µmole -
Iowa Black RQ * 5' MW: 420.4
Ab max 656 nm 3' MW: 654.4
®
SCALE 5' INT. 3'
100 nmole -
250 nmole -
1.0 µmole -
* HPLC purification required
e-mail: oligo@mbl.co.jp
60

Dark Quenchers
Black Hole Quencher® -1 * MW: 554.5
Ab max 538 nm
®
SCALE 5' INT. 3'
100 nmole - -
250 nmole - -
1.0 µmole - -
Black Hole Quencher®-2 * MW: 556.5
Ab max 584 nm
6 Modifications
® ®
SCALE 5' INT. 3'
100 nmole - -
250 nmole - -
1.0 µmole - -
Dabcyl * MW: 757.8
Ab max 478 nm
SCALE 5' INT. 3'
HN
O
O
O N
H
O
N N N
100 nmole - -
N
250 nmole - -
'5
O
O
O
N
1.0 µmole - -
O
O
P O -
O -
* HPLC purification required
61

Spacers
C3 Spacer
MW: 138.1
6 Modifications
SCALE 5' INT. 3'
100 nmole
250 nmole
1.0 µmole
PC Spacer
'5
O
MW: 344.3
O
O P O -
O
3'
O
SCALE 5' INT. 3'
'5
O
N
H
100 nmole -
NO 2
250 nmole -
1.0 µmole -
O
O P O -
O
3'
Spacer 9
MW: 212.1
SCALE 5' INT. 3'
'5
O
O
O
100 nmole -
250 nmole -
1.0 µmole -
O
O P O -
O
3'
e-mail: oligo@mbl.co.jp
62

Spacers
Spacer 18
MW: 344.3
SCALE 5' INT. 3'
100 nmole -
250 nmole -
'5
O
O
O
O
O
O
1.0 µmole -
1',2'-Dideoxyribose (dSpacer)
MW: 180.1
O
O P O -
O
3'
6 Modifications
SCALE 5' INT. 3'
'5
O
O
100 nmole -
250 nmole -
1.0 µmole -
O
O P O -
O
Internal dSpacer
3'
Modified Bases
2-Aminopurine
MW: 313.2
SCALE 5' INT. 3'
N
N
100 nmole -
'5
H 2 N
N
N
250 nmole -
O
O
1.0 µmole -
O
O P O -
O
Internal 2-Aminopurine
3'
63

Modified Bases
2,6-Diaminopurine * (2-Amino-dA)
MW: 328.2
SCALE 5' INT. 3'
N
N
NH 2
O
100 nmole -
'5
H 2 N
N
N
250 nmole -
O
1.0 µmole -
O
6 Modifications
Reference:
1. The use of diaminopurine to investigate structural properties of nucleic acids and molecular recognition between ligands and DNA.
Bailly, C., and Waring, M.J., Nucleic Acids Research, 26:4309-14 (1998).
5-Bromo dU *
MW: 369.1
O P O -
O
Internal 2,6-Diaminopurine
3'
HN
O
Br
SCALE 5' INT. 3'
O
N
100 nmole -
250 nmole -
'5
O
O
1.0 µmole -
O
O P O -
O
3'
deoxyUridine
MW: 290.2
Internal 5-Br dU
O
SCALE 5' INT. 3'
HN
100 nmole
250 nmole
'5
O
O
O
N
1.0 µmole
O
O P O -
* HPLC purification required Internal deoxyUridine
O
3'
e-mail: oligo@mbl.co.jp
64

Modified Bases
Inverted dT
MW: 304.2
SCALE 5' INT. 3'
'5
O
100 nmole - -
250 nmole - -
1.0 µmole - -
dideoxy-C
O
HO
O
HN
MW: 273.2
N
O
6 Modifications
NH 2
SCALE 5' INT. 3'
N
100 nmole - -
250 nmole - -
1.0 µmole - -
'5
O
O
O
N
5-Methyl dC
MW: 303.2
in vivo
NH 2
N
SCALE 5' INT. 3'
'5
O
N
100 nmole -
250 nmole -
1.0 µmole -
O
O
O
O P O -
O
3'
Internal 5-Me dC
65

Modified Bases
deoxyInosine
MW: 314.2
O
SCALE 5' INT. 3'
HN
N
6 Modifications
100 nmole
250 nmole
1.0 µmole
'5
O
O
N
O
O P O -
N
O
3'
Internal deoxyInosine
Locked Nucleic Acids (LNAs)
LNA A MW: 341.2 LNA G MW: 357.2
LNA C MW: 331.2 LNA T MW: 332.2
SCALE 5' INT. 3'
'5
O
O
Base
100 nmole -
250 nmole -
1.0 µmole -
O
O P O -
O
3'
O
Internal LNA Bases
Reference:
1. Design considerations and effects of LNA in PCR primers. Latorra, D., Arar, K., and Hurley, J.M., Mol. Cell. Probes., 17:253-9 (2003).
2. Antisense inhibition of gene expression in cells by oligonucleotides incorporating locked nucleic acids: effect of mRNA target sequence
and chimera design. Braasch, D.A., Liu, Y., and Corey, D.R., Nucleic Acids Res., 30:5160-7 (2002).
e-mail: oligo@mbl.co.jp
66

Modified Bases
5-Nitroindole
MW: 340.2
Reference:
SCALE 5' INT. 3'
100 nmole -
250 nmole -
1.0 µmole -
1. The applications of universal DNA base analogues. Loakes, D., Nucleic Acids Res.,
29:2437-2447 (2001).
'5
O 2 N
O
O
O
O P O -
O
3'
Internal 5-Nitroindole
N
6 Modifications
2'-O-Methyl RNA Bases
mA MW: 343.2 mG MW: 359.2
mC MW: 319.2 mU MW: 320.2
O
'5
Base
SCALE
Price Per Insertion
O
O
100 nmole
250 nmole
1.0 µmole
O
O P O -
O
3'
OCH 3
Internal 2'-O-Me RNA Bases
67

