1 - Eppendorf

Appendix 

259

Info | Appendix 

260 

Info 

General information for the lab 

Description Page 

I. General information for the lab: data, facts, tips and tricks 

1. Abbreviations, symbols, conversion factors and data 

1.1. Conversions and foreign units 261 

1.1.1. Volume and weight 261 

1.1.2. Units and rates of decay 261 

1.1.3. Foreign units 261 

1.2. Conversion factors, old units to actual units 261 

1.3. Metric prefixes 261 

1.4. Greek alphabet 261 

2. Elements, reagents, chemicals and isotopes 

2.1. Atomic numbers and atomic weights of elements 262 

2.2. Acids and bases 263 

2.3. Isotopes—physical properties of commonly used isotopes 263 

3. Fundamentals of dispensing 

3.1. Air-cushion principle (air displacement) 264 

3.2. Principle of positive displacement 266 

4. Dispensing techniques 

4.1. Air-cushion pipettes 267 

4.2. Optimum handling of manual pipettes 268 

4.3. Possibility and prevention of contamination 269 

5. Calibration 

5.1. Gravimetric test procedure 270 

6. Application tips for liquid handling 

6.1. Decontamination and cleaning of air-cushion pipettes 271 

6.2. Possible sources of error when pipetting with air-cushion pipettes 272 

6.3. Conversion of different pressure units 272 

6.4. Physical data of liquids (relevant examples) 273 

6.5. Chemical resistance of disposables 274 

6.6. Error limits in accordance with EN ISO 8655 275 

6.7. Conformity 276 

7. Application tips for centrifugation 

7.1. Conversion table for rpm/rcf (nomogram) 277 

7.2. k-factors and centrifugation times 278 

II. Practical information for Molecular Biology: data, facts, tips and tricks 279 

Product appearance, specifications, and/or prices are subject to change without notice.


1.1. Conversions and foreign units 

1.1.1. Volume and weight 

Volume: Weight: 

1 nl 1 µg 

1 µl 1 mg 

1 ml 1 g 

1 L 1,000 g (1 kg) 

1.1.2. Units and rates of decay 

Conversion factors: 

1 day = 1.44 x 10 3 min = 8.64 x 10 4 s 

1 year = 5.26 x 10 5 min = 3.16 x 10 7 s 

1.1.3. Foreign units 

Lengths: 

1 inch (in) = 2.54 cm 

1 foot (ft) = 12 in = 30.48 cm 

Volumes (GB): 

1 pint (pt) = 0.5679 L 

1 quart (qt) = 2 pints = 1.1359 L 

1 gallon (gal) = 4 quarts = 4.5435 L 

Volumes (US): 

1 pint (pt) = 0.4729 L 

1 quart (qt) = 2 pints = 0.9458 L 

1 gallon (gal) = 4 quarts = 3.7832 L 

Temperature: 

1° Kelvin (K) = °C + 273.151° 

Fahrenheit (°F) to Celcius (°C) = [(°C - 32) x 10] ÷ 18 

1.2. Conversion factors, old units to actual units 

Size: Old unit resp. 

commonly used unit: 

Actual unit: 

Pressure 1 at 0.980665 bar 

1 Atm (=760 Torr) 1.01325 bar 

1 Torr (mm Hg) 1.3332 mbar 

1 mWS 0.0980665 bar 

1 mmWS 0.0980665 mbar 

Energy 1 mkp 9.80665 J 

Radioactive 

decay 

1 kcal 4.1868 kJ 

1 erg 10 -7 J 

1 dpm 60 Bq 

1 Ci = 2.22 x 10 12 dpm 3.7 x 10 10 Bq 

1 mCi = 2.22 x 10 9 dpm 3.7 x 10 7 Bq 

1 µCi = 2.22 x 10 6 dpm 4.7 x 10 4 Bq 

1.3. Metric prefixes 

E = exa = 10 18 

P = peta = 10 15 

T = tera = 10 12 

G = giga = 10 9 

M = mega = 10 6 

k = kilo = 10 3 

h = hecto = 10 2 

da = deca = 10 1 

d = deci = 10 -1 

c = centi = 10 -2 

m = milli = 10 -3 

µ = micro = 10 -6 

n = nano = 10 -9 

p = pico = 10 -12 

f = femto = 10 -15 

a = atto = 10 -18 

z = zepto = 10 -21 

1.4. Greek alphabet 

a A Alpha 

b B Beta 

g G Gamma 

d D Delta 

e E Epsilon 

z Z Zêta 

h H Êta 

θ Q Thêta 

i I Iota 

k K Kappa 

l L Lambda 

m M Mu 

n N Nu 

x X Xi 

o O Omicron 

p P Pi 

r R Rho 

s S Sigma 

t T Tau 

u U Upsilon 

j F Phi 

c C Chi 

y Y Psi 

w W Omega 

In the U.S.: Eppendorf North America 800-645-3050 • In Canada: Eppendorf Canada Ltd. 800-263-8715 

Info 

email: info@eppendorf.com • www.eppendorf.com 

261 

Appendix | General information for the lab

General information for the lab | Appendix 

262 

Info 


2.1. Atomic numbers and atomic weights of elements 

Element Symbol Atomic number Atomic weight 

Actinium Ac 89 227.03 

Aluminum Al 13 26.98 

Americium Am 95 243.06 

Antimony Sb 51 121.75 

Argon Ar 18 39.95 

Arsenic As 33 74.92 

Astatine At 85 210.99 

Barium Ba 56 137.34 

Berkelium Bk 97 247.07 

Beryllium Be 4 9.01 

Bismuth Bi 83 208.98 

Boron B 5 10.81 

Bromine Br 35 79.9 

Cadmium Cd 48 112.4 

Caesium Cs 55 132.91 

Calcium Ca 20 40.08 

Californium Cf 98 249.07 

Carbon C 6 12.01 

Cerium Ce 58 140.12 

Chlorine Cl 17 35.45 

Chromium Cr 24 52 

Cobalt Co 27 58.93 

Copper Cu 29 63.55 

Curium Cm 96 245.07 

Dysprosium Dy 66 162.5 

Einsteinium Es 99 254.09 

Erbium Er 68 167.26 

Europium Eu 63 151.96 

Fermium Fm 100 252.08 

Fluorine F 9 18.99 

Francium Fr 87 223.02 

Gadolinium Gd 64 157.25 

Gallium Ga 31 69.72 

Germanium Ge 32 72.59 

Gold Au 79 196.97 

Hafnium Hf 72 178.49 

Helium He 2 4 

Holmium Ho 67 164.93 

Hydrogen H 1 1.01 

Indium In 49 114.82 

Iodine I 53 126.9 

Iridium Ir 77 192.22 

Iron Fe 26 55.58 

Khurchatovium Kh 104 260 

Krypton Kr 36 83.8 

Lanthanum La 57 138.91 

Lawrencium Lr 103 256 

Lead Pb 82 207.2 

Lithium Li 3 6.94 

Lutetium Lu 71 174.97 

Magnesium Mg 12 24.31 

Manganese Mn 25 54.94 

Product appearance, specifications, and/or prices are subject to change without notice. 

2.1. Atomic numbers and atomic weights of elements 

Element Symbol Atomic number Atomic weight 

Mendelevium Md 101 255.09 

Mercury Hg 80 200.59 

Molybdenum Mo 42 95.94 

Neodymium Nd 60 144.24 

Neon Ne 10 20.18 

Neptunium Np 93 237.05 

Nickel Ni 28 58.71 

Niobium Nb 41 92.91 

Nitrogen N 7 14.01 

Nobelium No 102 255 

Osmium Os 76 190.2 

Oxygen O 8 16 

Palladium Pd 46 106.4 

Phosphorus P 15 30.97 

Platinum Pt 78 195.09 

Plutonium Pu 94 242.06 

Polonium Po 84 208.98 

Potassium K 19 39.1 

Praseodymium Pr 59 140.91 

Promethium Pm 61 145 

Protactinium Pa 91 231.04 

Radium Ra 88 226.03 

Radon Rn 86 222.02 

Rhenium Re 75 186.2 

Rhodium Rh 45 102.91 

Rubidium Rb 37 85.47 

Ruthenium Ru 44 101.07 

Samarium Sm 62 150.4 

Scandium Sc 21 44.96 

Selenium Se 34 78.96 

Silicon Si 14 28.09 

Silver Ag 47 107.87 

Sodium Na 11 22.99 

Strontium Sr 38 87.62 

Sulfur S 16 32.06 

Tantalum Ta 73 180.95 

Technetium Tc 43 98.91 

Tellurium Te 52 127.6 

Terbium Tb 65 158.93 

Thallium Tl 81 204.37 

Thorium Th 90 232.04 

Thulium Tm 69 168.93 

Tin Sn 50 118.69 

Titanium Ti 22 47.9 

Tungsten W 74 183.85 

Uranium U 92 238.03 

Vanadium V 23 50.94 

Xenon Xe 54 131.3 

Ytterbium Yb 70 173.04 

Yttrium Y 39 88.91 

Zinc Zn 30 65.37 

Zirconium Zr 40 91.22


2.2. Acids and bases 

Acids 

Molecular weight % by weight Molarity (approx.) 1 M solution (ml/L) Specific gravity 

Acetic acid (glacial) 60.05 99.6 17.4 57.5 1.05 

Formic acid 46.03 90 23.6 42.4 1.205 

98 25.9 38.5 1.22 

Hydrochloric acid 36.46 36 11.6 85.9 1.18 

Nitric acid 63.01 70 15.7 63.7 1.42 

Perchloric acid 100.46 60 9.2 108.8 1.54 

72 12.2 82.1 1.70 

Phosphoric acid 98.00 85 14.7 67.8 1.70 

Sulfuric acid 98.07 98 18.3 54.5 1.835 

Bases 

Ammonium hydroxide 35.0 28 14.8 67.6 0.90 

Potassium hydroxide 56.11 45 11.6 82.2 1.447 

Sodium hydroxide 40.0 50 19.1 52.4 1.53 

2.3. Isotopes—physical properties of commonly used isotopes 

Nuclide Half-life Emission Energy, 

max. (MeV) 

Range of 

emission, max. 

