I didn't understand how only 10 pair were chosen in the 1997 PNAS paper (A unified view of polymer, dumbbell) by Santalucia. I don't know on what basis these 10 sets have been chosen. The parameter for . AA/TT, AT/TA, TA/AT, CA/GT, GT/CA, CT/GA, GA/CT, CG/GC, GC/CG, GG/CC have been given in the paper but what will be the parameter for AG/TC, AC/TG, TG/AC, TC/AG, TT/AA, CC/GG which are not given in the paper.
HI Himanshu,
You should have called me over phone or dropped a mail. this is my bread and butter. :)
Good that i saw it in RG, some more points to mr RGScore :)
Ok, coming to your question.
DNA is made of four bases A,T,G and C. and A pairs with T and G pairs with C. a sequence of DNA which forms a duplex will have one base pair stacked over the other. The paper talks about wat is known as "dinucleotide steps.". Its nothing but the combination of base pair stacked. a total of 16 possible combination can occur. Take "AA/TT" as a example. It refers to stacking of Adenine bases in strand_I and Thymine base in strand_II. Ur question is why is that they have not calculate the energy for TT/AA. "TT/AA " has thymine in strand_I and Adenine in strand_II. if u pass a pseudo-symmetry axis in the center of the step. u can go btw AA/TT and TT/AA.
I suggest u take coordinates of these two steps . superpose n observe that 5' to 3' direction is maintained even after 180 degree rotation.
Thus, Instead of 16 steps there is only 10 possible unique combination of steps.
Hope this helps.
Thanks Senthil,
I got it, basically it converges with the following identities
AA/TT = TT/AA
CA/GT = TG/AC
GT/CA = AC/TG
CT/GA = AG/TC
GA/CT = TC/AG
CC/GG = GG/CC
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