Structural Variability and New Intermolecular Interactions of Z-DNA in Crystals of d(pCpGpCpGpCpG)

Malinina, Lucy; Tereshko, V.; Иванова, Е. М.; Subirana, Juan A.; Zarytova, V.; Nekrasov, Yurii S.

doi:10.1016/s0006-3495(98)77956-1

Cited by 14 publications

(17 citation statements)

References 44 publications

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“…To this purpose, MD and TMD simulations are carried out for the double-helical hexanucleotide 39-(CGCGCG)-59 in water. The self-complementary (CGCGCG) 2 duplex (melting temperature: T m % 320 K (96)) has been investigated previously in a number of experimental and theoretical studies (1,(97)(98)(99)(100)(101)(102), and is known to show a high propensity to form Z-DNA due to the presence of CG repeats (103). Six independent MD simulations at room temperature involve the hexamer duplex starting from either the B or the Z conformation, and either without counterions, with a neutralizing amount of sodium counterions, or with an excess amount (4 m) of sodium and chloride counterions.…”

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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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 molecular structure is rigid and all geometrical parameters have values close to those found in the fibre model. However, when the helix adopts a different packing scheme, the structure ceases to be rigid and shows a range of variability (Malinina et al, 1998).…”

Section: Introductionmentioning

confidence: 99%

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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“…Other researchers (Malinina et al, 1998), however, did lodge their raw diffraction data and structure factors derived from X-ray diffraction from crystals of d-CGCGCG. Their Z-DNA structure factor file, 392D, defines a supercell, that is, their chosen unit cell is larger than the crystallographic data requires.…”

Section: The Paranemic Dna Duplexmentioning

confidence: 99%

“…For example, researchers report (Sadasivan et al, 1994) that their refinement of the structure factors of a Z form hexamer was carried out using the algorithm NUCLSQ. This contains within it the sub-routine NAHELIX (Malinina et al, 1998) which contains a model double helix. Therefore a double helical computational outcome is the only possibility.…”

Section: The Paranemic Dna Duplexmentioning

confidence: 99%

Extending the Repertoire of Structures in DNA Nanotechnology

Delmonte¹

2015

American Journal of Nanotechnology

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DNA nanotechnology remains an active area of research and advances have been reviewed recently. DNA nanotechnology seeks to deploy molecules at an atomic level and on a small molecule scale. Other techniques in biophysics and biochemistry do not need to address the issue of the true structure of the nucleic acids at an atomic level but, rather, at a macro-atomic level such as in genetics and in immunology, for example. Accordingly, DNA nanotechnology is perhaps uniquely dependent upon exact clarity in the secondary and tertiary structures of the nucleic acids, as well as that can ever be achieved. Challenges include expanding the use of DNA in medicine, and the construction of detectors with higher sensitivity for biological and chemical settings. Though increasingly complex architectures have been constructed, novel approaches to a greater rôle in biological computation and data storage remain important goals. Here a repertoire of structures for DNA at an atomic level is described which offers a new conjecture with which to move forward. The DNA double helix model faces many problems which have become apparent in the 62 years of research in molecular biology that have elapsed since it was formulated by Watson and Crick in 1953. Experimental evidence is set out seeking to show that the only truly side-by-side alternative, the paranemic model, accounts better for the wide range of phenomena otherwise inexplicable with the double helix model. This paranemic model can engage in a repertoire of structural options denied to the DNA double helix model. Without the requirement to postulate unwinding of the DNA strands, the nucleotide base sequence is immediately accessible to complementary DNA sequences to promote rapid detection of specific molecules in biological and medical settings. Rapid switching between Watson-Crick and Hoogsteen base pairing and four-stranded structures can allow greater complexity in the construction of molecular switches and digital programming.

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Structural Variability and New Intermolecular Interactions of Z-DNA in Crystals of d(pCpGpCpGpCpG)

Cited by 14 publications

References 44 publications

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

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

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

Extending the Repertoire of Structures in DNA Nanotechnology

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