3 H 12.43 years b 0.0186 0.42 cm (air) – 

14 C 5,370 years b 0.156 21.8 cm (air) – 

Rec. shielding 

(half value layer) 

32 P 14.3 days b 1.71 610 cm (air) Acrylic (1 cm) 

0.8 cm (water) – 

0.76 cm (acrylic) – 

33 P 25.4 days b 0.249 49 cm Acrylic (1 cm) 

35 S 87.4 days b 0.167 24.4 cm (air) – 

125 I 60 days g 0.27–0.035 0.2 mm (lead) Lead (0.02 mm) 


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Dispensing systems function by one of two different physical 

principles: dispensing of liquid takes place either via an air 

cushion or by positive displacement. These two different 

3.1. Air-cushion principle (air displacement) 

Fig.1: Cutaway model of an air-cushion pipette (Eppendorf Reference ®1 ) 

Air-cushion pipettes consist of a piston-cylinder system that 

performs the actual measurement (Fig. 1). An air cushion is what 

separates the aspirated sample in the pipette tip from the piston 

inside the pipette. 

Upward movement of the piston produces partial vacuum in 

the tip, which causes the liquid to be drawn into the tip. The air 

cushion, moved by the piston, acts like an elastic spring from 


principles are described in detail in this section. Directly below we 

describe piston-stroke pipettes and their ergonomic function, a key 

feature for anyone using a manual dispensing system. 

Pushbutton 

which the volume of liquid in the tip is suspended. Due to 

expansion of this air volume, the volume moved by the piston 

is approx. 2% to 4% greater than the aspirated volume of liquid 

required. Such expansion is compensated for by a factor that 

takes into account the dead volume and the lift height in the tip 

of the pipette. The air-cushion pipette is specially designed to 

minimize the influences of temperature, air pressure and humidity 

so that the dispensing accuracy is not impaired. 

1 U.S. Pat. 5,511,433 

2 On volumes above 20 µl 

Digital indicator (adjustable pipettes) 

Piston (ceramic 2 ) 

Piston seal 

Air cushion 

Tip ejection spring 

Ejection sleeve 

Pipette cone


Fig. 2: Function of an air-cushion pipette (Eppendorf Research ® *) 

Rest position 

1. Stop 

(Measuring stroke) 

Rest 

position 

Piston 

moves 

down 

Preparation for 

liquid aspiration 

� � � 

� � 

� 

Figure 2 shows the design principle of the air-cushion pipette 

based on the rest position (1). To prepare for aspiration of the 

liquid (2) press the pushbutton down to the first stop (measuring 

stroke). The piston moves down, displacing a volume of air that 

corresponds to the selected aspirating volume of the liquid. 

To aspirate liquid (3) vertically immerse the pipette tip a few 

millimeters into the liquid. As the pushbutton slowly moves 

back, a partial vacuum is created in the pipette tip, aspirating 

the required volume through the tip opening. To dispense 

liquid (4), slowly press the pushbutton down to the first stop 

Liquid 

aspiration 

(measuring stroke). The piston moves down, emptying the tip. 

Rest position 

Liquid 

dispensing 

1. Stop (Measuring stroke) 

2. Stop 

(Blow-out) 

Piston 

moves 

down 

To empty the tip completely (“blow-out”, 5), press the pushbutton 

down to the second stop (blow-out), raise the pipette with the 


Info 

pushbutton still depressed and wipe against the wall of the vessel. 

After the pushbutton has moved back, the piston returns to the 

rest position (6). 

The immersion depth of the pipette tip has a significant effect on 

the result. If the tip is immersed too deeply into the liquid, drops 

form on the outside, possibly falsifying the dispensing volume. If 

the tip is not immersed deeply enough into the liquid, turbulence 

is produced, and an incorrect volume will be aspirated. 

*U.S. Pats. 5,531,131/6,199,435 

Blow-out 

Blow-out Tip 

ejection 

Tip ejector 

is pressed 

Tip 

ejector 

moves 

down 


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3.2. Principle of positive displacement 

Dispensing systems that operate according to the principle of 

positive displacement are subject to physical influences other 

than those that occur with the air-cushion systems. Air-cushion 

effects are not applicable here, which makes these devices 

suitable for dispensing liquids as well as for applications that 

are considered critical in conjunction with air-cushion systems. 

Such applications include: liquids with high vapor pressure, high 

viscosity or high density, and applications in molecular biology 

such as the Polymerase Chain Reaction, which calls for an 

absence of aerosols. 

Compared with air-cushion systems, the dispensing accuracy 

of positive-displacement systems depends even more on the 

disposable plastic tip used. Unlike the tips used with air-cushion 

systems, the tips of positive-displacement systems have an 

integrated piston, which is coupled to the piston rod of the 

dispensing device during the pipetting (Fig. 3)—and performs the 

Fig. 3: Coupling of a positive-displacement pipette 

with a matching pipette tip: 

The tip has an integrated piston (2) that securely connects to the 

piston rod of the pipette during pipetting (1). The liquid in the tip 

only reaches up to the hermetic sealing lip (3), thus preventing 

aerosols from entering the pipette. 


actual dispensing process. These tips are specially designed for 

use in positive-displacement systems and cannot be replaced by 

standard pipette tips or a tip type that may be foreign to the system. 

Figure 4 shows how a positive-displacement system functions. To 

prepare for aspiration of the liquid (1) press the pushbutton down 

to the first stop, which moves the piston down to the corresponding 

position. To aspirate the liquid (2) vertically immerse the pipette tip 

a few millimeters into the liquid, then allow the pushbutton to slide 

back slowly so that the piston moves up, and the required volume 

of liquid is aspirated into the tip by the partial vacuum produced. 

To dispense the liquid into a vessel (3) slowly press the pushbutton 

down to the first stop (measuring stroke), which allows the piston 

rod in the pipette to move the tip down and thus displace the liquid 

from the tip. Hold the pushbutton down and draw the tip up against 

the wall of the vessel. To eject the tip (4) press the pushbutton all 

the way down. 

Fig. 4: Function of the Eppendorf ® 

positive-displacement pipette 

Rest position 

1. Stop (measuring stroke) 

Tip ejection 

Preparation 

for liquid 

aspiration 

Liquid 

aspiration 

Liquid 

dispensing 

� � � 

� 

Tip 

ejection


4.1. Air-cushion pipettes 

Fig. 5: Forward pipetting 

1: Press key down to first stop. 

Immerse tip a few millimeters 

into liquid. 

Fig. 6: Reverse pipetting 

1: Press key down to second 

stop. Immerse tip a few 

millimeters into liquid. 

The dispensing techniques used most frequently are forward 

pipetting, reverse pipetting, dispensing, sequential dispensing and 

diluting. While mechanical pipettes are only suitable for forward and 

reverse pipetting, electronic dispensing systems frequently cover all 

of these functions. Each dispensing technique that may be suitable 

for a particular application may have a different impact on the 

analysis results. 

2: Release key slowly. 

Tip will fill up. 

2: Release key slowly. 

Tip will fill up. 

The foward pipetting technique is suitable for aqueous solutions 

that may contain low concentrations of protein or detergents; 

prewetting the tip improves the analysis result. With viscous or 

foaming liquids or when dispensing very small sample volumes, 

the results may be greatly improved by reverse pipetting. Here, the 

liquid is aspirated with blow-out and dispensed without blow-out. 

A residue of liquid remains in the plastic tip, and it is subsequently 

3: Dispense liquid by pressing 

key down to first stop. Then 

blow out remaining liquid by 

pressing key down to second 

stop. 

3: Dispense liquid by pressing 

key down to first stop. Some 

liquid will remain in the tip. 

discarded or returned to the aspirating vessel. During the dispen- 

sing process the aspirated liquid is dispensed in defined stages. 

This technique is often used when processing long test series 

or filling microtest plates. With sequential dispensing, different 

volumes of a solution are dispensed one after the other in a 

specified sequence. This technique is often used with serologic 

work processes or with similar applications. 

Prewet tip when working with 

volumes greater than 10 µl. 

When diluting liquids, an initial volume is first aspirated and then 


Info 

This application is 

recommended for standard 

solutions, such as water, 

buffers, diluted saline solutions 

and diluted acids/alkalis. 

