Molecular mechanical studies of base-pair opening in d(CGCGC):d(GCGCG), dG5·dC5, d(TATAT):d(ATATA), and dA5·dT5 in the B and Z forms of DNA
✍ Scribed by Joe Keepers; Peter A. Kollman; Thomas L. James
- Publisher
- Wiley (John Wiley & Sons)
- Year
- 2007
- Tongue
- English
- Weight
- 720 KB
- Volume
- 23
- Category
- Article
- ISSN
- 0006-3525
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✦ Synopsis
Molecular mechanical energy refinement of double-helical pentanucleotide tetraphosphates, d(CGCGC):d(GCGCG), dG5 . dC5, d(TATAT):d(ATATA), and dA5 . dT5 g e e metries, are presented in order to examine the energy required to open the Nl(purine) ---N3(pyrimidiae) distance (base-pair opening) of a Watson-Crick base pair from its normal value of 3 A to a value of 6 A. The structural consequences of forcing base-pair opening is sequence dependent. For both dA, -dT, and d(TATAT):d(ATATA), forcing the N1 (AdekN3 (Thy) distance of the central base pair to a value of 6 . & slides the bases perpendicular to the helix axis forming a lowenergy non-Watson-Crick base pair having an adenine amine hydrogen.. . thymine carbonyl oxygen hydrogen bond.
The two GC sequences behave differently from both AT sequences and differently from each other. Forcing the Nl(Gua) * -. N3(Cyt) distance to 6 A leads to unconventional structures in which hydrogen bonds are formed between the separated bases and the bases above or below them. These structures appear to be trapped in true local minima 6-10 kcal/mol higher in energy than the WatsonCrick structures. Preliminary simulations on d(CGCGC):d(GCGCG) in the Z geometry suggest the reason the Z form may be more refractory to proton exchange than the B form, consistent with experimental observations.