Molecular Mechanisms for the B−Z Transition in the Example of Poly[d(G−C)·d(G−C)] Polymers. A Critical Review

Fuertes, Miguel A.; Cepeda, Victoria; Alonso, Carlos; Pérez, Jose

doi:10.1021/cr050243f

Cited by 88 publications

(65 citation statements)

References 164 publications

(413 reference statements)

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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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“…[1] It has been reported that in a low temperature crystal structure of the spermine complexed with Z-DNA duplex, the spermine in the minor groove decreases the cross-groove electrostatic repulsions between the phosphate anions within the Z-DNA. [12] The crystal structure has been reported to bind two molecules of tetra-amine, NH 2 A C H T U N G T R E N N U N G ((CH 2 ) 3 NH) 3 H, in the minor groove of ZdA C H T U N G T R E N N U N G (CGCGCG) 2 formed at high MgCl 2 concentrations.…”

Section: Resultsmentioning

confidence: 99%

“…The organic layers were dried over Na 2 SO 4 , and evaporated to give a crude residue, which was purified by column chromatography (silica gel, hexane/AcOEt, 7:1) to give 1-benzyl-3,4-bis(2-naphthyl)-pyrrole-2,5-dione (0.38 g, 99 %) as a yellow solid. 1 …”

Section: Isothermal Titration Calorimetry (Itc)mentioning

confidence: 99%

“…Z-DNA is a lefthanded helix in which the purines are in the syn conformation and the pyrimidines in the anti conformation. [1] It has been shown that Z-DNA exists in vivo under physiological conditions as a transient structure occasionally induced by a biological process, such as transcription, the methylation of cytosine, and the level of DNA supercoiling. [2,3] Several proteins have been identified that bind to Z-DNA.…”

Section: Introductionmentioning

confidence: 99%

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The Spermine–Bisaryl Conjugate as a Potent Inducer of B‐ to Z‐DNA Transition

Doi

Tsuji

Kawakami

et al. 2010

Chemistry A European J

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DNA containing alternating purine and pyrimidine repeats has the potential to adopt the Z-DNA structure, one of the well-studied structures besides A- and B-DNA. Despite a number of molecular models that have been proposed to explain the mechanism for B→Z transition, there is continued discussion on the mechanism and physiological role of this transition. In this study, we have found that the bis(2-naphthyl)-maleimide-spermine conjugate (3c) exhibits a remarkable ability to cause the B→Z transition of d(CGCGCG)(2) at low salt concentrations. Using isothermal titration calorimetry (ITC) we show that the B→Z transition induced by 3c is both enthalpically and entropically favorable. The ligand might effect the dehydration of B-DNA, which leads to the B→Z transition. Interestingly, an intermediate CD between the B and Z forms was observed in the pH-dependent transition in the presence of the ligand. The unique structure and characteristics of the ligand designed in this investigation will be useful for the study of Z-DNA.

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“…[4] In dieser "B-ZNanomaschine" sind zwei DNA-Doppelkreuzungsstrukturen (double-crossover DNA structures) durch einen Doppelstrang der Sequenz (CG) 10 verbunden, die C5-methyliertes Cytosin enthält und die für den B-Z-Übergang besonders anfällig ist. [103] Der Übergang wird durch die ¾nderung der [Co(NH 3 ) 6 ] 3+ -Konzentration von 0 auf 0.25 mm ausgelöst. Durch den B-Z-Übergang des d(CG) 10 -Abschnitts wird eine Doppelkreuzungs(DX)-Einheit bezüglich der jeweils anderen um 3.5 Helixwindungen gedreht.…”

Section: Pufferabhängige Molekulare Schalterunclassified

Nukleinsäure‐basierte molekulare Werkzeuge

2011

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In der Biologie sind die Nukleinsäuren die Träger der molekularen Information: Die DNA‐Basensequenz speichert und vermittelt genetische Anweisungen, während die RNA‐Sequenz der Weitergabe der Information sowie der Regulation der Genexpression dient. Als Biopolymere haben Nukleinsäuren auch interessante physikochemische Eigenschaften, die sich darüber hinaus auf unzählige Weise über die Basensequenz rational verändern lassen. Es verwundert daher nicht, dass Nukleinsäuren in den letzten Jahren wichtige Bausteine für die Bottom‐up‐Nanotechnologie geworden sind: als Moleküle für die Selbstorganisation molekularer Nanostrukturen, aber auch als Material zum Aufbau maschinenähnlicher Nanobauteile. In diesem Aufsatz werden wir die wichtigsten Entwicklungen auf dem wachsenden Gebiet der Nukleinsäure‐Nanobauteile zusammenfassen. Wir werden auch einen Überblick über die biochemischen und biophysikalischen Hintergründe des Gebiets sowie über die “historischen” Einflüsse, von denen es geprägt wurde, geben. Besonderes Augenmerk wird molekularen DNA‐Motoren, der molekularen Robotik, der molekularen Datenverarbeitung sowie Anwendungen von Nukleinsäure‐Nanobauteilen in der Biologie gelten.

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Molecular Mechanisms for the B−Z Transition in the Example of Poly[d(G−C)·d(G−C)] Polymers. A Critical Review

Cited by 88 publications

References 164 publications

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

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

The Spermine–Bisaryl Conjugate as a Potent Inducer of B‐ to Z‐DNA Transition

Nukleinsäure‐basierte molekulare Werkzeuge

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