This application is 

recommended for viscous 

solutions, solutions with a 

high vapor pressure and 

wetting agents. 

followed by an air bubble and the second volume. Both volumes are 

then dispensed in one step. This dispensing technique increases 

throughput, and it reduces fatigue as compared with performing 

aspiration and dispensing twice with manual pipettes—particularly 

in the case of sizeable volumes and multichannel pipettes. 


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4.2. Optimum handling of manual pipettes 

Regardless of which dispensing technique is performed, the 

following items should be taken into consideration when pipetting: 

‡ In the case of air-cushion pipettes, select a pipette tip that 

minimizes the air cushion between the pipette piston and the 

surface of the liquid. The smaller the tip, the lower the air volume, 

and the greater the accuracy of the results will be. 

‡ When aspirating the liquid, the tip should only be immersed a 

few millimeters in the medium (Tab. 1, Fig. 7). 

‡ The filled tip should be moved up against the wall of the vessel 

to avoid residues of liquid on the outside of the tip. 

‡ Prewetting the tip two or three times will improve the accuracy 

and precision of the results. 

‡ Liquid should be aspirated slowly and evenly. 

‡ A waiting period of 1s to 3 s should be allowed for the liquid to 

rise in the tip. 

Table. 1: Optimum immersion depth for 

different pipetting volumes 

Volume (µl) Optimum immersion depth (mm) 

0.1–1 1 

1–500 2–3 

101–1,000 2–4 

1,001–10,000 3–6 

The pipette should be held vertically during aspiration. When 

aspirating, the hydrostatic pressure of the liquid column in the tip 

falls as the pipette‘s angle of inclination increases. This will result 

in an increased aspiration volume (Fig. 7). The deviation in volume 

can be estimated for any pipette volume and angles of inclination. 

At a pipette angle of 45° the extra volume with a 1,000 µl pipette 

is 2.9 µl or 0.29%; for a 100 µl pipette at an angle of 60°, an extra 

volume of 0.53 µl or 0.53% will result (Fig. 7). 


Fig. 7: Influence of immersion depth and holding angle of 

pipette during aspiration of liquid 

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Research 

Research 

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Systematic �� Systematic �� Systematic 

�� 

measurement 

�� 

measurement 

�� measurement 

�� 

�� 

�� 

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deviation 

deviation 

deviation 

0.2–0.4% 

0.6–0.8% 

1.0–1.2% 

Pipette vertical, 

immersion depth 

of tip in liquid 

approx. 1 cm 

The fact that different people do not pipette exactly the same 

volume with exactly the same pipette can also be explained by 

factors such as different angles of inclination when aspirating liquid. 

Although the effect is small in each instance, the error may be 

much greater when all of the differing factors are added together. 

Research 

Research 

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Pipette vertical, 



approx. 3 cm 

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Research 

Research 

Pipette held at an 

angle of 30° to 40°, 



approx. 3–4 cm


4.3. Possibility and prevention of contamination 

A distinction is made between three possible sources of contamination: 

‡ From the pipette to the sample 

‡ From the sample to the pipette 

‡ From sample to sample, also known as carryover. 

Fig. 8: 

Preventing contamination of a piston-stroke pipette Contamination from sample to sample 

Piston-stroke 

pipette 

with 

Standard tip 

Risk of 

contamination 

via aerosols 

Filter 

Unprotected 

area 

The first source of contamination is via a contaminated pipette 

tip or pipette. The contamination of samples can be prevented by 

using sterile pipette tips and cleaning or autoclaving the pipette. 

The second type of contamination involves infiltration of the sample 

or its aerosols into the pipette itself. To prevent this, the pipette 

should be held vertically when aspirating the liquid. It is also recom- 

mended to immediately eject the pipette tip after usage to prevent 

vapors from entering the pipette and to store the pipette upright 

in the pipette stand. In addition, the pushbutton should be slowly 

moved up when aspirating. 

Piston-stroke 

pipette 

with 

Filter tip 

Protected 

area 

Aerosol 

barrier 

No risk of 

contamination 

via aerosols 

Positivedisplacement 

with 

integrated 

piston 

in the tip 

Sealing lip 

of 

piston 

Rest of sample A 

in the 

pipette tip 

Contamination 

of 

sample B 

For pipettes the most effective protection against contamination 


Info 

is the use of filter tips. They prevent aerosols from penetrating and 

thus, contaminating the pipette (Fig. 8 left). The use of positive-dis- 

placement pipettes, whose tips feature a piston with an integrated 

leakage seal, also safeguard against contamination (Fig. 8 left). 

The third type of contamination occurs during the dispensing of 

samples. Carryover takes place when part of sample A adheres to 

the inside surface of the pipette tip in droplet form. It is then mixed 

with sample B, thus producing a false test result (Fig. 8 right). To 

prevent sample-to-sample contamination, the pipette tip should be 

discarded after the dispensing of each sample. 


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5. Calibration 

5.1. Gravimetric test procedure 

The prerequisite for a gravimetric test procedure is an analytical 

balance or equivalent weighing device. The scale graduation value 

must correspond to the selected volume of the dispensing system 

to be examined (Tab. 2). In order to minimize the evaporation loss 

during weighing—particularly with small volumes (< 50 µl)—a 

weighing vessel that is suitable for the volume and, possibly, 

an evaporation trap (Fig. 9) should be used. 

In addition, the following points must be taken into account 

during gravimetric calibration: 

‡ Testing must take place in a room that is free from drafts. 

‡ The test room must have a relative humidity > 50% and a 

constant temperature (± 0.5 °C) between 15 °C and 30 °C. 

‡ Prior to testing, the dispensing system and the test liquid should 

stand in the test room for a minumum of two hours to equalize with 

the room conditions. 

‡ The test cycles must be as uniform as possible. It is important 

for the measuring time to be as identical as possible within 

each cycle, as well as from cycle to cycle, in order to reliably 

calculate and compensate for evaporation effects during a 

measurement series. 

‡ Degassed and distilled—or ion-free water—must be used as 

the test liquid. 

With adjustable-volume pipettes three different volumes 

are tested: 

‡ Nominal volume (greatest volume that can be adjusted by 

the user and set by the manufacturer) 

‡ 50% of the nominal volume 

‡ The lower limit of the useful volume, which must be 10% of the 

nominal volume. 

‡ Fig. 9: Pipette calibration at analytical balance with 

evaporation trap. 


Generally 10 measurements per test volume are performed. 

However, the number of test volumes, of measurements per test 

volume and, with multichannel pipettes, channels tested may be 

altered in a manner that best satisfies the users’ specific testing 

requirements. 

According to initial adjustment by the manufacturer, pipettes 

and dispensers must be tested for the dispensing of test liquid 

into a weighing vessel. The test procedure is as follows: 

‡ The weighing vessel is filled with test liquid up to a level of 

min. 3 mm. 

‡ The temperature of the liquid, the room temperature and the 

air pressure should be measured. (The temperatures and the air 

pressure are necessary for selection of the correction factor Z). 

‡ The pipette is equipped with the appropriate pipette tip, and 

the pipette tip prewetted five times with test liquid to produce 

a humidity balance in the “dead” air volume. 

‡ The tip is then changed and prewetted once more. 

‡ The balance is calibrated. 

‡ The pipette is held vertically and the pipette tip is immersed a 

few millimeters (see page 268, Tab. 1) in the test liquid. 

‡ The volume to be tested should be aspirated slowly and evenly. 

Here, a waiting period of 1s to 3 s should be taken into account. 

‡ The pipette tip is then removed slowly from the liquid, 

wiping it against the wall of the vessel. 

‡ The filled tip is slanted against the wall of the weighing vessel, 

and the test liquid is slowly dispensed to the first stroke 

(measuring stroke). 

‡ The residual liquid is dispensed by pressing the pushbutton 

to the second stop (blow-out). 

‡ The pushbutton is held down, and the tip drawn up against 

the wall of the vessel. 

‡ The weighing value, i.e., the mass of liquid pipetted, 

is then calculated. 

All measurements in a measurement series are performed as 

described. 

Table 2: Standard values for 

gravimetric testing of pipettes 

Random 

measurement 

deviation 

(imprecision) 

(µl) 

Scale 

graduation 

value 

(mg) 

Type of balance 

up to 0.01 0.001 Microbalance 

up to 0.01 0.01 Semi-microbalance 

up to 0.01 0.1 Analytical balance


6.1. Decontamination and cleaning of air-cushion pipettes 

Substance classification Handling, special features Decontamination and cleaning 

Aqueous solutions and buffers Pipette is calibrated with distilled water. 

Results are extremly accurate. 

Inorganic acids It is advisable to occasionally rinse the 

lower part of the pipette with distilled 

water if high-concentration acids are 

pipetted frequently; using epTIPS Filter 

is also recommended. 

Alkalis It is advisable to occasionally rinse the 

lower part of the pipette with distilled 

water if high-concentration alkalis are 

pipetted frequently; using epTIPS Filter 

is also recommended. 

Potentially infectious liquids To avoid contamination, epTIPS Filter 

should be used; alternatively, positivedisplacement 

systems can be used. 

Cell cultures To ensure sterility, epTIPS Filter should 

be used. 

Organic solvents 1. Density is different than water; 

therefore, it is necessary to adjust the 

pipette. 

2. Due to the high vapor pressure and 

the changes in the wetting behaviors, 

pipetting should be carried out rapidly. 

