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Re: Water movement around DNA (fwd)
Sender: vkitzing@sunny.mpimf-heidelberg.mpg.de (Eberhard von Kitzing)
Subject: Re: WSN: Water movement around DNA
>WSN colleagues:
>
>I am interested in finding references about water molecules around nucleic
>acids. While there may be some experimental references (like neutron
>diffraction) I would expect mostly simulation references. I am particularly
>interested in references that discuss the mobility of waters/ions close
>to the nucleotide and numbers of shells of water.
I found the following references:
Wolfram Saenger (1987). "Structure and Dynamics of Water surrounding
Biomolecules." Annual Reviews in Biophysics and Biophysical Chemistry 16
93-114.
F. Briki and D. Genest (1994). "Canonical-analysis of correlated atomic
motions in dna from molecular-dynamics simulation." Biophysical Chemistry
52(1) 35-43.
J. Garcia de la Torre, S. Navarro and M.C. Lopez Martinez (1994).
"Hydrodynamic Properties of a Double Helical Model for DNA." Biophysical
Journal
B. Schneider, D.M. Cohen, L. Schleifer, A.R. Srinivasan, W.K. Olson and
H.M. Berman (1993). "A systematic method for studying the
spatial-distribution of water-molecules around nucleic-acid bases ."
Biophysical Journal 65(N6) 2291-2303.
Peter Ahlstrom, Olle Teleman and Bo Jonsson (1989). "Interfacial Water
Studied by Molecular Dynamics Simulations." Chemica Scripta 29A 97-101.
H. M. Berman (1994). "Hydration of dna - take 2." Current Opinion in
Structural Biology 4(3) 345-350.
D. L. Beveridge and G. Ravishanker (1994). "Molecular-dynamics studies of
DNA." Current Opinion in Structural Biology 4(2) 246-255.
H. Lee, T. A. Darden and L. G. Pedersen (1995). "Molecular-dynamics
simulation studies of a high-resolution z- dna crystal." Journal of
Chemical Physics 102(9) 3830-3834.
R. V. Gessner, Gary J. Quigley and M. Egli (1994). "Comparative-studies of
high-resolution z-dna crystal-structures .1. common hydration patterns of
alternating dc-dg." Journal of Molecular Biology 236(4) 1154-1168.
B. H. M. Mooers, G. P. Schroth, W. W. Baxter and P. S. Ho (1995).
"Alternating and non-alternating dg-dc hexanucleotides crystallize as
canonical a-dna." Journal of Molecular Biology 249(4) 772-784.
Enrico Clementi (1989). "Computer Simulations of Hydrated Proteins."
Journal of Molecular Liquids 41 233-239.
D. A. Zichi (1995). "Molecular-dynamics of rna with the opls force-field -
aqueous simulation of a hairpin containing a tetranucleotide loop." Journal
of the American Chemical Society 117(11) 2957-2969.
L. W. Tari and A. S. Secco (1995). "Base-pair opening and spermine binding
- b-dna features displayed in the crystal-structure of a gal operon
fragment - implications for protein-dna recognition." Nucleic Acids
Research 23(11) 2065-2073.
D. Hochberg, T. W. Kephart and D. Edwards (1994). "Structural information
in the local electric-field of dissolved b-dna." Physical Review E 49(N1)
851-867.
Gerhard Hummer and D. Mario Soumpasis (1994). "Statistical mechanical
treatment of the structural hydration of biological macromolecules: Results
for B-DNA." Physical Review E 50(6) 5085-5095.
Eric Westhof (1993). Structural Water Bridges in Nucleic Acids. Water and
Biological Macromolecules. Houndsmills, MacMillan Press. 226-243.
F. Vovelle and J. M. Goodfellow (1993). Hydration Sites and Hydration
Bridges around DNA Helices. Water and Biological Macromolecules.
Houndsmills, MacMillan Press. 244-265.
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Eberhard von Kitzing
Max-Planck-Institut fuer Medizinische Forschung
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