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How Does the Extent of Hydration of Minor and Major
Grooves Control the Thermal Stability of DNA Duplexes and Triplexes?
All PDF files with the numbers refer to paper numbers in the
The tertiary structure, dynamics of conformational transition of DNA and
its interaction with protein and water determine the fidelity of the base-pairing,
mismatch and mutation in the DNA replication. We have recently produced
convincing NMR evidence [Nucleic Acid Res., 21, 4246 (1993),
Tetrahedron 51, 5501-5508 (1995), PDF
248] that water both in the minor and major grooves has a destabilizing
influence on the DNA structure. As the water activity inside the DNA duplex
increases, the Tm decreases and vice versa. This work has provided the
first thermodynamic evidence that the presence of water around a Watson-Crick
base-pair would weaken the H-bond and hence would promote random mismatch,
frame-shift and mutation. We are presently studying the hydration behaviour
DNA and DNA polymerase complex and determine the role of hydration in the
DNA replication by specific 15N/ 13C/ 2H labeling experiments using our
We also like to understand the exact role of water molecules in the stability
of A, B and Z form of DNA and process of transition from the B to Z form
by influence of salt concentration by our new ROESY-NOESY method [see our
Nucleic Acid Res., 21, 4288 (1993), PDF
220] and also locate the site of binding of water molecule to the DNA.
The role of water in mediating interactions between drugs and nucleic acids
is of enormous interest. Water is displaced when a drug and nucleic acid
bind to one another as shown by X-ray studies. The formation of triple-stranded
structures by DNA and RNA is of considerable interest. The specificity
of the hydrogen-bonding interactions that stabilize the triple helix structure
would enable the design of DNA recognition elements of sequence-specificity.
Dep't of Bioorg. Chem. | Last mod.: Feb. 27,
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