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INTEGRATEDDNATECHNOLOGIESSpacersPRODUCTSMODIFICATIONSSpacer 9 MW: 212.1Spacer 9 is a triethylene glycol spacer that can be incorporated at the 5’-end of an oligo or internally. Multiple insertions canbe used to create long spacer arms.5’ INT. 3’a a —'5OOOOO P O -O3'Spacer 18 MW: 344.3Spacer 18 is an 18-atom hexa-ethyleneglycol spacer. It is the longest spacer arm that can be added as a single modification.5’ INT. 3’a a —'5OOOOOOOO P O -O3'1’,2’-Dideoxyribose (dSpacer) MW: 180.1The 1’,2’-Dideoxyribose modification is used to introduce a stable abasic site within an oligonucleotide.5’ INT. 3’a a —'5OOOO P O -Hexanediol MW: 180.1Hexanediol is a six carbon glycol spacer that is capable of blocking extension by DNA polymerases. This 3’ modification iscapable of supporting synthesis of oligos up to 100 bases.O3'5’ INT. 3’'5OOH— — a©2008 Integrated DNA Technologies www.idtdna.com75
INTEGRATEDDNATECHNOLOGIESModified BasesPRODUCTSMODIFICATIONS2-Aminopurine MW: 313.22-Aminopurine can substitute for dA in an oligonucleotide. It is a naturally fluorescent base that is sensitive to the localenvironment making it a useful probe for monitoring the structure and dynamics of DNA hairpins and for detecting the basestacking state of a duplex. 2-Aminopurine can be destabilizing and can slightly lower the T m .5’ INT. 3’NNa a —'5H 2NONONOO2,6-Diaminopurine(2-Amino-dA) MW: 328.23'This modified base can form three hydrogen bonds when base-paired with dT and can increase the T m of short oligos by asmuch as 1-2°C per insertion. This effect, however, is complex and is dependent on sequence context 1 .O P O -NH25’ INT. 3’NNa a —HPLC purification required'5H 2NONONOOReference:3'1. 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).O P O -5-Bromo dU MW: 369.15-Bromo-deoxyuridine (5-BrdU) is a photoreactive halogenated base that can be incorporated into oligonucleotides tocrosslink them to DNA, RNA or proteins with exposure to UV light. Crosslinking is maximally efficient with light at 308 nm.5’ INT. 3’OBra a —OHNNHPLC purification required'5OOOO P O -deoxyUridine MW: 290.2DeoxyUridine (dU) can be substituted for dT in DNA oligonucleotides. The base can be removed by the enzyme uracil-Ndeglycosylase(UNG), which renders the oligo susceptible to strand scission. One common use of this strategy is to eliminateamplified DNA and prevent cross-contamination.O3'O5’ INT. 3’HNa a a'5ONOO5' deoxyUridineOO P O -O3'©2008 Integrated DNA Technologies 76 www.idtdna.com
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