3. After pipetting is finished, open 

the pipette and allow the liquid to 

evaporate. 

Radioactive solutions To avoid contamination, epTIPS Filter 



Proteins/nucleic acids To avoid contamination, epTIPS Filter 



*U.S. Pat. 5,511,433 

Open pipette, rinse contaminated parts well with 

distilled water. Allow to dry at maximum 60 °C in 

dryer compartment. Lubricate piston if necessary. 


Info 

The plastics used in Eppendorf ® pipettes are 

acid-resistant, as are the ceramic pistons (except to 

hydrofluoric acid); however, aerosols from the acids can 

enter the lower part of the pipette and affect performance. 

Clean as described above in “Aqueous solutions and 

buffers.” 

The plastics used in Eppendorf pipettes are 

alkali-resistant, as are the ceramic pistons; however, 

aerosols from the alkalis can enter the lower part of the 

pipette and affect its performance. Clean as described 

above in “Aqueous solutions and buffers.” 

Autoclave the contaminated parts at 121 °C for 20 min 

(the Eppendorf ® Reference Series 2000* pipette can be 

completely autoclaved; partially disassemble beforehand 

by unscrewing twice) or immerse the lower parts in normal 

laboratory disinfectants, rinse with distilled water, and 

allow to dry as described above. 

Proceed as described above in “Potentially infectious 

liquids.” 

This evaporation process is normally sufficient 

for liquids with high vapor pressure. Alternatively, 

immerse the contaminated parts in detergent, 

rinse well with distilled water and dry as described 

above. Lightly lubricate piston. 

Open pipette and place contaminated parts in complex 

solutions or special cleaning solutions. Rinse well with 

distilled water and dry as described above. 

1. Proteins: Open pipette, rinse pipette with detergent, 

rinse with distilled water and dry as described above. 

2. Nucleic acids: Decontaminate by boiling in glycine/HCL 

buffer (pH = 2) for 10 minutes (this prevents unwanted DNA 

from being detected on an agarose gel). Rinse well with 

distilled water and dry as described above. Lightly 

lubricate piston. 

3. Clean with sodium hypochlorite (5%), rinse well with 

distilled water and dry as described above. Lightly lubricate 

piston. 


271 



272 

Info 


6.2. Possible sources of error when pipetting with air-cushion pipettes 

Influencing parameter Effect* Can be corrected by Can be recognized by 

Difference in density of the liquid to be 

pipetted versus that of the water used for 

adjustment 

Difference in vapor pressure of the liquid to 

be pipetted versus that of the water used 

for adjustment 

Uneven piston movement 

Uneven rhythm and timing during pipetting 

Plunging depth of the pipette tip and 

handling angle during pipetting 

Failure to prewet pipette tip 

Failure to wipe pipette tip on the vessel 

wall 

Leaky pipette tips 

up to 1.0% Readjusting the pipette (observe 

user information) 

up to 2.0% Sufficient prewetting of the pipette 

tip; observe EN ISO 8655-6 

up to 0.5% Smooth operation of piston; 

cleaning and lubricating of 

the piston 


Comparing the density of the liquid 

to be pipetted with that of water 

Dripping tip 

Monitoring your pipetting 

technique 

up to 1.5% Even pipetting technique Maximum permitted errors 

are exceeded 

up to 1.0 Holding pipette in vertical position. 

Observe user information or 

EN ISO 8655-6 

Visual control of plunging depth 

and handling angle 

up to 2% Prewetting of pipette tip Maximum permitted errors 

are exceeded 

up to 3.0% Wiping of the pipette tip on the 

vessel wall 

Observe EN ISO 8655-6 

0.5% up to 50% Using Eppendorf epTIPS or 

recommended pipette tips 

*The possible measurement deviations are reference values and are quoted in percent from the nominal value. 

6.3. Conversion of different pressure units 

Conversion Multiply 

by 

from into 

bar Pascal (Pa) 10 5 

bar Hectopascal (hPa) 10 3 

bar Kilopascal (kPa) 10 2 

millibar (mbar) Pascal (Pa) 10 2 

millibar (mbar) Hectopascal (hPa) 1 

millibar (mbar) Kilopascal (kPa) 0.1 

Maximum permitted errors 

are exceeded 

Dripping tip or maximum 

permitted errors are exceeded


6.4. Physical data of liquids (relevant examples) 

Substance Formula Boiling point 

(°C) 

Density 

mg/µl 

(20 °C) 

Vapor pressure 

hPa 

(20 °C) 

Viscosity 

mPas 

(20 °C) 

Acetic acid CH 3COOH 118 1.06 15.4 1.53 (25 °C) 

Acetone C 3H 6O 56.5 0.79 233 0.32 

Ammonia NH 3 37.7 0.91 500 

Butanol C 4H 9OH 117.2 0.81 6.7 

Chloroacetic acid CH 2ClCOOH 189 1.60 

Chloroform CHCl 3 61.7 1.47 213 

Ethanol C 2H 5OH 78.5 0.79 59 1.2 

Formic acid HCOOH 100.7 1.23 42 1.8 

Glycerol C 3H 8O 3 290 1.26 

Hydrochloric acid HCl 1.15 213 2 

Hydrofluoric acid HF 112 1.13 

Methanol CH 3OH 65 0.79 128 0.597 

Nitric acid HNO 3 121.8 1.41 9 1.49 (40 °C) 

Phenol C 6H 5OH 181.4 1.06 1.099 (100 °C) 

Phosphoric acid H 3PO 4 1.71 2 

Potassium hydroxide solution KOH 1.29 

2-Propanol (isopropanol alcohol) C 3H 7OH 82.4 0.78 42.5 2.2 

Sodium hydroxide solution NaOH 1.33 19 

Sulfuric acid H 2SO 4 1.84 0.0016 26.9 

Trichloroacetic acid CCl 3COOH 196 1.62 


Info 


273 



274 

Info 


6.5. Chemical resistance of disposables 

Substance Formula Concentration 

(%) 

PE 

(Polyethylene) 


PP 

(Polypropylene) 

PC 

(Polycarbonate) 

Acetaldehyde CH 3CHO 40 0 4 2 2 4 4 4 4 

Acetic acid CH 3COOH 96 1 2 1 2 3 3 3 4 

Aqua regia 4 4 3 4 4 4 3 4 

Benzene 100 3 4 3 4 4 4 4 4 

Benzine 100 3 4 3 4 2 2 3 4 

Butanol C 4H 9OH 100 1 3 1 3 1 1 1 1 

Dichloromethane CH 2Cl 2 100 4 4 3 4 0 0 0 0 

Diethyl ether (C 2H 5) 2O 100 2 3 3 0 4 4 4 0 

Dioxan C 4H 8O 2 100 2 3 3 3 4 4 4 4 

Glycerol C 3H 5(OH) 3 1 1 1 1 1 1 1 1 

Hydrofluoric acid* HF up to 40 2 2 2 2 4 0 1 1 

Methanol CH 3OH 100 2 3 2 2 2 2 1 1 

Petroleum ether 100 3 3 2 3 2 3 3 3 

Phenol C 6H 5OH watersaturated 1 1 1 1 3 3 3 4 

Polyethylene glycol (PEG) 40 1 1 0 0 0 0 0 0 

Pyridine 100 2 3 3 3 3 3 4 4 

Sodium hydroxide solution up to 40 1 1 1 1 3 3 1 1 

Sodium hypochlorite diluted 2 3 1 2 2 0 2 3 

Trichloroacetic acid CCl 3COOH 100 3 4 1 1 2 2 0 0 

*Warning! Attacks the ceramic piston of the pipette. 

First number: chemical resistance at 20 °C, second number: at 50 °C 

1 = Resistant; the material does not change even after longer contact with the respective substance. 

2 = Practically resistant; the material does not change after longer contact with the substance over several weeks. 

3 = Conditionally resistant; if the material was in contact with the substance for only a short time, it does not change. 

4 = Non-resistant; the material changes even after brief contact with the substance. 

0 = No value available. 

PS 

(Poly- 

styrene)


6.6. Error limits in accordance with EN ISO 8655 

The following tables contain the error limits of the latest draft of 

the EN ISO 8655 standard in accordance with the volume used. 

These error limits are based on the overall pipette and tip system. 

The maximum permissible systematic errors of adjustable-volume 

piston pipettes with a volume range between 10 µl and 100 µl are 

± 0.8 µl, and the maximum permissible random errors are ± 0.3 µl 

for every measured value. 

For the maximum permissible errors of piston pipettes with 

intermediate nominal volumes between those given in Table 1, 

the absolute values for the next greater nominal volume shall apply. 

The conversion formula for the relative error limits based on the 

nominal volume is as follows: 

Error limit [µl] x 100% 

Nominal volume [µl] 

In the case of adjustable-volume piston pipettes, the nominal 

volume is the greatest possible user-selectable volume that is 

specified by the manufacturer. 


Info 

Systematic error: the difference between the dispensed volume 

and the nominal volume or selected volume of the piston-operated 

volumetric apparatus. The systematic error is ascertained by taking 

the mean of 10 measurements. 