Modified Bases
3'-Ribo Primers
Ribo A MW: 329.2 Ribo C MW: 305.2
Ribo G MW: 345.2 Ribo U MW: 306.2
N
N
SCALE 5' INT. 3'
'5
NH 2
O
N
N
100 nmole - -
O
6 Modifications
Reference:
250 nmole - -
1.0 µmole - -
1. Use of PCR primers containing a 3'-terminal ribose residue to prevent cross-contamination of amplified sequences. Walder, R.Y.
and Walder, J.A. Nucleic Acids Research, 21:4339-43 (1993).
OH
3' Ribo A
OH
Iso-dC and Iso-dG
Iso-dC*
5' MW: 303.2
Int. MW: 303.2
SCALE 5' INT. 3'
H
N
N
100 nmole -
250 nmole -
1.0 µmole -
Price per insertion of Iso-dG and Iso-dC.
* IE-HPLC required
N
H
O
H
N
N N
5-Me-Iso-dC
H
N
H
O
N
N
Iso-dG
H H
N
N
N
5-Me-dC
O
H
O
N
H
N
N
N
H
dG
Reference:
1. Enzymatic recognition of the base pair between isocytidine and isoguanosine. Switzer, C.Y., Moroney, S.E., and Benner, S.A. Biochemistry,
32:10489-96 (1993).
e-mail: oligo@mbl.co.jp
68

Modified Bases
Iso-dG*
5' MW: 329.2
Int. MW: 329.2
H
N
N
SCALE 5' INT. 3'
100 nmole -
250 nmole -
1.0 µmole -
Price per insertion of Iso-dG and Iso-dC.
* IE-HPLC required
Reference:
N
H
O
H
N
N N
5-Me-Iso-dC
H
N
H
O
N
N
Iso-dG
H H
N
N
N
5-Me-dC
O
H
O
N
H
N
N
N
H
dG
6 Modifications
1. Enzymatic recognition of the base pair between isocytidine and isoguanosine. Switzer, C.Y., Moroney, S.E., and Benner, S.A. Biochemistry,
32:10489-96 (1993).
Phosphorothioate Bond
N
O
NH
5'
N
N
NH 2
SCALE
Price Per Insertion
O
O
NH2
N
O
OMe
100 nmole
250 nmole
1.0 µmole
O
P S -
O
O
O P
O
S -
N
N
N
O
O
N
NH
NH 2
O
O
O
O P S -
O
3'
69

Molecular Biology
Products
7 Molecular Biology Products
Phone: 03-5248-3066
Fax: 03-5248-2930
e-mail: oligo@mbl.co.jp
70

RNaseAlert Substrate and Nuclease Detection System
PRODUCT
PRICE
RNaseAlert - (25) single-use 50 pmole tubes
RNaseAlert Substrate - Two 2-nmole bulk tubes (enough for 200 reactions)
RNaseAlert Kit
RNaseAlert Buffer (10) 2mL tubes
7 Molecular Biology Products
RNaseAlert Kit Components:
(25) 50 pmole Fluorescent Substrate tubes
250 µl 10x RNaseAlert Buffer
2 ml Nuclease-Free water
50 µl RNase A
50 ml Nuclease Decontamination Solution
Kit quality guaranteed for six months from date received when stored at -20°C.
RNaseAlert Positive
Control
Examination of RNase-free sample versus RNase positive control.
71

DNaseAlert Substrate and Nuclease Detection System
7 Molecular Biology Products
PRODUCT
DNaseAlert Substrate - (25) single-use 50 pmole tube
DNaseAlert Substrate - Two 2-nmole bulk tubes (enough for 200 reactions)
DNaseAlert Kit
PRICE
DNaseAlert Kit Components:
(25) 50 pmole Fluorescent Substrate tubes
250 µl DNaseAlert Buffer
2 ml Nuclease-Free water
25 µl 2U/ml DNase I Enzyme
50 ml Nuclease Decontamination Solution
Kit quality guaranteed for six months from date received when stored at -20°C.
Phone: 03-5248-3066
Fax: 03-5248-2930
e-mail: oligo@mbl.co.jp
72
Examination of DNase-free sample versus DNase positive control.

Nuclease-free
Buffers & Reagents
7 Molecular Biology Products
73

Nuclease-free Buffers and Reagents
IDTE (10 mM Tris, pH 7.5 or 8.0, 0.1 mM EDTA)
7 Molecular Biology Products
Duplex Buffer (30 mM Hepes, pH 7.5, 100 mM Potassium Acetate)
Nuclease-Free Water
Quantity IDTE Duplex Buffer NucleasepH
7.5 or 8.0
Free Water
10x2 mL
250 mL
1 Liter
4x1 Liter
Nuclease Decontamination Solution
Phone: 03-5248-3066
Fax: 03-5248-2930
e-mail: oligo@mbl.co.jp
74
Product
Nuclease Decontamination
Solution
250 mL Spray Bottle
6x250 mL Spray Bottle Refill Kit

®
Nucleic Acid Labeling System
®
®
StarFire® Complete Kit
StarFire® Universal Template
Sufficient for 25 labeling reactions
Includes:
StarFire® 10X Buffer Mix
StarFire® Stop Buffer
One PAGE-purified StarFire®
Custom Probe (up to 50 bases)
StarFire® Universal Template
StarFire® Custom Probes (up to 50 bases)
Desalted
/base
PAGE Purified*
/base + StarFire® PAGE,
Sufficient for 300 labeling reactions
0.5 OD (in single tube)
HPLC Purified
Quality Control checked by mass spectrometry
and CE
StarFire® Refill Kit
Sufficient for 25 labeling reactions
StarFire® 10X Buffer Mix
StarFire® Stop Buffer
*For optimal labeling efficiency, IDT recommends using PAGE purification for custom StarFire® probes.
References:
1. Use of high specific activity
StarFire® oligonucleotide probes
to visualize low-abundance premRNA
splicing intermediates in
S. pombe. Behlke, M.A., Dames,
S.A., McDonald, W.H., Gould,
K.L., Devor, E.J., and Walder, J.A.,
BioTechniques, 29:892-897 (2000).
2. Temporal regulation of
microRNA expression in Drosophila
melanogaster mediated by hormonal
signals and Broad-Complex gene
activity. Sempere, L.F., Sokol, N.S.,
Dubrovsky, E.B., Berger, E.M.,
Ambros, V., Development Biology
259: 9 (2003).
3. The Expression of the let-7 Small
Regulatory RNA Is Controlled by
Ecdysone during metamorphosis in
Drosophila melanogaster. Sempere,
L.F., Dubrovskaya, V.A., Dubrovsky,
E.B., Berger, E.M., Ambros, V.,
Development Biology, vol. 244: 170
(2002).
7 Molecular Biology Products
75

