BioHackerLab/Equipment

An overview of available equipment and equipment of interest.

See also: http://www.mlo-online.com/the-quest-for-the-500-home-molecular-biology-laboratory.php

Thermocyclers

http://www.the-scientist.com/?articles.view/articleNo/18812/title/How-Low-Can-You-Go---Nineteen-Thermal-Cyclers-Priced-Under--5000/

DNA quantification

GeneQuant/Genequant II

GeneQuant Manual: http://www.americaninstrument.com/pdf/1976E-DNA.pdf

• Light path height = 15 mm

Eppendorf biophotometer 6131

Manual: http://arboretum.harvard.edu/wp-content/uploads/Biophotometer-manual.pdf

• Device: Single-beam filter photometer with reference beam and fixed wavelengths.

Cuvette types (min volume):

• 10 mm macro (1000 uL)
• 10 mm semi-micro (400 uL)
• 10 mm suction (300 uL)
• 10 mm ultra-micro (70 uL)

Wavelengths: 230,260,280,320,562,595

• Photometric random error: <= 0.005A at 1A.
• Photometric systemic error: +- 1% at 1A.

Height of light beams in cuvette: 8.5 mm

Kompatible kuvetter:

https://www.brandtech.com/product/uv-cuvettes/

See also: http://www.biocompare.com/Application-Notes/138277-Reproducible-photometric-determination-of-DNA-concentrations-using-the-Eppendorf-UVette-in-the-Eppendorf-BioPhotometer-plus/

Biophotometer test

Performed August 7 2016. All measurments were performed with previously unused Brand "UV-cuvette micro" cuvettes. For these cuvettes, the specified minimum sample volume is 70 uL.

The oligo program was selected. Programmed factor: 1A260 = 30.0 ug/mL.

The program was blanked with 100 uL nuclease-free water (Dongsheng biotech)

100 uL NF water in another cuvette was measured as a control. Result = 0.000 ug/uL.

50 uL of a solution of ITS1 single-strand DNA oligomer supplied by Macrogen Inc with expected concentration 10 uM [Note 1] was mixed with 50 uL DSBio NF water to give a solution with expected concentration 5 uM. Somewhat less than 100 uL was measured as sample. Result: 0.0498 ug/uL ~0.05 ug/uL (50 ng/uL)

Complete results: 1.343 A230, 1.661 A260, 0.945 A280, 0.027 A320)

The sample was removed from the photometer, then later replaced and remeasured once with the following result: 0.0492 ug/uL (1.320 A230, 1.639 A260, 0.930 A280, 0.010 A320)

Without being removed from the photometer, the sample was then remeasured thrice in quick succession with the following results [ug/uL]:

• Measurement #6: 0.0494
• Measurement #7: 0.0493
• Measurement #8: 0.0493

The sample was then removed from the photometer, placed back into the photometer and remeasured. This was repeated twice. The results were as follows [ug/uL]:

• Measurement #9: 0.0496
• Measurement #10: 0.0498
• Measurement 11: 0.0502

The cuvette was then measured in one orientation, rotated 180 degress and the sample remeasured. This was repeated once, for a total of four measurements, the results being as follows [ug/uL]:

• Measurement #12: 0.0496 (Original orientation. Logo on cuvette towards front of instrument. Arrow on cuvette towards back of instrument)
• Measurement #13: 0.0509 (Reversed)
• Measurement #14: 0.0506 (Original orientation)
• Measurement #15: 0.0499 (Reversed)

20 uL of a solution of ITS4 primer with expected concentration 10 uM [Note 2] was mixed with 80 uL DSBio NF water. The sample was measured twice, using the dilution correction feature for the second measurement. The results were as follows.

• First measurment: 15.4 ng/uL. A260/A280 = 1.39. Dilution specified: N/A
• Second measurement: 77.3 ng/uL. A260/A280 = 1.40. Dilution specified: 20 uL sample + 80 uL diluent.

Note 1: The 10 uM solution was previously prepared by mixing 10 uL of a solution prepared from dry DNA received from Macrogen Inc. by resuspension in 220 uL DSBio NF water for an expected concentration of 100 pmol/uL. A concentration of 5 uM gives the following expected concentration by mass: 5 * 10^-6 mol/L * ~ 6000 g/mol = 0.03 g/L (0.03 ug/uL, 30 ug/mL, 30 ng/uL). Using a conversion factor of 1 A260 = 30 ug/mL, the expected A260 is thus ~ 1.0 A260. The photometric measuring range according to the Biophotometer manual is up to 2.6A at 260 nm when using Eppendorf UVette cuvettes.

Centrifugation

Eppendorf 5415D

Manual: http://www.nist.gov/ncnr/upload/Eppendorf_5415R_Centrifuge_Manual.pdf

• Max speed: 13 200 rpm
• Max centrifugal force: 16 110 rcf
• Max load: 24 x 2,0 mL or 36 x 0,5 mL tubes (rotor dependent)
• Power requirement: 180 W
• Weight without rotor: 8.5 kg