Random error: the scatter of the dispensed volumes around the 

mean of the dispensed volume. The random error is ascertained 

by taking the repeatability standard deviation of 10 measurements. 

a) Single-channel piston pipettes 

Nominal volume µl 1 2 5 10 20 50 100 200 500 1,000 2,000 5,000 10,000 

Maximum 

permissible 

systematic errors 

±µl 0.05 0.08 0.125 0.12 0.2 0.5 0.8 1.6 4.0 8.0 16 40 60 

Maximum 

permissible 

random errors 

±µl 0.05 0.04 0.075 0.08 0.1 0.2 0.3 0.6 1.5 3.0 6.0 15.0 30.0 

b) The maximum permissible systematic and random errors of multichannel piston pipettes shall be equal to twice the values specified in 

Table 1 for single-channel piston pipettes. Each channel of the multichannel piston pipette, considered independently, shall meet these 

specifications 

c) Multiple delivery dispensers (repetitive pipettes) 

Nominal volume ml 0.001 0.002 0.003 0.01 0.02 0.05 0.1 0.2 0.5 1 2 5 10 25 50 100 200 

Maximum 

permissible 

systematic errors 

±µl 0.05 0.1 0.075 0.2 0.3 0.5 1.0 2.0 5.0 10 16 30 50 125 250 500 1,000 

Maximum 

permissible 

random errors 

±µl 0.05 0.1 0.11 0.25 0.4 0.75 1.0 2.0 3.0 4.0 8.0 15 30 75 125 250 500 


275 



276 

Info 


6.7. Conformity 

Accurate analysis results in the medical 

laboratory can only be ensured by high- 

precision work practices across-the-board, 

starting with pipetting, continuing with 

analysis and ending with evaluation. 

The lower the error tolerances of each 

individual device, the more accurate and 

precise the result. 

To ensure safe practices in the laboratory 

from the very beginning, a conformity 

assurance document is available for 

pipettes and pipette tips. This document 

guarantees that the error limits stipulated in 

the EN ISO 8655 standard are not 

All Eppendorf ® pipettes are characterized by high accuracy and precision levels. 

We hereby confirm that the following products conform with standardization regulations: 

Single-channel, fixed-volume 

Research 1 All sizes 

Reference 2 All sizes 

Single-channel, adjustable-volume 

Reference All sizes 

Research 3 All sizes 

Research pro 4 All sizes 

Maxipettor ® All sizes 

exceeded and that the equipment in 

question complies with all legal 

requirements. This applies to the 

combination of pipette and tip. 

Maxipettor In all combinations 

Multichannel 

Research All sizes 

Research pro All sizes 

Repeater ® Plus 5 

In combination with all Combitips Plus ® tips 6 , with the 

exception of the two smallest sizes: 0.1 ml and 0.2 ml 

Repeater stream/Xstream 

In combination with all Combitips Plus tips (dispensing mode), 

with the exception of the two smallest sizes: 0.1 ml and 0.2 ml 

1 U.S. Pat. 6,199,435 

2 U.S. Pat. 5,511,433 

3 U.S. Pat. 5,531,131 

4 U.S. Pats. 6,499,365/6,778,917 

5 U.S. Pats. 5,620,660/5,620,661/5,591,408/5,573,729 

6 U.S. Pats. 5,620,660/5,620,661 


At Eppendorf, we offer both the instrument 

and the consumable for a complete system. 

Although non-Eppendorf pipette tips may 

be used with our pipettes, compliance 

with the EN ISO stipulations can only be 

guaranteed by the conformity assurance 

document issued for a specific pipette. 

Take advantage of the pipette/tip team 

that conforms.


7.1. Conversion table for rpm/rcf (nomogram) 

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Centrifugation radius r of a point at distance h from 

bottom of tube with fixed-angle rotors at a 45° angle: 

r = r max – h x 0.71 

Example (see diagram): 

r max = 7.2 cm 

n = 14,000 rpm 

rcf max = 16,000 x g 

Please note that MiniSpin ® plus, 5415 D, 5415 R, 5417 C,* 

5417 R,* 5418, 5424, 5430, 5702, 5702 R, 5702 RH, 5804, 5804 R, 

5810 and 5810 R* centrifuges have automatic rpm/rcf conversion, 

which eliminates time-consuming manual calculations. 

The max. radius of the MiniSpin is 6 cm. 

* U.S. Pat. 5,496,254 

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277 



278 

Info 


7.2. k-factors and centrifugation times 

The k-factor, a value that is primarily determined by the rotor, 

affects the sedimentation time necessary during centrifugation. 

It is a measure for the sedimentation distance in the test tube, 

i.e., for the difference between the longest and shortest distance 

between the sample and the rotor axis (see diagram). 

The duration of separation in the test tube increases in direct 

proportion to its distance. The k-factor clearly depends on the 

angle of the tubes in the rotor and on the type of tubes used. 

A small k-factor means more rapid separation. The k-factor is also 

affected by the rotational speed; the higher the rotational speed, 

the quicker the separation. 

The formula is 

n = rotational speed; r min and r max: see diagram 

A direct comparison of two rotors is possible by calculating 

the relative speed of a separation in both centrifuge rotors. 

The formula for calculating the relative 

centrifugation time is 

t = Centrifugation time in the comparative centrifuge, 

calculated from experiment 

t x 

= Centrifugation time required in centrifuge X 

k = k-factor of the comparative centrifuge 

k x 

Example: 

= k-factor of centrifuge X 

The 30-position fixed-angle rotor in Centrifuges 5417 C* and 

5417 R* has a k-factor of 377 (with Safe-Lock microcentrifuge 

tubes) at a maximum speed of 14,000 rpm and a maximum rcf of 

20,800 x g. With the same test tube, the same rotor angle (45°) 

and the same maximum speed (14,000 rpm), the 18-position 

fixed-angle rotor of Centrifuge 5415 C attains a maximum rcf of 

16,000 x g and a k-factor of 525. 

*U.S. Pat. 5,496,254 


In the case of Models 5417 C and 5415 C: a centrifugation time 

of only 7 minutes is required in the 5417 C to attain the same 

separation performance for the selected separation example; 

in contrast, the 5415 C requires 10 minutes. 

Separation example: 

When determining centrifugation times, it is therefore advisable 

to take into consideration the physical characteristics of the 

centrifuge used, particularly when using critical samples and 

small sample quantities.

Index: Practical information for Molecular Biology 

Description Page 

II. Practical information for Molecular Biology: data, facts, tips and tricks 


1.1. Metric prefixes 280 

1.2. Abbreviations and symbols 280 

1.3. Tris-HCl Buffer, pH values 280 

1.4. Nucleic acid conversions 280 

1.4.1. Conversion of weight to absolute quantity (mol) 280 

1.4.2. Conversion of absolute quantity (mol) to weight 280 

1.4.3. Molecular weight of DNA fragments 281 

1.4.4. Molecular weights for nucleotides 281 

1.5. Protein conversions 281 

1.5.1. Conversion of proteins to DNA length 281 

1.5.2. Conversion of absolute quantity (mol) to weight 281 

1.6. DNA content of various organisms 281 

2. Genetic code, properties and molecular structure of amino acids 

2.1. Genetic code 282 

2.2. Nomenclature and properties of amino acids 282 

2.3. Molecular structure of amino acids 283 

3. Detection of nucleic acids and proteins 

3.1. Electrophoretic resolution 284 

3.1.1. Recommended agarose gel percentages for resolution of DNA 284 

3.1.2. Recommended polyacrylamide gel percentages for resolution of DNA 284 

3.1.3. Recommended polyacrylamide gel percentages for resolution of proteins 284 

3.2. Dye migration in electrophoresis 284 

3.2.1. Dye migration in polyacrylamide nondenaturing gels 284 

3.2.2. Dye migration in polyacrylamide denaturing gels 284 

3.3. Spectrophotometric conversion of nucleic acids and proteins 285 

3.3.1. Physical properties of nucleotides 285 

3.3.2. Biophysical data for deoxynucleoside triphosphates 285 

3.3.3. Conversion to concentration (µg/ml) 285 

3.3.4. Quantification made easy 286 

4. Application tips for PCR 

4.1. Procedure and parameters for PCR 287 

4.2. Calculating primer quantity 289 

4.2.1. Conversion to absolute quantity (in pmol) 289 

4.2.2. Conversion to weight (in µg) 289 

4.2.3. Calculation of the molar concentration of the primer 289 

4.3. Using gradient PCR to optimize different reaction parameters 290 

4.4. Eppendorf ® thermal cycler and SteadySlope ® technology: Temperature control means quality 291 

4.5. Optimization of the primer concentration (primer matrix) 292 

PCR disclaimers 292 


Info 


279 

Appendix | Info

Practical information for Molecular Biology | Appendix 

280 

Info 


1.1. Metric prefixes 

E = exa = 1018 P = peta = 1015 T = tera = 1012 G = giga = 109 M = mega = 106 k = kilo = 103 h = hecto = 102 da = deca = 101 d = deci = 10-1 c = centi = 10-2 m = milli = 10-3 µ = micro = 10-6 n = nano = 10-9 p = pico = 10-12 f = femto = 10-15 a = atto = 10-18 z = zepto = 10-21 1.4. Nucleic acid conversions 

