A new approach to calculate the hydration of DNA molecules

Hummer, Gerhard; Soumpasis, Dikeos Mario

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A new approach to calculate the hydration of DNA molecules

Hummer, G., & Soumpasis, D. M.(1993). A new approach to calculate the hydration of DNA molecules (LA-UR-93-3013; CONF-9306237-3). Los Alamos: Los Alamos National Laboratory.

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Item Permalink: https://hdl.handle.net/21.11116/0000-0009-238F-F Version Permalink: https://hdl.handle.net/21.11116/0000-000B-9137-3

Genre: Report

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Creators:
Hummer, Gerhard¹, Author
Soumpasis, Dikeos Mario², Author

Affiliations:
1Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, USA, ou_persistent22
2External Organizations, ou_persistent22

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Abstract: A new method to calculate approximate water density distributions around DNA is presented. Formal and computational simplicity are emphasized in order to allow routine hydration studies. The method is based on the application of pair and triplet correlation functions of water-oxygen calculated by computer simulation. These correlation functions are combined with the configurational data of the electronegative atoms on DNA (oxygen and nitrogen)
taken from crystal structures. For three B-DNA structures water
density distributions are calculated and discussed. The observed characteristic
features agree well with the prevalent picture from experiments. The minor groove shows a more structured hydration than the major groove. Also, the minor groove hydration of A.T basepair tracts differs from that found in G.C basepair regions. In A.T tracts single peaks of high water density appear (spine of hydration), whereas in G.C regions the minor groove is occupied by two side-by-side ribbons of water.

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Language(s): eng - English

Dates: Date issued: 1993-09

Publication Status: Issued

Pages: 20

Publishing info: Los Alamos : Los Alamos National Laboratory

Table of Contents: -

Rev. Type: -

Identifiers: Report Nr.: LA-UR-93-3013; CONF-9306237-3
BibTex Citekey: hummer_new_1993

Degree: -

Event

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Title: Eighth Conversation in the Discipline Biomolecular Stereodynamics

Place of Event: Suny at Albany

Start-/End Date: 1993-06-22 - 1993-06-26

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