Mesoscopic model confirms strong base pair metal mediated bonding for T–Hg2+–T and weaker for C–Ag+–C

Silva, Luciano Gabriel; Weber, Gerald

doi:10.1016/j.cplett.2022.139847

Cited by 3 publications

(1 citation statement)

References 47 publications

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“…They found that helix stability is additive for high ion concentrations and long helices and non-additive for low ion concentrations and short helices [ 72 ]. Recently, Silva and Weber [ 73 ] used a mesoscopic model and published melting temperatures of sequences containing CC or TT mismatches in the presence of metal ions. These metal-mediated base pairs are becoming increasingly popular in sensing applications and DNA nanotechnology.…”

Section: Role Of Salt Concentrationmentioning

confidence: 99%

Structure and Dynamics of dsDNA in Cell-like Environments

Singh

Maity

Singh

2022

Entropy

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Deoxyribonucleic acid (DNA) is a fundamental biomolecule for correct cellular functioning and regulation of biological processes. DNA’s structure is dynamic and has the ability to adopt a variety of structural conformations in addition to its most widely known double-stranded DNA (dsDNA) helix structure. Stability and structural dynamics of dsDNA play an important role in molecular biology. In vivo, DNA molecules are folded in a tightly confined space, such as a cell chamber or a channel, and are highly dense in solution; their conformational properties are restricted, which affects their thermodynamics and mechanical properties. There are also many technical medical purposes for which DNA is placed in a confined space, such as gene therapy, DNA encapsulation, DNA mapping, etc. Physiological conditions and the nature of confined spaces have a significant influence on the opening or denaturation of DNA base pairs. In this review, we summarize the progress of research on the stability and dynamics of dsDNA in cell-like environments and discuss current challenges and future directions. We include studies on various thermal and mechanical properties of dsDNA in ionic solutions, molecular crowded environments, and confined spaces. By providing a better understanding of melting and unzipping of dsDNA in different environments, this review provides valuable guidelines for predicting DNA thermodynamic quantities and for designing DNA/RNA nanostructures.

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Section: Role Of Salt Concentrationmentioning

confidence: 99%

Structure and Dynamics of dsDNA in Cell-like Environments

Singh

Maity

Singh

2022

Entropy

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Nearest-neighbour parametrization of DNA single, double and triple mismatches at low sodium concentration

de Oliveira Martins,

Weber

2024

Biophysical Chemistry

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Molecular Dynamics Simulation of Melting of the DNA Duplex with Silver-Mediated Cytosine–Cytosine Base Pair

Gusarova,

Kovaleva

2024

Computation

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Metal-mediated base pairs in DNA double helix molecules open up broad opportunities for biosensors based on DNA clusters with silver due to their low toxicity and applicability in drug design. Despite intensive experimental and computational research, molecular mechanisms of stabilization of a double helix by silver-mediated base pairs are mainly unknown. We conducted all-atom molecular dynamics simulations of a dodecameric DNA double helix (sequence 5′-TAGGTCAATACT-3′-3′ATCCACTTATGA-5′) with either cytosine–cytosine or cytosine–Ag+–cytosine mismatch in the center of the duplex. We extended the previously proposed set of interaction parameters for a silver ion in the silver-mediated pair in order to allow for its dissociation. With this new potential, we studied how the addition of a silver ion could stabilize a DNA double helix containing a single cytosine–cytosine mismatch. In particular, we found out that the helix with cytosine–Ag+–cytosine mismatch has a greater melting temperature than the helix with cytosine–cytosine one. This stabilization effect of the silver ion is in qualitative agreement with experimental data. The central region of the duplex with cytosine–Ag+–cytosine mismatch (unlike with cytosine–cytosine mismatch) is stable enough to prevent bubble formation at moderate temperatures during melting. The results of this simulation can be used to devise novel metal-mediated DNA structures.

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Mesoscopic model confirms strong base pair metal mediated bonding for T–Hg2+–T and weaker for C–Ag+–C

Cited by 3 publications

References 47 publications

Structure and Dynamics of dsDNA in Cell-like Environments

Structure and Dynamics of dsDNA in Cell-like Environments

Nearest-neighbour parametrization of DNA single, double and triple mismatches at low sodium concentration

Molecular Dynamics Simulation of Melting of the DNA Duplex with Silver-Mediated Cytosine–Cytosine Base Pair

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