Noi/NOTES/2014-3-29

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DNA methylation sensitivity test assay - MONOD Project, MONOD_GP1_V4 probe set (BSPP capture)

[Link to calendar]

  • Continued from: [[1]]
File:MONOD-sensitivity-test-plans.png
- For all bis-DNA input, I will use the same concentration of probe in capture reaction by using 500:1 probe:target ratio for 300ng bis-DNA

BSPP capture set up

Probe calculation

Probe:target 500:1 Unit Calculation
Probe size (number of individual probe in oligo mix) 7,110 probes
Human bis-cvt gDNA required 300 ng
Human gDNA MW 1.822E+12 g/mole 3.0E+09 * 607.4Da/bp
Human gDNA( 300ng) 1.646E-19 mole 300E-09g / 1.822E+12g/mole
Probe required (500:1) 8.232E-17 mole 500 * 1.098E-19mole
Probe mix MW (size 7,110probes, 110nt) 2.381E+08 g/mole 7,110 probes * (110bp *303.7Da/bp+79Da)
Mass of probe required 1.960E-08 g 8.232E-17mole * 2.381E+08g/mole
Mass of probe required 19.60 ng
Probe conc 6.87 ng/ul
Volume of probe 2.85 ul