ReadyMade Primers
The Highest Quality
•
•
•
Easy Ordering
• Order online ; www.idtdna.com
• Email ; oligo@mbl.co.jp
• Fax ; 03-5248-2930
• 10 µg
•
7 Molecular Biology Products
Phone: 03-5248-3066
Fax: 03-5248-2930
e-mail: oligo@mbl.co.jp
ReadyMade Primer Name
Sequence
16S rRNA For
AG AGT TTG ATC CTG GCT CAG
16S rRNA Rev
ACG GCT ACC TTG TTA CGA CTT
3' RACE PCR GGC CAC GCG TCG ACT AGT AC
Anchored Oligo dT (20)
TTT TTT TTT TTT TTT TTT TV
Anchored Oligo dT (22)
TTT TTT TTT TTT TTT TTT TTV N
BGH Reverse
TAG AAG GCA CAG TCG AGG
Bluescript KS
TCG AGG TCG ACG GTA TC
Bluescript SK
CGC TCT AGA ACT AGT GGA TC
cDNA Cloning Primer
GGC CAC GCG TCG ACT AGT ACT TTT TTT TTT TTT TTT TV
EGFP-C
CAT GGT CCT GCT GGA GTT CGT G
EGFP-N
CGT CGC CGT CCA GCT CGA CCA G
G3PDH For
ACC ACA GTC CAT GCC ATC AC
G3PDH Rev
TCC ACC ACC CTG TTG CTG TA
IL-2 Exon 3 For (7329)
CTA GGC CAC AGA ATT GAA AGA TCT
IL-2 Exon 3 Rev (7652)
GTA GGT GGA AAT TCT AGC ATC ATC C
M13 Forward (-20)
GTA AAA CGA CGG CCA GT
M13 Forward (-41)
CGC CAG GGT TTT CCC AGT CAC GAC
M13 Reverse (-27)
CAG GAA ACA GCT ATG AC
M13 Reverse (-48)
AGC GGA TAA CAA TTT CAC ACA GG
Neomycin For
CTT GGG TGG AGA GGC TAT TC
Neomycin Rev
AGG TGA GAT GAC AGG AGA TC
Oligo dT, (20) w/5' Phos
/5Phos/TTT TTT TTT TTT TTT TTT TT
Oligo dT, 15-mer
TTT TTT TTT TTT TTT
Oligo dT, 16-mer
TTT TTT TTT TTT TTT T
Oligo dT, 18 mer
TTT TTT TTT TTT TTT TTT
Oligo dT, 20-mer
TTT TTT TTT TTT TTT TTT TT
PCMV Forward
CGC AAA TGG GCG GTA GGC GTG
pET 3'
CTA GTT ATT GCT CAG CGG
pET 5' (T7)
TAA TAC GAC TCA CTA TAG G
pET Upstream
ATG CGT CCG GCG TAG A
pGEX 3'
CCG GGA GCT GCA TGT GTC AGA GG
pGEX 5'
GGG CTG GCA AGC CAC GTT TGG TG
Random Hexamer
NNN NNN
Random Hexamer w/Biotin
/5Bio/NNN NNN
ROSA26 Promoter For
AAA GTC GCT CTG AGT TGT TAT
ROSA26 Promoter Rev
GGA GCG GGA GAA ATG GAT ATG
SP6
TAC GAT TTA GGT GAC ACT ATA G
SP6 upstream
ATT TAG GTG ACA CTA TAG
T3 Promoter
AAT TAA CCC TCA CTA AAG GG
T7 Promoter
TAA TAC GAC TCA CTA TAG GG
T7 Terminator
GCT AGT TAT TGC TCA GCG G
T-cell Receptor For
CAA ATG TTG CTT GTC TGG TG
T-cell Receptor Rev
GTC AGT CGA GTG CAC AGT TT
76

miRNA Cloning Linker
Specifications
Sequence:
/5rApp/CTGTAGGCACCATCAAT/3ddC/
Internal Ban-I site
Molecular weight: 5838
Yield:
Modifications:
Purification:
Quality Control:
Synthesis Scale
1-nmole miRNA Cloning Linker
1 nmole, 0.19 OD, 5.8 mg
5 nmole, 0.93 OD, 29.1 mg
31.4 mg/OD, 5.4 nmoles/OD
5'-Adenylated; fully activated and ready for use
3'-end blocked with a dideoxy-C base
HPLC purified
Identity confirmed by ESI Mass Spectrometry
Tested for reactivity with RNA ligase
Price
References:
1. Dinucleoside pyrophosphate are
substrates for T4-induced RNA
ligase. England, T.E., Gumport, R.I.,
and Uhlenbeck, O.C. Proc Natl Acad
Sci USA, 74:4839-42 (1977).
2. RNA-catalyzed nucleotide
synthesis. Unrau, P.J., and Bartel,
D.P. Nature, 395:260-63 (1998).
3. An abundant class of tiny RNAs
with probable regulatory roles in
Caenorhabditis elegans. Lau, N.C.,
Lim, L.P., Weinstein, E.G., and
Bartel, D.P. Science, 294:858-62
(2001).
7 Molecular Biology Products
5-nmole miRNA Cloning Linker
Technical Note!
Instructions for Use
77

Oligo Length Standards
10/60 Ladder
10, 15, 20, 25, 30, 40, 50, 60 base marker oligos
7 Molecular Biology Products
20/100 Ladder
20, 30, 40, 50, 60, 70, 80, 90, 100 base marker oligos
10/60 Ladder
20/100 Ladder
15% Acrylamide
7M Urea
12% Acrylamide
7M Urea
Technical Note!
Phone: 03-5248-3066
Fax: 03-5248-2930
e-mail: oligo@mbl.co.jp
Resuspension and Use Guidelines
µµµ
µ
78

Microarray-Related Products
DNA oligonucleotides
Microarray SpotQC
Oligo Spotting Buffer (OSB)
RNase Contamination
7 Molecular Biology Products
Microarray Bioinformatics
79

7 Molecular Biology Products
For further information,
including instructions for use,
please visit www.idtdna.com.
Microarray Products
SpotQC
IDT's SpotQC Image vs. Cellular RNA Hyb Results on a High-Density cDNA Array.
The left image was obtained from a 1 hour QC hybridization using the IDT SpotQC kit. The right image was obtained from an overnight hybridization of a
sister slide (same print run) done using Cy3 TM /Cy5 TM -labeled cellular RNA. The utility of SpotQC to distinguish between true negatives and false negatives is
demonstrated. White arrows indicate examples of real negatives where the absence of experimental hyb signal is due to absent (or very low) mRNA target and not
a printing defect. Other missing spots, which are spot dropouts, can be found in both the QC image and the cellular RNA hyb image; these data points can now be
eliminated from the final gene expression analysis done on the experimental array and thereby prevent false negative results. The SpotQC hybridization image is
5-micron resolution Cy3 scan using a ScanArray® 5000 (Perkin Elmer) at 70/70 laser (power/gain) settings. (Pseudo-color scale: black < blue < green < yellow
< orange < red < white). The cellular RNA hybridization image is 5-micron resolution Cy3/Cy5 composite using a GenePix (Axon) scanner. (Cy3, green;
Cy5, red; Cy3/Cy5, yellow).
Phone: 03-5248-3066
Fax: 03-5248-2930
e-mail: oligo@mbl.co.jp
SpotQC Kit
Includes:
1000 pmoles of Cy3-SpotQC detector oligo
500 µl of 1X Hybridization Buffer
Oligo Spotting Buffer (OSB)
80
Includes:
125 ml 1X Oligo Spotting Buffer

