Publisher's Note: “Breathing dynamics based parameter sensitivity analysis of hetero-polymeric DNA” [J. Chem. Phys. 140, 125101 (2014)]

Talukder, Srijeeta; Sen, Shrabani; Chakraborti, Prantik; Metzler, Ralf; Banik, Suman Kumar; Chaudhury, Pinaki

doi:10.1063/1.4871297

Cited by 2 publications

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“…Before going into the fundamental aspects of GA, it should be mentioned that the available stochastic search techniques in literature can be separated mainly into two categories . The first category deals with a single solution and during evolution the solution is subjected to be updated according to certain criteria as desired in that particular technique.…”

Section: Methodsmentioning

confidence: 99%

Controlling the isomerization dynamics of iodide acetonitrile dimer complex by optimally designed electromagnetic field: A wave packet based approach

Naskar

Talukder

Ghosh

2019

Int J of Quantum Chemistry

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Both symmetric and asymmetric forms of the iodide acetonitrile dimer complex are known to exist with a higher stability shown by the symmetric isomer. Dynamics of this isomerization has been investigated on reduced dimensional surface in absence/presence of external electromagnetic field using Gaussian wave packet as the starting wave function. When the symmetric isomer has been taken as the initial structure, isomerization does not takes place without the external field due to high energy barrier, whereas with the asymmetric isomer as the starting one, isomerization takes place spontaneously with an equal population of both isomers. Our target in this study has been to get a dominant population of asymmetric isomer which is not possible without the application of electromagnetic field. However, it has also been seen that a simple monochromatic field cannot achieve this goal. Only by application of optimally designed polychromatic field the dominating population of asymmetric isomer can be obtained.

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Section: Methodsmentioning

confidence: 99%

Controlling the isomerization dynamics of iodide acetonitrile dimer complex by optimally designed electromagnetic field: A wave packet based approach

Naskar

Talukder

Ghosh

2019

Int J of Quantum Chemistry

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“…Being not very rigid and stiff, the hairpin and the triplex so formed as a result of RH base pairing is expected to undergo brief melting and reforming that is illustrated as “breathing” in response to perturbations in the vicinity. − One of the major causes of the breathing is differential interactions in terms of direct and indirect contact of the cations with the DNA . The conformational fluctuation due to DNA breathing is also highly sequence-dependent .…”

Section: Introductionmentioning

confidence: 99%

Real-Time Monitoring of the Multistate Conformational Dynamics of Polypurine Reverse Hoogsteen Hairpin To Capture Their Triplex-Affinity for Gene Silencing by smFRET Microspectroscopy

Bandyopadhyay

Mishra

2020

J. Phys. Chem. B

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Single-molecule Förster resonance energy transfer microspectroscopic methods are employed for real-time monitoring and to gain deeper insights into the formation of the polypurine reverse Hoogsteen hairpin (PPRH) and its triplex-forming activity. The heterogeneity in the behavior of individual PPRHs has been documented, and it is seen that the degree of anharmonic plasticity of the antiparallel hairpin is stabilized by the formation of reverse Hoogsteen (RH) bonds. While being involved in the hairpin formation, they flip reversibly between the open and closed conformations, irrespective of the concentration of ions present in their microenvironment. However, the nature of the cation present in the buffer plays a crucial role in determining the structural stability. The Watson Crick (WC) bonds are found to be more dynamic in the triplex compared to that of the RH base pairs, indicating the involvement of progressive WC bonds during the triplex motif formation by the PPRH. The majority of the intact triplex DNA attained a semifolded relaxed state before progressing toward a tightly folded state, emphasizing the fact that the folding mechanism pursues an ambiguous path in the mode of acquiring the final step of the triple helix motif. Moreover, the presence of triplex-forming sequences in the regulatory regions of the genome further provides an intricate link between the experimental results and sequence occurrence.

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Publisher's Note: “Breathing dynamics based parameter sensitivity analysis of hetero-polymeric DNA” [J. Chem. Phys. 140, 125101 (2014)]

Cited by 2 publications

References 0 publications

Controlling the isomerization dynamics of iodide acetonitrile dimer complex by optimally designed electromagnetic field: A wave packet based approach

Controlling the isomerization dynamics of iodide acetonitrile dimer complex by optimally designed electromagnetic field: A wave packet based approach

Real-Time Monitoring of the Multistate Conformational Dynamics of Polypurine Reverse Hoogsteen Hairpin To Capture Their Triplex-Affinity for Gene Silencing by smFRET Microspectroscopy

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