Z-DNA crystallography

Ho, P Shing; Mooers, Blaine H. M.

doi:10.1002/(sici)1097-0282(1997)44:1<65::aid-bip5>3.0.co;2-y

Cited by 38 publications

(65 citation statements)

References 112 publications

(34 reference statements)

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“…In DinuHT1 the values are À11.5 and À48.5 . The basestep rise at all the steps in all three helices is similar to the values seen in other crystal structures of Z-type helices (Ho & Mooers, 1997).…”

Section: Molecular Structuresupporting

confidence: 86%

Structure of d(TGCGCG)·d(CGCGCA) in two crystal forms: effect of sequence and crystal packing in Z-DNA

Thiyagarajan¹,

Rajan²,

Gautham³

2005

Acta Cryst D

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The sequence d(TGCGCG).d(CGCGCA) crystallized in two crystal forms, orthorhombic and hexagonal, in the presence of cobalt hexammine chloride, a known inducer of the left-handed Z-form of DNA. The crystal structures have been solved and refined at 1.71 A resolution in space group P2(1)2(1)2(1) and 2.0 A resolution in space group P6(5). The orthorhombic structure contains one Z-DNA hexamer duplex, while the hexagonal structure contains two hexamer duplexes in the structure. Of the latter, one is situated on a crystallographic sixfold screw axis, leading to disorder. This paper reports the effects of sequence and crystal packing on the structure of Z-type DNA. The structures lend additional support to the authors' earlier conclusion that a stretch of four C.G base pairs is sufficient to nucleate and define the regular model of the left-handed helix based on the structure of d(CGCGCG)2.

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Section: Molecular Structuresupporting

confidence: 86%

Structure of d(TGCGCG)·d(CGCGCA) in two crystal forms: effect of sequence and crystal packing in Z-DNA

Thiyagarajan¹,

Rajan²,

Gautham³

2005

Acta Cryst D

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“…5-Methylation is known to stabilize B-Z transitions (Rich, 1984). Previous crystallographic studies showed that 5-methylation did not affect the global structures of DNA, with the exception of subtle changes in helical twist angles (Fujii et al, 1982;Ho & Mooers, 1997). It was suggested that 5-methylation is associated with a relative destabilization of the B-DNA structure and stabilization through hydrophobic bonding of Z-DNA structures.…”

Section: Effects Of the Local Environment On The Polymorphism Of Z-dnamentioning

confidence: 99%

DNA conformational transitions inferred from re-evaluation ofm|F_o| −D|F_c| electron-density maps

Sunami

Chatake

Kono

2017

Acta Cryst Sect D Struct Biol

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Edited by G. J. Kleywegt, EMBL-EBI, Hinxton, EnglandKeywords: crystallographic heterogeneity; DNA; flexibility of phosphate backbone; Z-DNA; ZI/ZII transition. Conformational flexibility of DNA plays important roles in biological processes such as transcriptional regulation and DNA packaging etc. To understand the mechanisms of these processes, it is important to analyse when, where and how DNA shows conformational variations. Recent analyses have indicated that conventional refinement methods do not always provide accurate models of crystallographic heterogeneities and that some information on polymorphism has been overlooked in previous crystallographic studies. In the present study, the m|F o | À D|F c | electron-density maps of double-helical DNA crystal structures were calculated at a resolution equal to or better than 1.5 Å and potential conformational transitions were found in 27% of DNA phosphates. Detailed analyses of the m|F o | À D|F c | peaks indicated that some of these unassigned densities correspond to ZI $ ZII or A/B ! BI conformational transitions. A relationship was also found between ZI/ZII transitions and metal coordination in Z-DNA from the detected peaks. The present study highlights that frequent transitions of phosphate backbones occur even in crystals and that some of these transitions are affected by the local molecular environment.

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“…However, already in 1972, Pohl and Jovin (7) were able to observe an almost complete inversion of the ultraviolet circular dichroism (CD) spectrum of poly(GC) double-helical oligonucleotides upon addition of large amounts of salt (e.g., 4 m NaCl). The explanation for this effect was provided by the subsequent determination of the corresponding three-dimensional structure through x-ray diffraction (1,8), resulting in a left-handed helicity with an alternating anti (pyrimidine) and syn (purine) orientation of the nucleotide bases together with Watson-Crick basepairing (1). Due to the particular zigzag pattern adopted by the sugar-phosphate backbone, this new DNA form was termed Z-DNA.…”

Section: Introductionmentioning

confidence: 99%

The Transition between the B and Z Conformations of DNA Investigated by Targeted Molecular Dynamics Simulations with Explicit Solvation

Kastenholz

Schwartz

Hünenberger

2006

Biophysical Journal

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The transition between the B and Z conformations of double-helical deoxyribonucleic acid (DNA) belongs to the most complex and elusive conformational changes occurring in biomolecules. Since the accidental discovery of the left-handed Z-DNA form in the late 1970s, research on this DNA morphology has been engaged in resolving questions relative to its stability, occurrence, and function in biological processes. While the occurrence of Z-DNA in vivo is now widely recognized and the major factors influencing its thermodynamical stability are largely understood, the intricate conformational changes that take place during the B-to-Z transition are still unknown at the atomic level. In this article, we report simulations of this transition for the 3'-(CGCGCG)-5' hexamer duplex using targeted molecular dynamics with the GROMOS96 force field in explicit water under different ionic-strength conditions. The results suggest that for this oligomer length and sequence, the transition mechanism involves: 1), a stretched intermediate conformation, which provides a simple solution to the important sterical constraints involved in this transition; 2), the transient disruption of Watson-Crick hydrogen-bond pairing, partly compensated energetically by an increase in the number of solute-solvent hydrogen bonds; and 3), an asynchronous flipping of the bases compatible with a zipperlike progression mechanism.

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Z-DNA crystallography

Cited by 38 publications

References 112 publications

Structure of d(TGCGCG)·d(CGCGCA) in two crystal forms: effect of sequence and crystal packing in Z-DNA

Structure of d(TGCGCG)·d(CGCGCA) in two crystal forms: effect of sequence and crystal packing in Z-DNA

DNA conformational transitions inferred from re-evaluation ofm|F_o| −D|F_c| electron-density maps

The Transition between the B and Z Conformations of DNA Investigated by Targeted Molecular Dynamics Simulations with Explicit Solvation

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Z-DNA crystallography

Cited by 38 publications

References 112 publications

Structure of d(TGCGCG)·d(CGCGCA) in two crystal forms: effect of sequence and crystal packing in Z-DNA

Structure of d(TGCGCG)·d(CGCGCA) in two crystal forms: effect of sequence and crystal packing in Z-DNA

DNA conformational transitions inferred from re-evaluation ofm|Fo| −D|Fc| electron-density maps

The Transition between the B and Z Conformations of DNA Investigated by Targeted Molecular Dynamics Simulations with Explicit Solvation

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DNA conformational transitions inferred from re-evaluation ofm|F_o| −D|F_c| electron-density maps