Custom Services
8 Custom Services
81

PrimerQuest TM
8 Custom Services
References:
1. Primer3 on the WWW for general users
and for biologist programmers. Rozen S. &
Skaletsky, H. J., Bioinformatics Methods
and Protocols: Methods in Molecular
Biology. M. S. Krawetz S., Totowa, N.J.,
Humana Press: 365-386 (2000).
2. Optimal computer folding of large RNA
sequences using thermodynamics and
auxiliary information. Zuker M. & Steigler
P., Nucleic Acids Research 9: 133-148
(1981).
3. Algorithms and thermodynamics for
RNA secondary structure prediction: A
practical guide in RNA Biochemistry and
Biotechnology. Zuker M., Mathews D.H.
& Turner D.H., 11-43, J. Barciszewski
& B.F.C. Clark, eds., NATO ASI Series,
Kluwer Academic Publishers (1999).
4. A unified view of polymer, dumbbell,
and oligonucleotide DNA nearest-neighbor
thermodynamics. SantaLucia Jr. J., Proc.
Natl. Acad. Sci., 95: 1460-1465 (1998).
5. Basic local alignment search tool.
Altschul S. F., Gish W., Miller W., Myers
E.W. & Lipman D.J., Mol. Biol. 215: 403-
410 (1990).
Phone: 03-5248-3066
Fax: 03-5248-2930
e-mail: oligo@mbl.co.jp
OligoAnalyzer 3.0
82
mFold

Packaging and Formulation
8 Custom Services
83

Mass Spectrometry and CE --
available FREE on the web!
Mass Spectrometry
Mass Spectrometry Analysis
8 Custom Services
Capillary Electrophoresis
CE Analysis
Phone: 03-5248-3066
Fax: 03-5248-2930
e-mail: oligo@mbl.co.jp
84

Service Pricing
Lab-Ready Oligo Service
25 nmole 100 nmole 250 nmole 1 µmole 10 µmole
FREE F R E E F R E E F R E E F R E E
N/A
N/A
N/A
µµ
Standard Mixed
Base Sites:
R = A,g
Y = C,T
M = A,C
K = g,T
S = g,C
W = A,T
H = A,C,T
B = g,T,C
V = g,C,A
D = g,A,T
N = A,C,g,T
Service Pricing
All
scales
8 Custom Services
85

Usage, Warranty
9 Usage, Warranty and Licenses
and Licenses
Phone: 03-5248-3066
Fax: 03-5248-2930
e-mail: oligo@mbl.co.jp
86

Usage, Warranty and Licenses
Usage
Oligonucleotides and nucleic acid products are manufactured and sold by IDT for the customer's research
purposes only. Resale of IDT products requires the express written consent of IDT. IDT products have not been
approved for use in any clinical, diagnostic or therapeutic applications. Obtaining license or approval to use IDT
products in proprietary applications or in any non-research (clinical) applications is the customer's exclusive
responsibility.
IDT will not be responsible or liable for any losses, costs, expenses or other forms of liability arising out of
the unauthorized or unlicensed use of IDT products. Purchasers of IDT products shall indemnify and hold
IDT harmless for any and all damages and/or liability, however characterized, related to the unauthorized or
unlicensed use of IDT products. Under no circumstances shall IDT be liable for any consequential damages
Warranties
IDT's products are guaranteed to meet or exceed our published specifications for quality and yield as measured
under normal laboratory conditions. If our product fails to meet such specifications, IDT will promptly replace
the product. All other warranties are hereby expressly disclaimed, including but not limited to, the implied
warranties of merchantability and fitness for a particular purpose, and any warranty that the products, or the use
of products, manufactured by IDT will not infringe the patents of one or more third-parties.
All orders received by IDT and all sales of IDT products are made subject to the aforementioned disclaimers of
warranties and customer indemnification of IDT.
9 Usage, Warranty and Licenses
Licenses / Trademarks
* Fluorescent Labeled Oligonucleotides
Alexa Fluor® / Oregon Green® / Texas Red® / Bodipy® / Rhodamine Red and Rhodamine Green
are trademarks of Molecular Probes, Inc (MPI). IDT is licensed to sell oligonucleotides labeled with MPI
dyes for non-commercial research purposes only.
Black Hole Quenchers®, BHQ-1® and BHQ-2® and CAL Fluor® are trademarks of Biosearch
Technologies, Inc. (BTI), and all BHQ products are licensed and sold under agreement with BTI. These
products are sold exclusively for research and development use by the purchaser. They may not be used for
any human or veterinary clinical or diagnostic purposes without express permission from BTI and they may
not be re-sold, distributed, re-labeled or re-packaged.
Cy Dyes and Cy -labeled oligonucleotides are covered by U.S. Patent Numbers 5,556,959 and
5,808,044 and are licensed and sold for non-commercial research purposes only. Any other use including
diagnostic, therapeutic or in vivo applications requires a license from Amersham Biosciences, Inc. Cy is a
trademark of Amersham Biosciences.
FAM, HEX, ROX, TAMRA and TET are trademarks of Applied Biosystems, Inc.
Iowa Black is a trademark of Integrated DNA Technologies, Inc.
Molecular Beacons are licensed under patents owned by The Public Health Research Institute of the City
of New York, Inc. and come with licensed rights for use only in the purchaser's research and development
activities.
Oyster® is a registered trademark of Denovo Biolabels, GmbH.
Notice: The 5' Nuclease Assay and other homogenous amplification methods used in connection with the
Polymerase Chain Reaction ("PCR") process are covered by patents owned by Roche Molecular Systems,
Inc. and F. Hoffman La-Roche Ltd ("Roche"). No license to use the 5' Nuclease Assay or any Roche patented
homogenous amplification process is conveyed expressly or by implication to the purchaser by the purchase
of the above listed products or any other IDT products.
87

