Nonspecificity Induces Chiral Specificity in the Folding Transition of Giant DNA

Ito, Michiko; Sakakura, Akira; Miyazawa, Naomi; Murata, Shizuaki; Yoshikawa, Kenichi

doi:10.1021/ja036745x

Cited by 13 publications

(20 citation statements)

References 19 publications

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“…Thus, several research groups studied this mode of compaction process using modified dendrimer surface by acetylation, PEGylation27 etc. Besides these substances, researchers have also studied the impact of chirality on DNA compaction by using chiral polycations and chiral polypeptide728. Interesting reports are also available about reversibly controlled compaction/decompaction process of DNA29.…”

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confidence: 99%

A Green Solvent Induced DNA Package

Satpathi

Sengupta

Hridya

et al. 2015

Sci Rep

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Mechanistic details of DNA compaction is essential blue print for gene regulation in living organisms. Many in vitro studies have been implemented using several compaction agents. However, these compacting agents may have some kinds of cytotoxic effects to the cells. To minimize this aspect, several research works had been performed, but people have never focused green solvent, i.e. room temperature ionic liquid as DNA compaction agent. To the best of our knowledge, this is the first ever report where we have shown that guanidinium tris(pentafluoroethyl)trifluorophosphate (Gua-IL) acts as a DNA compacting agent. The compaction ability of Gua-IL has been verified by different spectroscopic techniques, like steady state emission, circular dichroism, dynamic light scattering and UV melting. Notably, we have extensively probed this compaction by Gua-IL through field emission scanning electron microscopy (FE-SEM) and fluorescence microscopy images. We also have discussed the plausible compaction mechanism process of DNA by Gua-IL. Our results suggest that Gua-IL forms a micellar kind of self aggregation above a certain concentration (≥1 mM), which instigates this compaction process. This study divulges the specific details of DNA compaction mechanism by a new class of compaction agent, which is highly biodegradable and eco friendly in nature.

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confidence: 99%

A Green Solvent Induced DNA Package

Satpathi

Sengupta

Hridya

et al. 2015

Sci Rep

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“…[8][9][10][11][12][13] A few recent experiments concentrated on the kinetics of DNA compaction. They showed that DNA condenses continuously and linearly with time once the compaction process begins.…”

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confidence: 99%

Compaction Dynamics of Single DNA Molecules under Tension

Wang

Zhang

et al. 2006

J. Am. Chem. Soc.

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The compaction of DNA by multivalent cations has been the subject of many investigations, not only because it is biologically important, but also because it poses a fascinating challenge to our understanding of semiflexible polymers. [1][2][3][4][5] Polyelectrolyte theory has figured out that the attractive potential that leads to DNA compaction originates from correlated fluctuation of counterions shared between DNA segments. 6 Experimental observations have revealed that DNA condensates have generally a toroidal geometry with a typical size of ∼100 nm in diameter. It is generally believed that DNA within a toroid is organized in a hexagonal close-packed lattice, 7 but how such a structure is formed is still not fully understood.Single-molecule measurements have proven helpful to understanding the nucleation and growth of DNA condensates. [8][9][10][11][12][13] A few recent experiments concentrated on the kinetics of DNA compaction. They showed that DNA condenses continuously and linearly with time once the compaction process begins. [14][15][16][17] The results seemed to support the widely accepted opinion that the toroid is formed by continuously absorbing DNA to a primary loop randomly nucleated on DNA. The temporal resolution of the experiments was, however, relatively low. They might not be able to resolve the time trajectories of the DNA compaction.Exerting forces on DNA is a useful way to study processes relevant to DNA. 18 The force may slow down the dynamical process so that details can be observed using an apparatus of finite temporal resolution. Here we report single-molecule studies on the dynamics of hexaammine cobalt chloride-induced DNA compaction under tension. It turns out that the compaction process is more sophisticated than the static structural model has suggested. DNA condenses into toroid in a quantized manner.The measurements were performed using transverse magnetic tweezers similar to the one recently developed by Yan and Marko. 19 Two micrometer-sized beads are tethered to the two ends of a λ-phage DNA (16.4 µm). One bead is fixed in space by a micropipette, and the other is free in solution. A magnetic rod is inserted into the solution to generate a constant force to the free magnetic bead. The experiments were done in phosphate-buffered saline (10 mM PBS, 5 mM NaCl, pH ) 7.4). After adjusting the force on DNA, 10 µL of 10 mM hexaammine cobalt chloride solution was added into the sample cell. The final concentration of the trivalent cations was 100 µM. Figure 1a shows the time course of DNA compaction at a force F ) 0.5 pN. Time courses measured at other concentrations of the trivalent cations (from 35 to 200 µM) are quite similar. After addition of the cations, a long induction period was observed before the compaction started. The induction time becomes longer when a less concentrated solution of trivalent cations is added. The compaction is discontinuous and stepwise. The two big steps in Figure 1a consist of multiple small steps. Such discontinuous compactions were also observed...

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“…[1][2][3][4] In contrast to the wealth of information now available on the long-distance hole transfer, [5][6][7][8][9] less is known about the complementary excess-electron-transfer process in which an anion, instead of a cation, moves through the duplex. We, [10][11][12][13] and others, [14][15][16][17][18][19] have recently shown that excess electrons move through DNA by a hopping-type mechanism in which the pyrimidine bases dT and dC act as stepping stones. [17] Although the hopping of excess electrons through DNA is now a generally accepted model, conflicting data on the sequence dependence of this process were reported.…”

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Complex Sequence Dependence by Excess‐Electron Transfer through DNA with Different Strength Electron Acceptors

et al. 2005

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An independent jump: Excess electrons move through DNA by using a hopping‐type mechanism in which the pyrimidine bases dT and dC act as ‘stepping stones’. It was shown that GC base pairs, in contrast to AT base pairs, lower the efficiency of the excess‐electron transfer through the duplex. Through the use of the shown DNA hairpins, three different electron acceptors ( ) were investigated with the electron donor, reduced flavin ( ).

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Nonspecificity Induces Chiral Specificity in the Folding Transition of Giant DNA

Cited by 13 publications

References 19 publications

A Green Solvent Induced DNA Package

A Green Solvent Induced DNA Package

Compaction Dynamics of Single DNA Molecules under Tension

Complex Sequence Dependence by Excess‐Electron Transfer through DNA with Different Strength Electron Acceptors

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