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Title: B-DNA structure is intrinsically polymorphic: even at the level of base pair positions

Abstract

Increasingly exact measurement of single crystal X-ray diffraction data offers detailed characterization of DNA conformation, hydration and electrostatics. However, instead of providing a more clear and unambiguous image of DNA, highly accurate diffraction data reveal polymorphism of the DNA atomic positions and conformation and hydration. Here we describe an accurate X-ray structure of B-DNA, painstakingly fit to a multistate model that contains multiple competing positions of most of the backbone and of entire base pairs. Two of ten base-pairs of CCAGGCCTGG are in multiple states distinguished primarily by differences in slide. Similarly, all the surrounding ions are seen to fractionally occupy discrete competing and overlapping sites. And finally, the vast majority of water molecules show strong evidence of multiple competing sites. Conventional resolution appears to give a false sense of homogeneity in conformation and interactions of DNA. In addition, conventional resolution yields an average structure that is not accurate, in that it is different from any of the multiple discrete structures observed at high resolution. Because base pair positional heterogeneity has not always been incorporated into model-building, even some high and ultrahigh-resolution structures of DNA do not indicate the full extent of conformational polymorphism.

Authors:
; ; ; ; ;  [1]
  1. (GIT)
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
National Aeronautic and Space Administration (NASA)
OSTI Identifier:
1040914
Resource Type:
Journal Article
Journal Name:
Nucleic Acids Res.
Additional Journal Information:
Journal Volume: 40; Journal Issue: (8) ; 2012; Journal ID: ISSN 0305-1048
Country of Publication:
United States
Language:
ENGLISH
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; DIFFRACTION; DNA; ELECTROSTATICS; HYDRATION; MONOCRYSTALS; RESOLUTION; WATER; X-RAY DIFFRACTION

Citation Formats

Maehigashi, Tatsuya, Hsiao, Chiaolong, Woods, Kristen Kruger, Moulaei, Tinoush, Hud, Nicholas V., and Williams, Loren Dean. B-DNA structure is intrinsically polymorphic: even at the level of base pair positions. United States: N. p., 2012. Web. doi:10.1093/nar/gkr1168.
Maehigashi, Tatsuya, Hsiao, Chiaolong, Woods, Kristen Kruger, Moulaei, Tinoush, Hud, Nicholas V., & Williams, Loren Dean. B-DNA structure is intrinsically polymorphic: even at the level of base pair positions. United States. doi:10.1093/nar/gkr1168.
Maehigashi, Tatsuya, Hsiao, Chiaolong, Woods, Kristen Kruger, Moulaei, Tinoush, Hud, Nicholas V., and Williams, Loren Dean. Tue . "B-DNA structure is intrinsically polymorphic: even at the level of base pair positions". United States. doi:10.1093/nar/gkr1168.
@article{osti_1040914,
title = {B-DNA structure is intrinsically polymorphic: even at the level of base pair positions},
author = {Maehigashi, Tatsuya and Hsiao, Chiaolong and Woods, Kristen Kruger and Moulaei, Tinoush and Hud, Nicholas V. and Williams, Loren Dean},
abstractNote = {Increasingly exact measurement of single crystal X-ray diffraction data offers detailed characterization of DNA conformation, hydration and electrostatics. However, instead of providing a more clear and unambiguous image of DNA, highly accurate diffraction data reveal polymorphism of the DNA atomic positions and conformation and hydration. Here we describe an accurate X-ray structure of B-DNA, painstakingly fit to a multistate model that contains multiple competing positions of most of the backbone and of entire base pairs. Two of ten base-pairs of CCAGGCCTGG are in multiple states distinguished primarily by differences in slide. Similarly, all the surrounding ions are seen to fractionally occupy discrete competing and overlapping sites. And finally, the vast majority of water molecules show strong evidence of multiple competing sites. Conventional resolution appears to give a false sense of homogeneity in conformation and interactions of DNA. In addition, conventional resolution yields an average structure that is not accurate, in that it is different from any of the multiple discrete structures observed at high resolution. Because base pair positional heterogeneity has not always been incorporated into model-building, even some high and ultrahigh-resolution structures of DNA do not indicate the full extent of conformational polymorphism.},
doi = {10.1093/nar/gkr1168},
journal = {Nucleic Acids Res.},
issn = {0305-1048},
number = (8) ; 2012,
volume = 40,
place = {United States},
year = {2012},
month = {10}
}