Usage, Warranty and Licenses
* Gene Knockdown
Chimeric Antisense Oligos. In addition to the exclusive license under the University of Iowa Research
Foundation patents, IDT is the sole oligonucleotide supplier licensed under several patents owned or presently
controlled by ISIS Pharmaceuticals, Inc. to manufacture and sell Chimeric Antisense Oligonucleotides to
universities and other non-profit institutions for research purposes. Certain design, sequence, scale and
use restrictions may apply. IDT reserves the unlimited right to refuse any order for Chimeric Antisense
Oligos.
DNA-directed RNAi. Use of IDT oligos for DNA-directed RNAi research is protected by patents coowned
by Benitec Australia Ltd., and licensed exclusively to Promega Corporation in the human field
(excluding human therapeutics). For information regarding licensing of ddRNAi technology, please visit
www.promega.com/licensing. For licensing any human therapeutic purpose, contact Benitec Australia Ltd
at info@benitec.com.
Locked Nucleic Acids (LNAs). IDT is licensed under patents and patents applications assigned to Exiqon
A/S to sell oligonucleotides incorporating LNAs for research purposes only. Resale of LNA-oligos and
therapeutic applications are strictly prohibited.
9 Usage, Warranty and Licenses
RNAi. IDT's products are licensed under U.S. and international patent rights owned by the Carnegie
Institution of Washington that cover RNA interference. These products are accompanied by a limited nonexclusive
worldwide license under the Carnegie Institution of Washington's patent rights for researchers at
academic or other not-for-profit institutions to use the products for non-profit research. However, use of
dsRNA for RNA interference by for-profit organizations require a license from the Carnegie Institution of
Washington.
* Other Licenses
Acrydite. IDT is licensed under U.S. Patent Number 6,180,770, and 5,932,711 to sell oligos incorporating
Acrydite modifications for use solely in the purchaser's own life sciences research and development
activities. Resale, or use of this product in clinical or diagnostic applications, or other commercial
applications, requires separate license from Matrix Technologies, Inc. Acrydite is a trademark of Matrix
Technologies, Inc.
Iso dC and Iso dG. IDT is licensed by Eragen Biosciences, Inc., under United States Patent Numbers
5,432,272; 6,001,983; 6,037,120; and 6,140,496, and other pending applications to sell oligonucleotides for
non-commercial, research use in the life sciences research market.
RNaseAlert compositions and methods are protected under U.S. Patent No. 6,773,885 and other pending
IDT patent(s). RNaseAlert is a trademark of Ambion, Inc.
StarFire® is a trademark of IDT, and its compositions and methods are protected under pending IDT
patent(s).
SAGE is a trademark of Genzyme Molecular Oncology. Purchase of IDT oligos does not confer to
customer a license to perform SAGE methods. For more information, contact Genzyme or Johns Hopkins
University.
Uni-Link is a trademark of Clontech Laboratories, Inc.
Phone: 03-5248-3066
Fax: 03-5248-2930
e-mail: oligo@mbl.co.jp
88

