AMBER Archive (2006)

Subject: Re: AMBER: Creating an Intercalation site

From: Thomas Cheatham (
Date: Mon Jul 17 2006 - 15:13:54 CDT

> Can someone please suggest to me the best software / method in going
> about creating an intercalation site... for example intercalalting
> RNA/DNA with a small molecule?

ptraj has a facility to scale, translate, principal axis align, and center
coordinates. In general, when modifying coordinates gradual changes are
better than abrupt (i.e. smoothing out a stretch of a region over multiple
atoms rather than creating a long bond, as per work by the Santa Lucia

To do this for DNA, we have aligned the long axis along Z, centered the
intercalation site to the origin, scaled the central step by 2.0 and then
translated the top half and bottom halve in Z by 3.6 angstroms.

i.e. imagine duplex with intercalation site **'ed for the 7 base pair
duplex cartooned below

    \-/ -/-
    -/- /-\
  * /-\ | |
  * \-/ ---> \-/
    -/- -/-
    /-\ /-\
    \-/ \-/

center :3,4,11,12 mass origin
scale z 2.0 :3,4,11,12
translate z 3.6 :1-2,13-14
translate z -3.6 :5-10

(or some combination). In our experience, you will also have to play with
the orientation of the intercalator (i.e. assuming it is in the plane of
the bases, what is its twist relative to the bases?). The simple
procedure above (followed by minimization) works OK for us.

More complete control could like by engineering via NAB or 3DNA, albeit
with significantly more complication.

\-/ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
-/- Departments of Med. Chem. and of Pharmaceutics and Pharm. Chem.
/-\ Adjunct Asst Prof of Bioeng.; Center for High Performance Computing
\-/ University of Utah, 30 S 2000 E, SH 201, Salt Lake City, UT 84112
/-\ (801) 587-9652; FAX: (801) 585-9119
\-/ BPRP295A

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