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problems with DNA structures solved using CNS

Monika Ivancic ivancicm at ucs.orst.edu
Thu Mar 1 17:04:24 EST 2001

Fellow NMR spectroscopists,

I recently solved a structure of a DNA hexamer with a drug intercalator
bound in the central two base pairs using CNS.  I have generated a family
of 25 accepted structures with an RMSD of 0.50 Angstroms.  The
intercalator makes
the central base pairs separate by 7.0 Ang.  My problem is that the
stacking of the 3 base pairs above and below the intercalator is
incorrect.  The base pair rise is between 3.8 and 5.5 A, when it should be
under 3.5 A.  I haven't seen many pubs of solved DNA structures using CNS.
If you have any idea of how I could solve my problem, I would appreciate
your help.

Thank you,

Monika Ivancic                        email: ivancicm at ucs.orst.edu
Biochemistry and Biophysics Dept.
Oregon State University
Corvallis, OR 97331


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