10 Index
Index
General Information
IDT . . . . . . . Inside Front Cover
How to Order . . . . . . . . . . . . . Inside Front Cover
Shipping Information . . . . . . . Inside Front Cover
About IDT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
IDT Advantage . . . . . . . . . . . . . . . . . . . . . . . . . . 4
DNA Synthesis & Purification. . . . 6, 79
ddRNAi . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
DNA Bases. . . . . . . . . . . . . . . . . . . . . . . 6, 11, 16
DNA Modifications . . . . . . . . . . . . . . . . . . .40-69
DNA Purification . . . . . . . . . . . . . . . . . . . . . . . . 7
DNA Yield Guarantees. . . . . . . . . . . . . . . . . . . . 6
Large Scale Synthesis . . . . . . . . . . . . . . . . . . . . 6
Plates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Plates
ddRNAi Plates . . . . . . . . . . . . . . . . . . . . . . . . . 25
Entire Plate CE. . . . . . . . . . . . . . . . . . . . . . . 8, 85
Plate Oligos . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Plate Loading Options . . . . . . . . . . . . . . . . . . . . 8
Plate Oligo Modifications . . . . . . . . . . . . . . . . . 8
RNA Synthesis & Purification
Large Scale Synthesis . . . . . . . . . . . . . . . . . . . 12
2'-O-Methyl RNA Bases . . . . . . . . . . . 11, 16, 67
RNA Bases . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
RNA Modifications . . . . . . . . . . . . . . . . . . . . . 12
RNA Purification . . . . . . . . . . . . . . . . . . . . . . . 11
RNA Yield Guarantees. . . . . . . . . . . . . . . . . . . 11
Functional Genomics
Antisense . . . . . . . . . . . . . . . . . . . . . . . . . . 13, 15, 16
Antisense Design Tool . . . . . . . . . . . . . . . . .17-18
LNA . . . . . . . . . . . . . . . . . . . . . . . . 11, 15, 16, 66
2'-O-Me RNA bases . . . . . . . . . . . . . . . 11, 16, 67
5-Methyl dC . . . . . . . . . . . . . . . . . . 12, 15, 16, 65
Phosphorothioate Bond . . . . . . . . . . . . . . . 16, 69
RNAi . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13, 20, 21
RNAi Design Tool . . . . . . . . . . . . . . . . . . . .22-23
RNAi Modifications. . . . . . . . . . . . . . . . . . . . . 21
RNAi Yields . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
ddRNAi . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13, 25
ddRNAi Plates . . . . . . . . . . . . . . . . . . . . . . . . . 25
Yield Guarantees . . . . . . . . . . . . . . . . . . . . . . . 25
ddRNAi Design Tools . . . . . . . . . . . . . . . . .26-27
miRNA Cloning Linker . . . . . . . . . . . . . . . . . 13, 77
Fluorescent DNA & RNA Probes
Dual-Labeled Probes
5' CAL Fluor ® 560 / 3' IBFQ . . . . . . . . . . . 32
5' CAL Fluor ® 560 / 3' BHQ ® -2 . . . . . . . . . . . 32
5' CAL Fluor ® 610 / 3' IBRQ . . . . . . . . . . . 33
5' CAL Fluor ® 610 / 3' BHQ ® -2 . . . . . . . . . . . 33
5' Cy3 / 3' BHQ ® -2 . . . . . . . . . . . . . . . . . . . 32
5' Cy3 / 3' IBRQ. . . . . . . . . . . . . . . . . . . . 32
5' Cy5 / 3' BHQ ® -2 . . . . . . . . . . . . . . . . . . . 32
5' Cy5 / 3' IBRQ. . . . . . . . . . . . . . . . . . . . 32
5' 6-FAM / 3' BHQ ® -1 . . . . . . . . . . . . . . . . . 31
5' 6-FAM / 3' BHQ ® -2 . . . . . . . . . . . . . . . . . 31
5' 6-FAM / 3' IBFQ . . . . . . . . . . . . . . . . . 31
5' 6-FAM / 3' TAMRA . . . . . . . . . . . . . . . 31
5' 6-FAM / 3' TAMRA NHS Ester . . . . . . 31
5' HEX / 3' BHQ ® -1. . . . . . . . . . . . . . . . . . . 31
5' HEX / 3' BHQ ® -2. . . . . . . . . . . . . . . . . . . 31
5' HEX / 3' IBFQ . . . . . . . . . . . . . . . . . . . 31
5' HEX / 3' TAMRA NHS Ester. . . . . . . . 31
5' IBFQ / 3' 6-FAM . . . . . . . . . . . . . . . . . 35
5' IBFQ / 3' OrG488-X® . . . . . . . . . . . . . . . 35
5' IBFQ / 3' OrG514® . . . . . . . . . . . . . . . . . 35
5' IBRQ / 3' Cy3. . . . . . . . . . . . . . . . . . . . 35
5' IBRQ / 3' TAMRA . . . . . . . . . . . . . . . . 35
5' IBRQ / 3' TxRed® . . . . . . . . . . . . . . . . . . 35
5' JOE / 3' BHQ ® -1 . . . . . . . . . . . . . . . . . . . . . 33
5' JOE / 3' BHQ ® -2 . . . . . . . . . . . . . . . . . . . . . 33
5' JOE / 3' IBFQ. . . . . . . . . . . . . . . . . . . . . . 33
5' JOE / 3' TAMRA . . . . . . . . . . . . . . . . . . . 33
5' OrG® 488-X / 3' BHQ ® -1 . . . . . . . . . . . . . . 33
5' OrG® 488-X / 3' BHQ ® -2 . . . . . . . . . . . . . . 33
5' OrG® 488-X / 3' IBFQ . . . . . . . . . . . . . . 33
5' OrG® 488-X / 3' TAMRA . . . . . . . . . . . . 33
5' OrG® 514 / 3' BHQ ® -1 . . . . . . . . . . . . . . . . 34
5' OrG® 514 / 3' BHQ ® -2 . . . . . . . . . . . . . . . . 34
5' OrG® 514 / 3' IBFQ. . . . . . . . . . . . . . . . . 34
5' OrG® 514 / 3' TAMRA . . . . . . . . . . . . . . 34
5' ROX / 3' BHQ ® -2 . . . . . . . . . . . . . . . . . . 34
5' TAMRA / 3' BHQ ® -2. . . . . . . . . . . . . . . . 34
5' TAMRA / 3' IBRQ . . . . . . . . . . . . . . . . 34
5' TET / 3' BHQ ® -2 . . . . . . . . . . . . . . . . . . . 32
5' TET / 3' IBFQ. . . . . . . . . . . . . . . . . . . . 32
5' TET / 3' TAMRA . . . . . . . . . . . . . . . . . 32
5' TET / 3' TAMRA NHS Ester . . . . . . . . 32
5' TxRed®-X / 3' BHQ ® -2. . . . . . . . . . . . . . . . 34
5' TxRed®-X / 3' IBRQ . . . . . . . . . . . . . . . . 34
Dual-Labeled LNA Probes . . . . . . . . . . . . . . . . . 36
5' FAM / 3' IBFQ . . . . . . . . . . . . . . . . . . . 36
5' FAM / 3' BHQ ® -1. . . . . . . . . . . . . . . . . . . 36
5' Cy3 / 3' IBFQ . . . . . . . . . . . . . . . . . . . . 36
5' Cy3 / 3' BHQ ® -2 . . . . . . . . . . . . . . . . . . . 36
5' CAL Fluor ® 610 / 3' IBRQ. . . . . . . . . . . . 36
5' CAL Fluor ® 610 / 3' BHQ ® -2 . . . . . . . . . . . 36
5' Cy5 / 3' IBRQ . . . . . . . . . . . . . . . . . . . . 36
5' Cy5 / 3' BHQ ® -2 . . . . . . . . . . . . . . . . . . . 36
Dual-Labeled RNA Probes . . . . . . . . . . . . . . . . . 37
5' Cy5 / 3' BHQ ® -2 . . . . . . . . . . . . . . . . . . . 37
5' FAM / 3' BHQ ® -1 . . . . . . . . . . . . . . . . . . 37
5' FAM / 3' TAMRA. . . . . . . . . . . . . . . . . . . 37
5' HEX / 3' BHQ ® -1. . . . . . . . . . . . . . . . . . . 37
5' TET / 3' BHQ ® -1 . . . . . . . . . . . . . . . . . . . 37
Molecular Beacons. . . . . . . . . . . . . . . . . . . . . . . . 38
5' Cy3 / 3' BHQ ® -2 . . . . . . . . . . . . . . . . . . . 38
5' Cy5 / 3' BHQ ® -2 . . . . . . . . . . . . . . . . . . . 38
5' 6-FAM / 3' BHQ ® -1 . . . . . . . . . . . . . . . . . 38
5' 6-FAM / 3' Dabcyl . . . . . . . . . . . . . . . . . . 38
5' HEX / 3' BHQ ® -2. . . . . . . . . . . . . . . . . . . 38
5' HEX / 3' Dabcyl . . . . . . . . . . . . . . . . . . . . 38
5' TET / 3' BHQ ® -1 . . . . . . . . . . . . . . . . . . . 38
5' TET/ 3' Dabcyl . . . . . . . . . . . . . . . . . . . . . 38
89

