Common Conversions of Oligonucleotides

Molecular Weight
MW = 333 x N

Concentration of Oligonucleotides
C (µM or pmol/µl) = A260 / (0.01 x N)
C (ng/ml) = (A260 x MW) / (0.01 x N)

MW - molecular weight, Da 
A260 - absorbance at 260nm 
N - number of bases

 

 Common Conversions of Nucleic Acids

Molar Conversions


1µg of 1000 bp DNA = 1.52pmol 
1µg of pUC18/19 DNA (2686 bp) = 0.57pmol 
1µg of pBR322 DNA (4361 bp) = 0.35pmol 
1µg of SV40 DNA (5243 bp) = 0.29pmol 
1µg of PhiX174 DNA (5386 bp) = 0.28pmol 
1µg of M13mp18/19 DNA (7250 bp) = 0.21pmol 
1µg of lambda phage DNA (48502 bp) = 0.03pmol 

1pmol of 1000 bp DNA = 0.66µg 
1pmol of pUC18/19 DNA (2686 bp) = 1.77µg 
1pmol of pBR322 DNA (4361 bp) = 2.88µg 
1pmol of SV40 DNA (5243 bp) = 3.46µg 
1pmol of PhiX174 DNA (5386 bp) = 3.54µg 
1pmol of M13mp18/19 DNA (7250 bp) = 4.78µg 
1pmol of lambda phage DNA (48502 bp) = 32.01µg 

Spectrophotometric Conversions


1 A260 of dsDNA = 50µg/ml = 0.15mM (in nucleotides) 
1 A260 of ssDNA = 33µg/ml = 0.1mM (in nucleotides) 
1 A260 of ssRNA = 40µg/ml = 0.12mM (in nucleotides)

1mM (in nucleotides) of dsDNA = 6.7 A260 units 
1mM (in nucleotides) of ssDNA = 10.0 A260 units 
1mM (in nucleotides) of ssRNA = 8.3 A260 units 

The average MW of a deoxyribonucleotide base = 333 Daltons 
The average MW of a ribonucleotide base = 340 Daltons 

Estimation of Ends (3' or 5') Concentration

 

Circular DNA
pmol ends = pmol DNA x number of cuts x 2

Linear DNA
pmol ends = pmol DNA x (number of cuts x 2 + 2) 

1µg of 1000 bp DNA = 3.04pmol ends 
1µg of linear pUC18/19 DNA = 1.14pmol ends 
1µg of linear pBR322 DNA = 0.7pmol ends 
1µg of linear SV40 DNA = 0.58pmol ends 
1µg of linear PhiX174 DNA = 0.56pmol ends 
1µg of linear M13mp18/19 DNA = 0.42pmol ends 
1µg of lambda phage DNA = 0.06pmol ends

 

Melting Temperature of Duplex DNA and Oligonucleotides

For Duplex Oligonucleotide shorter than 25 bp, "The Wallace Rule" (1)
Tm (in °C) = 2(A+T) + 4(C+G), where 

(A+T) - the sum of the A and T residues in the oligonucleotide,
(C+G) - the sum of G and C residues in the oligonucleotide. 

Presence of m5C in oligonucleotide increases melting temperature of duplex.
Presence of m4C or m6A decreases melting temperature (2).

For Duplex DNA, <100 bp long (3)
Tm (in °C) = 81.5°C+16.6(log10[Na+])+0.41(%[G+C])-675/n-1.0m, where

n - number of bases in the oligonucleotide 
m - the percentage of base-pair mismatches