1.4.1. Conversion of weight to absolute quantity (mol) 

1 µg of 1,000 bp DNA = 1.52 pmol = 9.1 x 10 11 molecules 

1 µg of pUC18/19 DNA (2,686 bp) = 0.57 pmol = 3.4 x 10 11 molecules 

1 µg of pBR322 DNA (4,361 bp) = 0.35 pmol = 2.1 x 10 11 molecules 

1 µg of M13mp18/19 DNA (7,250 bp) = 0.21 pmol = 1.3 x 10 11 molecules 

1 µg of l-DNA (48,502 bp) = 0.03 pmol = 1.8 x 10 10 molecules 

1.4.2. Conversion of absolute quantity (mol) to weight 

1 pmol of 1,000 bp DNA = 0.66 µg 

1 pmol of pUC18/19 DNA (2,686 bp) = 1.77 µg 

1 pmol of pBR322 DNA (4,361 bp) = 2.88 µg 

1 pmol of M13mp18/19 DNA (7,250 bp) = 4.78 µg 

1 pmol of l-DNA (48,502 bp) = 32.01 µg 


1.2. Abbreviations and symbols 

ds double-stranded (as in dsDNA) 

ss single-stranded (as in ssDNA) 

bp base pair 

kb kilobase: 1,000 bases or base pairs, as appropriate 

nt nucleotides (base) 

Mb megabase: 1,000,000 bp 

Da Dalton, the unit of molecular mass; 

kDa = 1,000 Da, MDa = 1,000,000 Da 

MW molecular weight (g/mol) 

M Molar or molarity, moles of solute 

per liter of solution (mol/L) 

mol Mole, absolute amount of a substance 

(1 mol = 6.023 x 10 23 , Avogadro number) 

l wavelength 

l max 

wavelength at the absorption maximum 

1.3. Tris-HCl buffer, pH values 

5 ºC 7.76 7.89 7.97 8.07 8.18 8.26 8.37 8.48 8.58 8.68 8.78 8.88 8.98 9.09 9.18 9.28 

25 ºC 7.20 7.30 7.40 7.50 7.60 7.70 7.80 7.90 8.00 8.10 8.20 8.30 8.40 8.50 8.60 8.70 

37 ºC 6.91 7.02 7.12 7.22 7.30 7.40 7.52 7.62 7.71 7.80 7.91 8.01 8.10 8.22 8.31 8.42


1.4.3. Molecular weight of DNA fragments 

500 bp dsDNA = 325,000 Da 

500 nt (nucleotide) ssDNA = 162,500 Da 

1 kb dsDNA = 660,000 Da 

1 kb ssDNA = 330,000 Da 

1 kb ssRNA = 340,000 Da 

1 MDa dsDNA = 1.52 kb 

Average molecular weight of dNMP = 325 Da 

Average molecular weight of 

DNA base pair 

1.5. Protein conversions 

1.5.1. Conversion of proteins to DNA length 

= 650 Da 

1.4.4. Molecular weights for nucleotides 

Compound Molecular weight (in Dalton) 

ATP 507.2 

CTP 483.2 

GTP 523.2 

UTP 484.2 

dATP 491.2 

dCTP 467.2 

dGTP 507.2 

dTTP 482.2 

AMP 347.2 

CMP 323.2 

GMP 363.2 

UMP 324.2 

dAMP 312.2 

dCMP 288.2 

dGMP 328.2 

dTMP 303.2 

Protein with a molecular weight of 10,000 = 270 bp DNA 

Protein with a molecular weight of 30,000 = 810 bp DNA 

Protein with a molecular weight of 37,000 (corresponds to 333 amino acids) = 1,000 bp DNA 

Protein with a molecular weight of 50,000 = 1.35 kb DNA 

Protein with a molecular weight of 100,000 = 2.7 kb DNA 

1.5.2. Conversion of absolute quantity (mol) to weight 

100 pmoles of 100,000 Da protein = 10 µg 



1.6. DNA content of various organisms 

Organism DNA content (in bp) (haploid Genome) 

Escherichia coli 4.2 x 10 6 

Arabidopsis thaliana 4.7 x 10 6 

Saccharomyces cerevisiae 1.4 x 10 7 

Drosophila melanogaster 1.4 x 10 8 

Homo sapiens 3.3 x 10 9 

Triticum aestivum (hexaploid wheat) 1.7 x 10 10 


Info 


281 

Appendix | Practical information for Molecular Biology


282 

Info 


2.1. Genetic code 

1 st Codon position 

2 nd Codon position 

U C A G 

U UUU Phe UCU Ser UAU Try UGU Cys U 

UUC UCC UAC UGC C 

UUA Leu UCA UAA Stop UGA Stop A 

UUG UCG UAG Stop UGG Trp G 

C CUU Leu CCU Pro CAU His CGU Arg U 

CUC CCC CAC CGC C 

CUA CCA CAA Gln CGA A 

CUG CCG CAG CGG G 

A AUU Ile ACU Thr AAU Asn AGU Ser U 

AUC ACC AAC AGC C 

AUA ACA AAA Lys AGA Arg A 

AUG Met, Start ACG AAG AGG G 

G GUU Val GCU Ala GAU Asp GGU Gly U 

GUC GCC GAC GGC C 

GUA GCA GAA Glu GGA AA 

GUG GCG GAG GGG G 

2.2. Nomenclature and properties of amino acids 


Termination codons: 

UAA: ochre 

UAG: amber 

UGA: opal 

Amino acid 3-letter symbol 1-letter symbol Major properties of side chains 

Alanine Ala A Aliphatic 

Arginine Arg R Basic group 

Asparagine Asn N Amide group 

Aspartic acid Asp D Acidic group 

Cysteine Cys C Sulfur-containing 

Glutamic Acid Glu E Acidic group 

Glutamine Gln Q Amide group 

Glycine Gly G No side chain 

Histidine His H Imidazole group 

Isoleucine Ile I Aliphatic 

Leucine Leu L Aliphatic 

Lysine Lys K Basic group 

Methionine Met M Sulfur-containing 

Phenylalanine Phe F Aromatic group 

Proline Pro P Aliphatic 

Serine Ser S Hydroxyl group 

Threonine Thr T Hydroxyl group 

Tryptophan Trp W Aromatic group 

Tyrosine Tyr Y Aromatic group 

Valine Val V Aliphatic 

3 rd Codon position 

In yeast mitochondria, the AUA 

and UGA codons are used 

for Met and Trp, not for Ile and 

Stop as normally. 

Start codon: 

AUG: Methionine


2.3. Molecular structure of amino acids 

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283 



284 

Info 

3. Detection of nucleic acids and proteins 

3.1. Electrophoretic resolution 

3.1.1. Recommended agarose gel percentages 

for resolution of DNA 

Gel percentage DNA size range 

0.5% 1–30 kb 

0.7% 0.8–12 kb 

1.0% 0.5–10 kb 

1.2% 0.4–7 kb 

1.5% 0.2–3 kb 

3–4% sieved agarose 0.01–1 kb 

3.1.3. Recommended polyacrylamide gel percentages for 

resolution of proteins 

Gel percentage Protein size range 

5% 57–212 kDa 

7.5% 36–94 kDa 

10% 16–68 kDa 

15% 12–43 kDa 

3.2. Dye migration in electrophoresis 

3.2.1. Dye migration in polyacrylamide nondenaturing gels 

3.2.2. Dye migration in polyacrylamide denaturing gels 


3.1.2. Recommended polyacrylamide gel percentages 

for resolution of DNA 

Gel percentage DNA size range 

3.5% 1,000–2,000 bp 

5.0% 75–500 bp 

8.0% 50–400 bp 

12.0% 35–250 bp 

15.0% 20–150 bp 

20.0% 5–100 bp 

Gel percentage Bromophenol blue Xylene cyanol 

3.5% 100 bp 460 bp 

5.0% 65 bp 260 bp 

8.0% 45 bp 160 bp 

12.0% 20 bp 70 bp 

15.0% 15 bp 60 bp 

20.0% 12 bp 45 bp 

Gel percentage Bromophenol blue Xylene cyanol 

5.0% 35 nucleotides 130 nucleotides 




20.0% 8 nucleotides 28 nucleotides

3. Photometric detection of nucleic acids and proteins 

3.3. Spectrophotometric conversion of nucleic acids and proteins 

3.3.1. Physical properties of nucleotides 

Compound Molecular weight l max (pH 7.0) Absorbance at l max 

of a 1 M solution (pH 7.0) 

ATP 507.2 259 nm 15,400 

CTP 483.2 271 nm 9,000 

GTP 523.2 253 nm 13,700 

UTP 484.2 260 nm 10,000 

dATP 491.2 259 nm 15,400 

dCTP 467.2 272 nm 9,100 

dGTP 507.2 253 nm 13,700 

dTTP 482.2 267 nm 9,600 

3.3.2. Biophysical data for deoxynucleoside triphosphates 

Component Molecular weight (Daltons) Molar extinction coefficient and l max 

dATP 491 15,200 at 259 nm 

dCTP 467 9,300 at 271 nm 

dGTP 507 13,700 at 253 nm 

dTTP 482 9,600 at 267 nm 

3.3.3. Conversion to concentration (µg/ml) 

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Double-stranded DNA (dsDNA): 

A 260 = OD 260 = 1 for a 50 µg/ml dsDNA-solution* 

Single-stranded RNA: 

A 260 = OD 260 = 1 for a 40 µg/ml RNA-solution* 

Single-stranded DNA (ssDNA): 

A 260 = OD 260 = 1 for a 33 µg/ml ssDNA-solution* 

Absorbance is calculated as: 

Molar extinction coefficient x concentration x path length 

(usually cuvette width) 

* These values apply when using a neutral-to-light alkaline measuring medium and 

a cuvette optical path length of 1 cm. 


