Structural Waters in the Minor and Major Grooves of DNA鈥擜 Major Factor Governing Structural Adjustments of the A鈥揟 Mini-Helix

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• 作者：Tetiana Zubatiuk ; Oleg Shishkin ; Leonid Gorb ; Dmytro Hovorun ; Jerzy Leszczynski
• 刊名：Journal of Physical Chemistry B
• 出版年：2015
• 出版时间：January 15, 2015
• 年：2015
• 卷：119
• 期：2
• 页码：381-391
• 全文大小：523K
• ISSN：1520-5207

文摘

The role of microhydration in structural adjustments of the AT-tract in B-DNA was studied at the B97-D/def2-SV(P) level. The (dA:dT)₅ complexes with 10 water molecules in minor and 15 water molecules in major grooves were studied. The obtained network of hydrogen bonds revealed the dependence between the groove width and the types of water patterns. In the minor groove, the following patterns were observed: interstrand one-water bridges similar to that of the Dickerson 鈥渨ater spine鈥?and interstrand two-water bridges. The network of structural waters in the major groove is more diverse than that in the minor groove, which agrees with crystallographic data. As the major groove is wider, it is enriched by water molecules forming two- and three-water bridges. Results suggest the nucleobase鈥搘ater interactions in both grooves prevent AT-tract twisting and its 鈥渃ollapse鈥?along the minor groove. Whereby, a helix structure with narrow minor and wide major grooves is formed. The structural waters affect the polynucleotide conformation so that it becomes similar to poly(dA)路poly(dT) in fibers and acquires features of the A-tracts in DNA in solution. We suggest that formation of specific water patterns in both grooves is the factor responsible for stabilization of A-tracts with a narrowed minor groove, leading in turn to their strong intrinsic bending in DNA.