10 Index
Phone: 03-5248-3066
Fax: 03-5248-2930
e-mail: oligo@mbl.co.jp
Index
RNase Substrate. . . . . . . . . . . . . . . . . . . . . . . . . . 12
Modifications
Phosphorylation . . . . . . . . . . . . . . . . 8, 12, 21, 40
Attachment Chemistry/Linkers
Acrydite . . . . . . . . . . . . . . . . . . . 8, 12, 40
Amino Modifier C6 . . . . . . . . . . . . 8, 12, 40
Amino Modifier C12 . . . . . . . . . . . . . 12, 41
Amino Modifier C6 dT . . . . . . . . . . . 12, 41
Amino Modifier . . . . . . . . . . . . . . . . . . . . 41
Uni-Link Amino Modifier . . . . . . . 12, 42
Biotin . . . . . . . . . . . . . . . . . . . . 8, 12, 21, 42
Biotin dT. . . . . . . . . . . . . . . . . . . . . . . . . . 42
Biotin-TEG . . . . . . . . . . . . . . . . . . . . . . . . 43
Dual Biotin . . . . . . . . . . . . . . . . . . . . . . . . 43
PC Biotin . . . . . . . . . . . . . . . . . . . . . . . . . 43
Digoxigenin NHS Ester . . . . . . . . . . . . . . 44
I-Linker. . . . . . . . . . . . . . . . . . . . . . . 8, 44
Thiol Modifier C3 S-S . . . . . . . . . . . . . . . 44
Thiol Modifier C6 S-S . . . . . . . . . . . . . . . 45
Fluorophores
Alexa Fluor® 488 NHS Ester . . . . . . . . . 45
Alexa Fluor® 532 NHS Ester . . . . . . . . . 46
Alexa Fluor® 546 NHS Ester . . . . . . . . . 46
Alexa Fluor® 594 NHS Ester . . . . . . . . . 47
Alexa Fluor® 647 NHS Ester . . . . . . . . . 47
Alexa Fluor® 660 NHS Ester . . . . . . . . . 48
Alexa Fluor® 750 NHS Ester . . . . . . . . . 48
Bodipy® 630/650-X NHS Ester . . . . . . . 49
Bodipy® 650/665-X NHS Ester . . . . . . . 49
CAL Fluor® 560 . . . . . . . . . . . . . . . . . . . 50
CAL Fluor® 610 . . . . . . . . . . . . . . . . . . . 50
Cy3 . . . . . . . . . . . . . . . . . . . . . . . . . 21, 51
Cy5 . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
Cy5.5. . . . . . . . . . . . . . . . . . . . . . . . . . . 52
6-FAM. . . . . . . . . . . . . . . . . . . . . 8, 16, 52
Fluorescein (see 6-FAM)
Fluorescein dT . . . . . . . . . . . . . . . . . . . . . 53
HEX . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
JOE NHS Ester. . . . . . . . . . . . . . . . . . . . . 54
Oregon Green® 488-X NHS Ester. . . . . . 54
Oregon Green® 514 NHS Ester. . . . . . . . 55
Oyster® 556 NHS Ester. . . . . . . . . . . . . . 55
Oyster® 645 NHS Ester. . . . . . . . . . . . . . 56
Rhodamine Green-X NHS Ester . . . . . 56
Rhodamine Red-X NHS Ester . . . . . . . 57
ROX NHS Ester . . . . . . . . . . . . . . . . . . 57
TAMRA . . . . . . . . . . . . . . . . . . . . . . . . 58
TAMRA® NHS Ester. . . . . . . . . . . . . . . . 58
TET. . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Texas Red®-X NHS Ester . . . . . . . . . . . . 59
Dark Quenchers
Iowa Black FQ . . . . . . . . . . . . . . . . . . . 60
Iowa Black RQ . . . . . . . . . . . . . . . . . . . 60
Black Hole Quencher®-1. . . . . . . . . . . . . 61
Black Hole Quencher®-2. . . . . . . . . . . . . 61
Dabcyl. . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Spacers
C3 Spacer . . . . . . . . . . . . . . . . . . . . . . 12, 62
PC Spacer . . . . . . . . . . . . . . . . . . . . . . . . . 62
Spacer 9 . . . . . . . . . . . . . . . . . . . . . . . 12, 62
Spacer 18 . . . . . . . . . . . . . . . . . . . . . . 12, 63
dSpacer . . . . . . . . . . . . . . . . . . . . . . . . 12, 63
Modified Bases
2-Aminopurine . . . . . . . . . . . . . . . . . . 12, 63
2,6-Diaminopurine . . . . . . . . . . . . . . . . . . 64
90
5-Bromo dU . . . . . . . . . . . . . . . . . . . . . . . 64
Uridine . . . . . . . . . . . . . . . . . . . . . . . . 12, 64
Inverted dT . . . . . . . . . . . . . . . . . . . . . . . . 65
dideoxy-C . . . . . . . . . . . . . . . . . . . . . . . . . 65
5-Methyl dC . . . . . . . . . . . . . . 12, 15, 16, 65
Inosine . . . . . . . . . . . . . . . . . . . . . . . . 12, 66
LNA . . . . . . . . . . . . . . . . . . . . 11, 15, 16, 66
5-Nitroindole . . . . . . . . . . . . . . . . . . . 12, 67
2'-O-Methyl RNA Bases. . . . . 11, 15, 16, 67
3' Ribo Primers . . . . . . . . . . . . . . . . . . . . . 68
Iso-dC . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
Iso-dG . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
Phosphorothioate bond . . . . . . . . . . . . 16, 69
Molecular Biology Products
RNaseAlert . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
(25) 50pmole Single Use Tubes. . . . . . . . . . . . 71
(2) Bulk Tubes (200 reactions) . . . . . . . . . . . . 71
RNaseAlert Buffer . . . . . . . . . . . . . . . . . . . . 71
RNaseAlert Kit. . . . . . . . . . . . . . . . . . . . . . . 71
DNaseAlert . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
(2) Bulk Tubes . . . . . . . . . . . . . . . . . . . . . . . . . 72
(25) 50pmole Single-Use Tubes. . . . . . . . . . . . 72
DNaseAlert Kit. . . . . . . . . . . . . . . . . . . . . . . 72
Nuclease-Free Buffers & Reagents. . . . . . . . . . . 74
IDTE pH 7.5. . . . . . . . . . . . . . . . . . . . . . . . . . . 74
IDTE pH 8.0. . . . . . . . . . . . . . . . . . . . . . . . . . . 74
Duplex Buffer. . . . . . . . . . . . . . . . . . . . . . . . . . 74
Nuclease-free Water . . . . . . . . . . . . . . . . . . . . . 74
Nuclease Decontamination Solution. . . . . . . . . . 74
StarFire® . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
StarFire® Complete Kit . . . . . . . . . . . . . . . . . . 75
StarFire® Probe . . . . . . . . . . . . . . . . . . . . . . . . 75
StarFire® Refill Kit . . . . . . . . . . . . . . . . . . . . . 75
StarFire® Universal Template . . . . . . . . . . . . . 75
ReadyMade Primers . . . . . . . . . . . . . . . . . . . . 76
16S rRNA For . . . . . . . . . . . . . . . . . . . . . . . . . 76
16S rRNA Rev . . . . . . . . . . . . . . . . . . . . . . . . . 76
3' RACE PCR. . . . . . . . . . . . . . . . . . . . . . . . . . 76
Anchored Oligo dT (20). . . . . . . . . . . . . . . . . . 76
Anchored Oligo dT (22). . . . . . . . . . . . . . . . . . 76
BGH Reverse . . . . . . . . . . . . . . . . . . . . . . . . . . 76
Bluescript KS . . . . . . . . . . . . . . . . . . . . . . . . . . 76
Bluescript SK . . . . . . . . . . . . . . . . . . . . . . . . . . 76
cDNA Cloning Primer . . . . . . . . . . . . . . . . . . . 76
EGFP-C . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
EGFP-N . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
G3PDH For . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
G3PDH Rev . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
IL-2 Exon 3 For (7329) . . . . . . . . . . . . . . . . . . 76
IL-2 Exon 3 Rev (7652). . . . . . . . . . . . . . . . . . 76
M13 Forward (-20). . . . . . . . . . . . . . . . . . . . . . 76
M13 Forward (-41). . . . . . . . . . . . . . . . . . . . . . 76
M13 Reverse (-27) . . . . . . . . . . . . . . . . . . . . . . 76
M13 Reverse (-48) . . . . . . . . . . . . . . . . . . . . . . 76
Neomycin For. . . . . . . . . . . . . . . . . . . . . . . . . . 76
Neomycin Rev . . . . . . . . . . . . . . . . . . . . . . . . . 76
Oligo dT, (20) w/5' Phos . . . . . . . . . . . . . . . . . 76
Oligo dT, 15 mer . . . . . . . . . . . . . . . . . . . . . . . 76
Oligo dT, 16 mer . . . . . . . . . . . . . . . . . . . . . . . 76

