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

Shimada, Noritomo; Kano, Arihiro; Maruyama, Atsushi

doi:10.1002/adfm.200901169

Cited by 20 publications

(23 citation statements)

References 37 publications

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“…The mechanism behind the diverse effects of monomeric TMA + ion and MPLL-g-Dex multivalent ions are not yet understood. We previously reported that PLL-g-Dex induces B-form to Zform transitions of poly(dG-dC)•poly(dG-dC) dsDNA [23]. Interestingly, changes of the dsDNA conformation by MPLL-g-Dex were not observed in CD measurements (data not shown).…”

Section: Discussioncontrasting

confidence: 57%

Preparation of Cationic Comb-Type Copolymer Having Tetra-Alkylammonium Groups and its Interaction with DNA

Moriyama¹,

Mochida²,

Yamayoshi³

et al. 2011

CNANO

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The interactions between DNAs and cationic comb-type copolymers like those with quaternary ammonium with N-methylated groups have applications in nanotechnology. N-methylated poly(L-lysine)-graft-dextran copolymers (MPLL-g-Dex) were obtained by methylation of poly(L-lysine)-graft-dextran copolymers (PLL-g-Dex) using dimethyl sulfate under weak basic conditions. The resulting copolymers were characterized using NMR spectroscopy and gel permeation chromatography-multiangle light scattering (GPC-MALS). Both primary and secondary amino groups of the PLL backbones were thoroughly methylated to form quaternary ammonium groups without fragmentation of PLL-g-Dex chains or other detectable side reactions. The interactions of the copolymers with DNAs were assessed by UV melting curves and fluorescence correlation spectroscopic measurements. PLL-g-Dex interacts with double-stranded DNA (dsDNA) in a sequence-independent manner. In contrast the MPLL-g-Dex affinity was lower for dsDNA with higher GC content than for DNA with low GC content. The results suggest that MPLL-g-Dex interacts with DNAs not only through ionic interactions, but also by hydrophobic interactions.

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Section: Discussioncontrasting

confidence: 57%

Preparation of Cationic Comb-Type Copolymer Having Tetra-Alkylammonium Groups and its Interaction with DNA

Moriyama¹,

Mochida²,

Yamayoshi³

et al. 2011

CNANO

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“…US2 was subsequently studied for its detail characterization including binding and melting curve analysis. As indicated previously, two factors are mainly required to trigger B-Z transition, shielding of the electrostatic repulsion from phosphate groups of DNA and reducing water activity in Z-DNA stabilization484950. The preference for B- over Z-DNA has been ascribed to electrostatic repulsion between adjacent phosphate oxygen which are approximately 1 Å closer in the Z-form51.…”

Section: Resultsmentioning

confidence: 82%

Lanthanum induced B-to-Z transition in self-assembled Y-shaped branched DNA structure

Nayak

Mishra

Jena

et al. 2016

Sci Rep

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Controlled conversion of right-handed B-DNA to left-handed Z-DNA is one of the greatest conformational transitions in biology. Recently, the B-Z transition has been explored from nanotechnological points of view and used as the driving machinery of many nanomechanical devices. Using a combination of CD spectroscopy, fluorescence spectroscopy, and PAGE, we demonstrate that low concentration of lanthanum chloride can mediate B-to-Z transition in self-assembled Y-shaped branched DNA (bDNA) structure. The transition is sensitive to the sequence and structure of the bDNA. Thermal melting and competitive dye binding experiments suggest that La3+ ions are loaded to the major and minor grooves of DNA and stabilize the Z-conformation. Our studies also show that EDTA and EtBr play an active role in reversing the transition from Z-to-B DNA.

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“…The Z-DNA peaks of GC-DNA increased after gradually addition of SC-dots (Figure 2C). As the B-Z transition was accompanied by a change in the UV spectrum, a marked hypochromism and bathrochromic shift was also observed (Figure 2D) (17,20). UV spectral change of AT-DNA was also different from GC-DNA, and there was no obvious shift on SC-dots binding (Supplementary Figure S5B).…”

Section: Resultsmentioning

confidence: 90%

Lighting up left-handed Z-DNA: photoluminescent carbon dots induce DNA B to Z transition and perform DNA logic operations

Feng

Zhao

Ren

et al. 2013

Nucleic Acids Research

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Left-handed Z-DNA has been identified as a transient structure occurred during transcription. DNA B-Z transition has attracted much attention because of not only Z-DNA biological importance but also their relation to disease and DNA nanotechnology. Recently, photoluminescent carbon dots, especially highly luminescent nitrogen-doped carbon dots, have attracted much attention on their applications to bioimaging and gene/drug delivery because of carbon dots with low toxicity, highly stable photoluminescence and controllable surface function. However, it is still unknown whether carbon dots can influence DNA conformation or structural transition, such as B-Z transition. Herein, based on our previous series work on DNA interactions with carbon nanotubes, we report the first example that photoluminescent carbon dots can induce right-handed B-DNA to left-handed Z-DNA under physiological salt conditions with sequence and conformation selectivity. Further studies indicate that carbon dots would bind to DNA major groove with GC preference. Inspired by carbon dots lighting up Z-DNA and DNA nanotechnology, several types of DNA logic gates have been designed and constructed based on fluorescence resonance energy transfer between photoluminescent carbon dots and DNA intercalators.

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

Cited by 20 publications

References 37 publications

Preparation of Cationic Comb-Type Copolymer Having Tetra-Alkylammonium Groups and its Interaction with DNA

Preparation of Cationic Comb-Type Copolymer Having Tetra-Alkylammonium Groups and its Interaction with DNA

Lanthanum induced B-to-Z transition in self-assembled Y-shaped branched DNA structure

Lighting up left-handed Z-DNA: photoluminescent carbon dots induce DNA B to Z transition and perform DNA logic operations

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