AMBER Archive (2003)

Subject: mm_pbsa and B/Z DNA relative stabilities

From: Peter Gannett (pgannett_at_hsc.wvu.edu)
Date: Wed May 14 2003 - 06:54:47 CDT

Amber users:

We have been doing some simulations of 5'-CGCGCGCGCG-3' and a modified version (G6 from the 5' end) with respect to the relative stability of the B and Z DNA forms. We've run about 2ns of simulation on the B/Z forms of both the unmodified and modified forms (total of 4) and then have processed the trajectories (from ~200-1800 ns) with mm_pbsa. The control parms for the mm_pbsa were

IGB=1
SALTCON =0
EXTDIEL=80

SURFTEN=0.0072
SURFOFF=0.00
DIELC =4
MAXCYC=5000000
DRMS=0.0001.

The final energies (delG) are:

B(unmodified) = -3998.5
Z(unmodified) = -4013.8
B(modified) = -3954.8
Z(modified) = 3964.2

Experimentally, at 200 mM NaCl, the B form of the unmodified oligo is the only significant form while, under the same conditions, the modified form is roughly 1:1 B/Z.

Obviously, the calculated results are significantly different from the experimental results. I don't understand why the Z unmodified is calculated to be the most stable form when there is no way that it is. I don't mind the order for the modified form, but given the result for the unmodified, I don't give the result much weight.

Note, in case it helps, the mm_pbsa gets large differences in ELE between the B and Z forms (unmodified and modified), favoring the B form which I am willing to accept. The is counterbalanced by a large value for GB, favoring the Z form in both cases. Relatively speaking, small changes in these numbers could change the relative ordering of things. By small changes, I mean with respect to the STD reported on these values.

Also, we ran the mm_pbsa with SALTCON=1. This increased the stability of the Z forms relative to the B forms, but did not change the relative ordering of the four DNAs.

But, I don't think this is the whole story. Any suggestions, comments, etc? They would be appreciated.

Pete Gannett