Question

Calculate the melting temperature in 1 M NaCl of the following pieces of DNA (the pieces of DNA are double stranded - I've just given the sequence of one of the two strands). Assume a total DNA strand concentration of 0.1 mM. Carry out the calculations using the salt-corrected Marmur-Doty equation, and then repeat them using the nearest neighbor thermodynamic parameters. Explain any discrepancies between the two calculations for each sequence.:

a) CCGGAATTCCGG b) (AAGGTTCCGATACTGC)5 (note: the 5 is a subscript)

Answer 1

Answer-

Accoring to Marmur-Doty equation, the melting temp calculated based upon set of short oligonucleotide sequences ranging from 16 to 30 nt long, which span the whole range of CG-content.

Tm = (64.9 + 41.0) X {( yG + zC − 16.4)/ ( wA + xT + yG + zC )}

where x, y, w and z are the number of the bases of T, G, A and C, respectively...

The salt adjusted calculation of Tm is as follows:

Tm = 100.5 + ( 41.0) × [(yG + zC − 16.4)/(wA + xT + yG + zC )]– {(820.0 )/(wA + xT + yG + zC )} + 16.6 log([Na+]).