Raison d'être and structural model for the B‐Z transition of poly d(G‐C)<sup>∗</sup>poly d(G‐C)

Heinemann, Udo

doi:10.1016/0014-5793(89)81539-x

Cited by 24 publications

(26 citation statements)

References 35 publications

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“…A number of molecular mechanisms have been proposed for the B-Z transition. [31] There is no spectroscopic support for intermediates in three models, the Saenger-Heinemann model, [32] the stretched model, [33] and the zipper model, [34] probably owing to the short lifetime of the intermediates. Goto et al successfully observed an intermediate, designated as B Ã -DNA, in the B-Z transition induced under high salt conditions using a stopped-flow apparatus.…”

Section: Discussionmentioning

confidence: 99%

B–Z DNA Transition Triggered by a Cationic Comb‐Type Copolymer

Shimada

Kano

Maruyama

2009

Adv Funct Materials

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The conformational transition from right‐handed B–DNA to left‐handed Z–DNA—the B–Z transition—has received increased attention recently because of its potential roles in biological systems and its applicability to bionanotechnology. Though the B–Z transition of poly(dG–dC) · poly(dG–dC) is inducible under high salt concentration conditions (over 4 M NaCl) or by addition of multivalent cations, such as hexaamminecobalt(III), no cationic polymer were known to induce the transition. In this study, it is shown by circular dichroism and UV spectroscopy that the cationic comb‐type copolymer, poly(L‐lysine)‐graft‐dextran, but not poly(L‐lysine) homopolymer or a basic peptide, induces the B–Z transition of poly(dG–dC) · poly(dG–dC). At a cationic amino group concentration of 10−4 M the copolymer stabilizes Z–DNA. The transition pathway from the B to the Z form is different to that observed previously. We speculate that the cationic backbone of the copolymer, which reduces electrostatic repulsion among DNA phosphate groups, and the hydrophilic dextran chains, which reduce activity of water, cooperate to induce the B–Z transition. The copolymer specifically modified the micro‐environment around DNA molecules to induce Z–DNA formation through stable and spontaneous inter‐polyelectrolyte complex formation.

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Section: Discussionmentioning

confidence: 99%

B–Z DNA Transition Triggered by a Cationic Comb‐Type Copolymer

Shimada

Kano

Maruyama

2009

Adv Funct Materials

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“…A number of molecular mechanisms have been proposed to explain the change in the handedness of DNA double helix and the 180°base-pair plane rotation during the B-Z transition, including the Wang model, 1 the Harvey model, 12 the A-DNAlike intermediate model, 13 and the model based on the crystal structure of a B-Z junction. 14 The Wang model proposes that base-pair opening occurs before base-pair plane and phosphate backbone angle rotation.…”

Section: Introductionmentioning

confidence: 99%

Transition between B-DNA and Z-DNA: Free Energy Landscape for the B−Z Junction Propagation

Lee

Kim

et al. 2010

J. Phys. Chem. B

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Canonical, right-handed B-DNA can be transformed into noncanonical, left-handed Z-DNA in vitro at high salt concentrations or in vivo under physiological conditions. The molecular mechanism of this drastic conformational transition is still unknown despite numerous studies. Inspired by the crystal structure of a B-Z junction and the previous zipper model, we show here, with the aid of molecular dynamics simulations, that a stepwise propagation of a B-Z junction is a highly probable pathway for the B-Z transition. In this paper, the movement of a B-Z junction by a two-base-pair step in a double-strand nonamer, [d(GpCpGpCpGpCpGpCpG)] 2 , is considered. Targeted molecular dynamics simulations and umbrella sampling for this transition resulted in a transition pathway with a free energy barrier of 13 kcal/mol. This barrier is much more favorable than those obtained from previous atomistic simulations that lead to concerted transitions of the whole strands. The free energy difference between B-DNA and Z-DNA evaluated from our simulation is 0.9 kcal/mol per dinucleotide unit, which is consistent with previous experiments. The current computation thus strongly supports the proposal that the B-Z transition involves a relatively fast extension of B-DNA or Z-DNA by sequential propagation of B-Z junctions once nucleation of junctions is established.

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“…A third hypothesis assumes a transition through an intermediate (A-type) conformation without disruption of Watson-Crick hydrogen bonds and without sterical interference (50,51).…”

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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Raison d'être and structural model for the B‐Z transition of poly d(G‐C)^∗poly d(G‐C)

Cited by 24 publications

References 35 publications

B–Z DNA Transition Triggered by a Cationic Comb‐Type Copolymer

B–Z DNA Transition Triggered by a Cationic Comb‐Type Copolymer

Transition between B-DNA and Z-DNA: Free Energy Landscape for the B−Z Junction Propagation

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

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Raison d'être and structural model for the B‐Z transition of poly d(G‐C)∗poly d(G‐C)

Cited by 24 publications

References 35 publications

B–Z DNA Transition Triggered by a Cationic Comb‐Type Copolymer

B–Z DNA Transition Triggered by a Cationic Comb‐Type Copolymer

Transition between B-DNA and Z-DNA: Free Energy Landscape for the B−Z Junction Propagation

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

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Raison d'être and structural model for the B‐Z transition of poly d(G‐C)^∗poly d(G‐C)