10 Index
Index
ReadyMade Primers, cont. . . . . . . . . . . . . . . . 76
Oligo dT, 18 mer . . . . . . . . . . . . . . . . . . . . . . . 76
Oligo dT, 20 mer . . . . . . . . . . . . . . . . . . . . . . . 76
PCMV Forward . . . . . . . . . . . . . . . . . . . . . . . . 76
pET 3' . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
pET 5' (T7). . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
pET Upstream . . . . . . . . . . . . . . . . . . . . . . . . . 76
pGEX 3' . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
pGEX 5' . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
Random Hexamer. . . . . . . . . . . . . . . . . . . . . . . 76
Random Hexamer w/Biotin . . . . . . . . . . . . . . . 76
ROSA26 Promoter For. . . . . . . . . . . . . . . . . . . 76
ROSA26 Promoter Rev . . . . . . . . . . . . . . . . . . 76
SP6 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
SP6 upstream . . . . . . . . . . . . . . . . . . . . . . . . . . 76
T3 Promoter . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
T7 Promoter . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
T7 Terminator. . . . . . . . . . . . . . . . . . . . . . . . . . 76
T-cell Receptor For . . . . . . . . . . . . . . . . . . . . . 76
T-cell Receptor Rev . . . . . . . . . . . . . . . . . . . . . 76
RNaseAlert Substrates . . . . . . . . . . . . . . . . . . . . 12
Oligo Length Standards . . . . . . . . . . . . . . . . . . . 78
10/60 Ladder . . . . . . . . . . . . . . . . . . . . . . . . . . 78
20/100 Ladder . . . . . . . . . . . . . . . . . . . . . . . . . 78
Microarray Products . . . . . . . . . . . . . . . . . . . . . . 79
DNA Synthesis. . . . . . . . . . . . . . . . . . . . . . . 6, 79
Oligo Spotting Buffer (100 mL 1X) . . . . . 79, 80
SpotQC Kit. . . . . . . . . . . . . . . . . . . . . . . . . 79, 80
Usage, Warranty and Licenses . . .87-88
Additional Information
Purifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Dual HPLC Purification. . . . . . . . . . . . . . . . . . . 7
Dual PAGE & HPLC Purification . . . . . . . . . . . 7
IE HPLC Purification. . . . . . . . . . . . . . . . . . . . . 7
HPLC Purification . . . . . . . . . . . . . . . . . . . . 7, 16
PAGE Purification . . . . . . . . . . . . . . . . . . . . . . . 7
RNase-Free HPLC . . . . . . . . . . . . . . . . . . . . . 7,11
Bases
ddRNAi Bases . . . . . . . . . . . . . . . . . . . . . . . . . 25
DNA Bases. . . . . . . . . . . . . . . . . . . . . . . 6, 11, 16
LNA Bases . . . . . . . . . . . . . . . . . . . 11, 15, 16, 66
2'-O-Methyl RNA Bases . . . . . . . . 11, 15, 16, 67
Plate Bases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
RNA Bases . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Yield Guarantees
ddRNAi . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
DNA Synthesis. . . . . . . . . . . . . . . . . . . . . . . . . . 6
Dual-Labeled LNA Probes. . . . . . . . . . . . . . . . 36
Dual-Labeled Probes . . . . . . . . . . . . . . . . . .31-35
Dual-Labeled RNA Probes. . . . . . . . . . . . . . . . 37
Purified Oligos . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Molecular Beacons. . . . . . . . . . . . . . . . . . . . . . 38
RNAi . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
RNA Synthesis . . . . . . . . . . . . . . . . . . . . . . . . . 11
Standard Desalted Oligos. . . . . . . . . . . . . . . . . . 6
Custom Services
SciTools
Antisense Design . . . . . . . . . . . . . . . . . . . . .17-18
ddRNAi Design . . . . . . . . . . . . . . . . . . . . . .26-27
mFOLD . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
Oligo Analyzer 3.0 . . . . . . . . . . . . . . . . . . . . . . 82
PrimerQuest . . . . . . . . . . . . . . . . . . . . . . . . . 82
RNAi Design . . . . . . . . . . . . . . . . . . . . . . . .22-23
Packaging & Formulation. . . . . . . . . . . . . . . . . . 83
Mass Spectrometry and CE . . . . . . . . . . . . . . . . 84
Analytical Services. . . . . . . . . . . . . . . . . . . . . . . . 85
CE. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84, 85
Conductivity. . . . . . . . . . . . . . . . . . . . . . . . . . . 85
Entire Plate CE. . . . . . . . . . . . . . . . . . . . . . . . . 85
ESI Mass Spectrometry . . . . . . . . . . . . . . . . . . 84
Fluorometric Scan . . . . . . . . . . . . . . . . . . . . . . 85
IE HPLC Trace. . . . . . . . . . . . . . . . . . . . . . . . . 85
Mass Spectrometry. . . . . . . . . . . . . . . . . . . . . . 84
RP HPLC Trace . . . . . . . . . . . . . . . . . . . . . . . . 85
Preparative Services . . . . . . . . . . . . . . . . . . . . . . 85
Annealing . . . . . . . . . . . . . . . . . . . . . . . . . . 11, 85
Custom Plate Loading . . . . . . . . . . . . . . . . . . . . 8
Lab-Ready Oligo Service. . . . . . . . . . . . . . . . . 85
Mixed Base Sites . . . . . . . . . . . . . . . . . . . . . . . 85
Na + Salt Exchange . . . . . . . . . . . . . . . . . . . 16, 85
91

137191-5111030E