Info 


285 



286 

Info 

3. Photometric detection of nucleic acids and proteins 

3.3.4. Quantification made easy 

With the aid of spectroscopy, the quantitative analysis of nucleic 

acids and proteins has established itself as a routine method in 

many laboratories. It includes absorption measurements in the 

ultraviolet and visible ranges. Proteins are measured (directly) 

at 280 nm and nucleic acids at 260 nm; colorimetric protein 

determination is performed in the 550 nm to 600 nm range. 

The Eppendorf ® BioPhotometer offers the following preinstalled 

test procedures: 

1. Nucleic acid determination 

DNA, RNA, oligonucleotides and even mononucleotides can be 

measured directly in aqueous solutions. Aqueous buffers with 

low ion concentrations (e.g., TE buffer) are ideal for this method. 

The concentration is determined by measuring at 260 nm against 

a blank and then calculating via a factor. Normally, the user has 

to calculate the concentration of the measured sample using the 

appropriate factor. The BioPhotometer can change these factors 

easily and will do all necessary calculations. 

The absorption of 1 OD at 260 nm is equivalent to approximately 

50 µg/ml dsDNA, 37 µg/ml ssDNA, 40 µg/ml RNA or 30 µg/ml 

for oligonucleotides. Purity determination of DNA interference by 

contaminants can be recognized by ratio calculations. The ratio 

A260/A280 is used to estimate the purity of nucleic acid since proteins 

absorb at 280 nm. Pure DNA should have a ratio of approximately 

1.8, whereas pure RNA should give a ratio of approximately 2.0. 

Absorption at 230 nm reflects contamination of the sample by 

substances such as carbohydrates, peptides, phenols or aromatic 

compounds. In the case of pure samples, the ratio A260/A230 should 

be > 2.0. 

2. Protein determination 

The protein content of a sample can be determined by various 

analytical procedures using the BioPhotometer. Calculations 

can be performed via factor or via a calibration curve with up 

to 10 standards. 

2.1 Absorption measurement at 280 nm (A280) A280 method may be used in concentrations of up to approximately 

4 mg/ml (3.0 A). This method is simple and rapid, but it may be 

disturbed by the parallel absorption of nonproteins (e.g., DNA). 

Unlike the colorimetric process, this method is less sensitive, 

requires higher protein concentrations and should thus be used 

with pure protein solutions. In addition to the direct absorbance 

display, evaluation is possible with the BioPhotometer via the 

Warburg formula or against a standard. 


2.2 Colorimetric determination (dye tests) 

Protein samples often consist of a complex mixture of many 

different proteins. The quantitative detection of the protein 

content is usually based on the reaction shown by functional 

groups of the proteins to dye-forming reagents. The intensity 

of the dye correlates directly with the concentration of the 

reacting groups and can be measured exactly. Different methods 

for dye-quantification are available depending on the type of dye 

being used: 

2.2.1 Lowry assay 

Specialist literature contains a multitude of modifications for the 

Lowry assay. The principal goal is to reduce the high susceptibility 

to interference. In comparison to the pure Biuret assay, the 

sensitivity of this assay is greatly increased. However, the Lowry 

method is adversely affected by a wide range of nonproteins. 

Additives such as EDTA, ammonia sulfate or Triton ® X-100, 

in particular, are incompatible with the test. 

2.2.2 Bicinchoninine acid assay (BCA) 

This test represents a highly regarded alternative to the Lowry 

assay. It is easier to perform, sensitivity can be varied using 

different temperatures and the dye complex is very stable. 

In addition, its sensitivity to detergents is similar to that of the 

Lowry method. This test is also highly susceptible to interference. 

2.2.3 Bradford assay 

This most rapid and easiest method to use is twice as sensitive as 

the Lowry or BCA tests and is thus the most sensitive quantitative 

dye assay. Its additional advantage is that a number of reducing 

substances (e.g., DTT and mercaptoethanol), which interfere with 

the Lowry or BCA test, have no adverse effect on results; however, 

it is sensitive to several detergents. The main disadvantage is 

that identical amounts of different standard proteins can cause 

considerable differences in the resulting absorption coefficients. 

3. Bacterial cell density 

The density of bacterial suspensions may be measured 

photometrically at OD600 without adding dyes. This applies, 

for example, to the preparation of competent cells, which 

must be in a specific phase of growth.


4.1. Procedure and parameters for PCR 

This PCR table is intended to provide all PCR newcomers with an 

overview of the common rules and concentrations that should be 

observed when developing their experiments. 

There are, of course, a number of exceptions and special points 

that we are unable to accommodate in the table. 

Steps Basic rules Comments 

1 

No. of source molecules No. of cycles Only perform as many cycles as necessary to 

10 

obtain sufficient PCR product. Too many cycles 

may cause the formation of unspecific products. 

5 25–30 

104 30–35 

No. of cycles 10 3 35–40 

2 

Denaturation step 

3 

Annealing step 

4 

Elongation step 

5 

Basic thermocycling 

protocol 

50 and less 20–30 followed by a second 

PCR with “nested” primers, 

i.e., with a primer pair that 

binds between the first 

two primers of the target 

sequence 

‡ 95 °C for 30 s or 97 °C for 15 s 

‡ For complex templates (e.g., genomic DNA) begin 

with an initial denaturation for 2–3 min before the 

actual cycles 

‡ G/C content greater than 50% increases the 

denaturation temperature 

For standard primers 

(approx. 20 nucleotides [nt]; 1 µM; 100% match) 

‡ Approx. 20 s, Tm should be approx. 55 °C–72 °C 

For calculation of molecule number please refer 

to table 1.4.1 and 1.4.2 on page 280. 

Inefficient denaturation is a frequent cause 

of errors. However: 

‡ T½ Taq at 92.5 °C = 2 h 

‡ T½ Taq at 95.0 °C = 40 min 

‡ T½ Taq at 97.5 °C = 5 min 

(T½ = half life of Taq at a specific temperature) 

We invite you to send us any comments or tips of general interest on this topic. References: Sambrook, J., Fritsch EF., Maniatis T. Molecular cloning, 2nd ed. New York; 

Cold Spring Harbor Laboratory Press: 1989 


Info 

‡ Low concentrations and long primers extend 

necessary annealing times. The optimal 

annealing temperature is normally 5 °C–10 °C 

lower than the primer melting temperature 

(Tm). The Tm value can be calculated using 

the following formulas: 

‡ Tm = (A+T) x 2 + (C+G) x 4 [Wallace], 

up to approx. 20 nt 

‡ Tm = 81.5 °C + 16.6 (log[Na + ]) + 0.41 (%G+C) 

– (500/n) – 0.61 (%FA) [Meinkoth and Wahl]; 

FA = Formamide 

‡ 1 kb require approx. 1 min ‡ The shorter the fragment, the easier it is to 

control the reaction 

‡ 200–500 bp fragments are sufficient for 

most detection reactions 

Initial denaturation: 2 min 94 °C 

Denaturation: 0.5 min 94 °C 

Annealing: 0.5 min 50 °C–68 °C 25–35 cycles 

Elongation: 1 min/kb 72 °C 

Final elongation: 10 min 72 °C 


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4.1. Procedure and parameters for PCR 

Reagents Basic rules Comments 

The most common components (as 10x buffers): 

Buffers 

‡ 500 mM KCl 

‡ 100 mM Tris-HCl, pH 8.3 (at 25 °C) or 150–200 mM 

(NH4) 2SO4 with 500–750 mM Tris-HCl, pH 9 (at 25 °C) 

‡ 1–2% Triton ® X-100 or 0.1% Tween ® 

‡ 10–15 mM Mg2+ ‡ The buffers delivered with the polymerase 

are specially tailored to this variety, and it 

is often not possible to use them with 

enzymes from other manufacturers 

‡ NaCl concentrations greater than 50 mM 

inhibit the Taq polymerase 

(usually available separately) 

‡ Mg2+ must be added (if not present in 

buffer), as Mg2+ is essential as a cofactor 

for the DNA polymerase 

Mg 2+ 

Taq Polymerase 

dNTP 

Primer 

‡ 0.5–3.5 mM in the assay 

‡ Essential as a cofactor of the DNA polymerase 


‡ If dUTP is used instead of dTTP, the Mg2+ concentration usually must be increased 

(max. 5 mM) 

‡ Concentration too high: promotes the 

amplification of nonspecific fragments 

(smears appear); increases the melting 

temperature 

‡ Concentration too low: reduces 

annealing efficiency and the synthesis rate 

of the polymerase 

‡ 0.5 - 2.5 units per PCR reaction ‡ Concentration too high: reduced specificity 

‡ Concentration too low: reduced efficiency 

‡ Please see step 2, “Denaturation step” 

‡ Storage in 10 mM, pH 7.0 aliquots 

‡ 20–200 µM in the assay 

‡ 0.1–1 µM in the assay 

‡ Length: approx. 15–30 nt 

‡ Concentration too high: leads to mispriming 

and the misincorporation of nucleotides 

‡ Following a successful PCR, theoretically 

the major part of the dNTPs are left over 

‡ All nucleotides must have the same 

concentration 

‡ Modified nucleotides must have a higher 

concentration 

‡ Secondary structures should not be able to 

form (Stemloop, Hairpin) 

‡ Primer must not be complementary at the 

3' ends, as this will lead to the formation 

of primer-dimers 

‡ Both primers should have the same Tm ‡ No stretches of individual nucleotides 

‡ G or C at the 3' end improves binding


4.2. Calculating primer quantity 

4.2.1. Conversion to absolute quantity (in pmole) 

Primer in pmole = 

Example: 0.1 µg of 20 oligomer: 

0.1 x 1,000,000 

20 x 327 

Weight in µg x 1,000,000 

Length x 327 

= 15.3 pmole primer 

4.2.3. Calculation of the molar concentration of the primer 

Micromolar concentration of primer = pmol/µl 

Example 1 Example 2 

20 pmol of primer in 100 µl PCR mixture = 0.20 micromolar (µM) Primer is 24 nucleotides in length and dissolved in 0.1 ml of water 

A 10 µl aliquot is diluted to 1.0 ml for A 260 measurement: A 260 = 0.76. 

