# DNA Concentration Formulas for EpiMark™ Nucleosome Assembly Kit (E5350)

## Protocol

1. Formulas
To determine the concentration of binding sites:
• 1.0 A260 unit double stranded DNA = 50 µg/ml
• MW of double stranded DNA= # base pairs x 650 daltons/base pairs
• pmol/µl of double stranded DNA= µg/µl DNA x 106 pg per µg/MW
• µM double stranded DNA = pmol/µl of double stranded DNA
• Size of DNA in bp / 150 bp = # of potential binding sites
• µM of binding sites =# potential binding sites x µM DNA

Example #1: 1 kb DNA at 1 µg/µl has 6 possible binding sites = 9 µM binding site DNA solution or 9 pmol/µl binding site DNA solution.

• MW = 1000 bp x 650 daltons/base pairs = 650,000 daltons
• µM = pmol/µl = 1 µg/µl DNA x 106 pg per µg/650,000 = 1.5
• # of potential binding sites = 1000 bp/150 bp =6
• conc. of binding sites = 1.5 x 6 = 9 µM or 9 pmol/µl
In the described assembly reaction for dilution assembly with 25 pmol of DNA substrate, use 2.7 µl of 9 µM binding site DNA solution per reaction and vary the amount of octamer.

Example #2:
0.5 kb DNA at 1 µg/µl has 3 possible binding sites = 4.5 µM binding site DNA solution.
• MW = 500 bp x 650 daltons/base pairs = 325,000 Daltons
• µM = pmol/µl = 0.5 µg/µl DNA x 106 pg per µg/325,000 = 1.5
• # of potential binding sites = 500 bp/150 bp = 3
• µM of binding sites = 1.5 µM x 3 = 4.5 µM or 4.5 pmol/µl
In the described assembly reaction for dilution assembly with 25 pmol of DNA substrate, use 5.5 µl of 4.5 µM binding site DNA solution per reaction and vary the amount of octamer.