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Shchyolkina, Anna K.

doi:10.1023/a:1023393521207

Cited by 18 publications

(4 citation statements)

References 35 publications

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“…This structural limitation also prevents the model from capturing the antiparallel directionality of DNA association (5 -end aligns with 3end and vice versa). Neglecting the antiparallel preference is not as drastic as it may appear, since parallel stranded DNA hybridization is known to be possible, [67][68][69] although it carries a much reduced stability and produces noncanonical helical structures. In the present work, sequence complementarity will be the only constraint driving the antiparallel pairing between single-stranded oligonucleotides.…”

Section: A Coarse-grained Lattice Model Of Oligonucleotidesmentioning

confidence: 99%

Lattice model of oligonucleotide hybridization in solution. I. Model and thermodynamics

Araque

Panagiotopoulos

Robert

2011

The Journal of Chemical Physics

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A coarse-grained lattice model of DNA oligonucleotides is proposed to investigate the general mechanisms by which single-stranded oligonucleotides hybridize to their complementary strands in solution. The model, based on a high-coordination cubic lattice, is simple enough to allow the direct simulation of DNA solutions, yet capturing how the fundamental thermodynamic processes are microscopically encoded in the nucleobase sequences. Physically relevant interactions are considered explicitly, such as interchain excluded volume, anisotropic base-pairing and base-stacking, and single-stranded bending rigidity. The model is studied in detail by a specially adapted Monte Carlo simulation method, based on parallel tempering and biased trials, which is designed to overcome the entropic and enthalpic barriers associated with the sampling of hybridization events of multiple single-stranded chains in solution. This methodology addresses both the configurational complexity of bringing together two complementary strands in a favorable orientation (entropic barrier) and the energetic penalty of breaking apart multiple associated bases in a double-stranded state (enthalpic barrier). For strands with sequences restricted to nonstaggering association and homogeneous pairing and stacking energies, base-pairing is found to dominate the hybridization over the translational and conformational entropy. For strands with sequence-dependent pairing corresponding to that of DNA, the complex dependence of the model's thermal stability on concentration, sequence, and degree of complementarity is shown to be qualitatively and quantitatively consistent both with experiment and with the predictions of statistical mechanical models.

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Section: A Coarse-grained Lattice Model Of Oligonucleotidesmentioning

confidence: 99%

Lattice model of oligonucleotide hybridization in solution. I. Model and thermodynamics

Araque

Panagiotopoulos

Robert

2011

The Journal of Chemical Physics

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“…First, the most striking feature of ps DNA is that the two strands of the duplex are parallel, which means the two 5′ ends are at the same end of the duplex. Second, the sequence of the strand that can form the ps duplex is specific, such as the reported parallel TA base pair, alternative d(GA) and d(GGA) sequence, , and so on. ,− Lastly, these ps duplexes are usually only stable in special solution conditions. For example, Mg 2+ , Zn 2+ or proton were needed to stabilize the corresponding ps DNA duplex depending on the specific DNA sequence …”

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confidence: 99%

Lighting Up the Thioflavin T by Parallel-Stranded TG(GA)n DNA Homoduplexes

et al. 2018

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Thioflavin T (ThT) was once regarded to be a specific fluorescent probe for the human telomeric G-quadruplex, but more other kinds of DNA were found that can also bind to ThT in recent years. Herein, we focus on G-rich parallel-stranded DNA and utilize fluorescence, absorbance, circular dichroism, and surface plasmon resonance spectroscopy to investigate its interaction with ThT. Pyrene label and molecular modeling are applied to unveil the binding mechanism. We find a new class of non-G-quadruplex G-rich parallel-stranded ( ps) DNA with the sequence of TG(GA) n can bind to ThT and increase the fluorescence with an enhancement ability superior to G-quadruplex. The optimal binding specificity for ThT is conferred by two parts. The first part is composed of two bases TG at the 5' end, which is a critical domain and plays an important role in the formation of the binding site for ThT. The second part is the rest alternative d(GA) bases, which forms the ps homoduplex and cooperates with the TG bases at the 5' end to bind the ThT.

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“…For all these systems we considered the classic Watson-Crick (cWW) and the reverse Watson-Crick (tWW) geometries, characteristic of antiparallel and parallel duplexes respectively, both in gas phase and in water. For the base pairs in the tWW geometry, the isoguanine-cytosine (iG:C) and guanine-isocytosine (G:iC) pairs have been used as reference systems, as the iG:C/G:iC pairs have been shown to stabilize parallel-stranded nucleic acid duplexes, [24] while the classical tWW G:C pair has been shown to destabilize them. [21a, 24a, 25] Therefore, DAiG and all its modifications with the above substituents on the C7 atom have also been modeled (Figure 1).…”

Section: Introductionmentioning

confidence: 99%

Structural and Energetic Impact of Non‐natural 7‐Deaza‐8‐azaguanine, 7‐Deaza‐8‐azaisoguanine, and Their 7‐Substituted Derivatives on Hydrogen‐Bond Pairing with Cytosine and Isocytosine

Chawla

Minenkov

et al. 2019

ChemBioChem

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We theoretically characterized the impact that the 7-deaza-8-azaguanine (DAG) and 7-deaza-8azaisoguanine (DAiG) modifications have on the geometry and stability of the G:C Watson-Crick (cWW) base pair and of the G:iC and iG:C reverse Watson-Crick (tWW) base pairs. In addition, we investigated the effect on the same base pairs of seven C7-substituted DAG and DAiG, some of which have been previously experimentally characterized. Our calculations indicate that all these modifications have a negligible impact on the geometry of the above base pairs, and that the modification of the heterocycle skeleton has small impact on the base pair interaction energies. Instead, base pair interaction energies are dependent on the nature of the C7 substituent. For the 7substituted DAG-C cWW systems we found a linear correlation between the base pair interaction energy and the Hammett constant of the 7-substituent, with higher interaction energies corresponding to more electron-withdrawing substituents. Therefore, the explored modifications are expected to be accommodated in both parallel and antiparallel nucleic acid duplexes without perturbing their

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Cited by 18 publications

References 35 publications

Lattice model of oligonucleotide hybridization in solution. I. Model and thermodynamics

Lattice model of oligonucleotide hybridization in solution. I. Model and thermodynamics

Lighting Up the Thioflavin T by Parallel-Stranded TG(GA)n DNA Homoduplexes

Structural and Energetic Impact of Non‐natural 7‐Deaza‐8‐azaguanine, 7‐Deaza‐8‐azaisoguanine, and Their 7‐Substituted Derivatives on Hydrogen‐Bond Pairing with Cytosine and Isocytosine

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