The stock solution has an absorbance at 260 nm (A 260) of 76. 

The stock solution (0.1 ml) contains 2.6 A 260 units. 

The base composition of the primer is: 

A = 6 

C = 6 

G = 6 

T = 6 

The molar extinction coefficient at 260 nm for the primer = k (15,200) + l (12,010) + m (7,050) + n (8,400) where: 

k = number of A’s 

m = number of G’s 

l = number of C’s 

n = number of T’s 

The molar extinction of the PCR primer = 6 (15,200) + 6 (12,010) + 6 (7,050) + 6 (8,400) = 255,960a 

The molar concentration of the PCR primer stock solution is 

4.2.2. Conversion to weight (in µg) 

Weight in µg = 

Example: 10 pmol of 25 oligomer: 

10 x 25 x 327 

76 

255,960 

1,000,000 

= 297 micromolar 

pmol x Length x 327 

1,000,000 

= 0.081 µg primer 

For more information on DNA quantification, see page 286. 


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4.3. Using gradient PCR to optimize different reaction parameters 

Gradient PCR is a technique that allows the empirical determination 

of optimal PCR conditions using the least number of steps. 

This optimization can often be achieved in just one experiment. 

Thermal cyclers from the Mastercycler ® ep system and from the 

classic Mastercycler series provide a gradient function that, in a 

single run, evaluates up to 12 different annealing, elongation 

and/or denaturation temperatures. During the same run, a number 

of other possible reaction variables can also be tested row by row. 

Problems with the amplification of a specific DNA fragment are 

an everyday occurrence in the lab. In many cases, nonspecific 

bands form during the PCR reaction, which hinder, or even prevent, 

downstream analyses or an unequivocal assessment of the PCR 

result. In such cases, PCR conditions must be optimized. 

1 2 3 4 5 6 7 8 9 10 11 12 13 14 

53 °C 67 °C 

‡ Fig. 1: Determination of the ideal annealing temperature 

Annealing temperature 

300 bp 

The selection of the annealing temperature is possibly the most 

critical component for optimizing the specificity of a PCR reaction. 

In most cases, this temperature must be empirically tested. 

The formation of nonspecific bands shows that the optimum 

temperature is often much higher than the calculated temperature 

(up to 12 °C). 

Licensed and authorized for PCR, see page 292. 


Eppendorf ® gradient cyclers enable rapid testing of the optimum 

temperature conditions on one block* and in one experiment. 

During the annealing step, a temperature gradient is built up 

consisting of 12 or 24 continuously increasing temperatures 

across the block. At the same time, each row with 8 or 16 wells 

shows perfect temperature homogeneity, allowing the possibility 

to simultaneously test additional reaction components, such as 

enzyme, primer and template DNA quantities. 

Denaturing temperature 

As a rule, the denaturation temperature for most DNA samples 

is between 94 °C and 96 °C. Depending upon its GC content, 

complexity and structure, the melting point of a DNA fragment can 

lie considerably above or below this range. However, to ensure 

minimum reduction of the polymerase activity, the temperature and 

the dwell time must be kept as low as possible. In these cases, 

determining the optimal denaturing temperature is greatly facilitated 

by the Eppendorf ® gradient cyclers. For this method, a gradient 

between 90 °C and 99 °C is set, thus empirically allowing an ideal 

compromise between enzyme-friendly reaction conditions and 

more efficient denaturing of DNA. 

Elongation temperature 

For most standard applications with Taq polymerase, optimization 

is seldom required. This is not the case for complex protocols, 

for example, the amplification of long fragments with a mixture 

of different polymerases. In this case, the optimization of the 

elongation temperature can play an important role because 

the ideal temperature for Taq polymerases and proofreading 

enzymes can vary considerably. 

*U.S. Pat. 6,767,512 

‡ Fig. 2: Thermograph recording of the thermoblock of the 

Mastercycler gradient


4.4. Eppendorf ® thermal cycler and SteadySlope ® technology: Temperature control means quality 

Row homogeneity in the gradient mode 

Triple Circuit Technology (TCT) provides an additional heating and 

cooling zone, thereby ensuring precise control of the temperature 

for all gradient profiles. 

‡ Additional temperature control via TCT 

‡ SteadySlope technology 

Constant temperature 

characteristics in the 

gradient mode 

‡ Comparison device with 

“dynamic” temperature 

control characteristic 

Changing temperature control 

characteristic (various cooling 

speeds) in gradient operation 

mode 

Temperature control characteristics 

Temperature control characteristics, i.e., the temperature 

profile and the speed at which temperature control of the samples 

changes (heating and cooling between the individual PCR steps), 

play a key role in PCR. The best-known PCR application, which 

highlights the significance of a reproducible temperature control 

speed, is random-amplified polymorphic DNA analysis (RAPD) for 

detecting polymorphisms during DNA fingerprint tests. Variations 

on the temperature control speed alter the resulting band pattern, 

as do thermal inaccuracies, making it much more difficult to 

interpret the results. 

A prerequisite for gradient cyclers to successfully transfer PCR 

protocols from gradient operation to routine operation is to have 

the temperature curves in both operating modes as similar as 

possible. With SteadySlope technology gradient temperatures 

are always attained with the same temperature characteristics, 

i.e., each temperature with the optimal speed. For standard PCR 

applications this is always the highest possible speed, which is 

clearly defined and is, therefore, reproduced identically in the 

normal mode. This ensures reliable and uncomplicated transfer 

of reaction conditions between the two operating modes and 

rules out any reduction in the yield or specificity caused by 

changes to the temperature characteristics. 

Block Control and Tube Control 

Block Control is the preferred operating mode for long, static 

incubation. However, for short incubation times—such as those 

that occur during the PCR—the programmed holding time may 

deviate greatly from the actual holding time for the selected 

temperature in the reaction mix. Tube Control ensures automatic 

compensation of this time and that the reaction mix is held 

at the temperature you have selected for as long as you have 

programmed it to do so. This is applied identically for all tube 

types across all Mastercyclers, allowing you to use the entire 

block for your samples. 

Licensed and authorized for PCR, see next page. 


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4.5. Optimization of the primer concentration (primer matrix) 

A primer matrix that spans a range of common concentrations 

of the forward and reverse primer is recommended to find the 

optimal combination of concentrations for both primers. Normally 

a range between 50 nM and 900 nM will be tested. A commonly 

used primer matrix is featured in the table below. To achieve the 

most reliable results, each combination should be performed with 

3 replicates and additional negative controls. 

Typical forward and reverse primer combinations for a primer matrix 

Reverse 

PCR disclaimers 

Eppendorf Mastercycler ® family 

Practice of the patented polymerase chain reaction (PCR) 

process requires a license. The Mastercycler is an Authorized 

Thermal Cycler and may be used with PCR licenses available 

from Applied Biosystems. Its use with Authorized Reagents 

also provides a limited PCR license in accordance with the 

label rights accompanying such reagent 

50 nM 100 nM 

Forward 

300 nM 600 nM 900 nM 

50 nM 50/50 100/50 300/50 600/50 900/50 

100 nM 50/100 100/100 300/100 600/100 900/100 

300 nM 50/300 100/300 300/300 600/300 900/300 

600 nM 50/600 100/600 300/600 600/600 900/600 

900 nM 50/900 100/900 300/900 600/900 900/900 


Eppendorf Mastercycler ep realplex 

Practice of the patented polymerase chain reaction (PCR) 

process requires a license. The Eppendorf Thermal Cycler 

is an Authorized Thermal Cycler and may be used with PCR 

licenses available from Applied Biosystems. Its use with Authorized 

Reagents also provides a limited PCR license in accordance with 

the label rights accompanying such reagents. This is a Licensed 

Real-Time Thermal Cycler under Applera’s United States Patent 

No. 6,814,934 and corresponding claims in non-U.S. counterparts 

thereof, for use in research and for all other applied fields except 

human in vitro diagnostics. No right is conveyed expressly, by 

implication or by estoppel under any other patent claim.

1 - Eppendorf

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