On Mon, Jun 25, 2012, barb fr wrote:
>
> I'm trying to estimate the free energy difference associated to the
> formation of a duplex B-DNA from the two single strand
> oligonucleotides within the mm-PBSA approach.
>
> A quick search in the literature pointed out that such a method has
> been extensively applied to dDNA-ligand system, but I could not find
> any attempt to calculate the free energy associated to the formation
> of the duplex from the two single strands sequence. So my first
> question is: are there some severe limitations of these method just
> considering one dna-strand like receptor and the other like ligand?
Yes, there are some severe limiations: first, no one knows what the ensemble
of conformations is that represents single-stranded DNA; second, the single
strands are presumably much more flexible than are double helices, but there
is no easy way to estimate the change in configurational entropy.
Most angels have feared to tread here. If you hope to learn things, look
carefully at the configurations you have that represent the single strand.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jun 25 2012 - 09:00:03 PDT
