Melting of DNA in confined geometries

Maity, Arghya; Singh, Navin

doi:10.1007/s00249-020-01462-9

Cited by 8 publications

(12 citation statements)

References 62 publications

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“…next part of the study, we have used Gromacs package, version 4.0.4, to study the change in the average size of the 1 BNA molecule with the changing size (radius) of the cylinder.With the change in the cylinder's size (radius only), we have calculated the RMSD (root mean square deviation) values of the confined DNA at different temperatures. The RMSD calculations showed that the molecule is more stable when it is placed inside a cylinder.The results are trivial and well in agreement with the first part of the current investigation and our earlier work[1,2]. The reason for the stability is as follows: the decrease in the cylinder's radius, the confining wall becomes closer, which suppresses the molecule's entropy and hence the RMSD value decreases.…”

supporting

confidence: 92%

“…Several researchers have extended the model to three-dimensions [17,18]. The PBD model has been extended to study the effect of molecular crowders as well as the effect of confinement on the thermal stability of DNA molecule [1,2,17]. The mathematical form of the model that contains N base pairs, is as follows:…”

Section: Methodsmentioning

confidence: 99%

“…The parameter, b, describes the range of anharmonicity. For our studies, we choose model parameters k = 0.015 eV Å−2 , ρ = 5.0, and b = 0.35 Å−1 [2]. The value of the parameter ρ defines the sharpness in the transition from double-strand to single-strand [19].…”

Section: Methodsmentioning

confidence: 99%

“…To study the thermodynamics of DNA in the cylindrical confinement we adopt the scheme proposed in our earlier work [2]. Due to the surrounding cellular environment, the movement of base pairs will be restricted, which in turn affects the overall movement of the molecule.…”

Section: Melting Of 1 Bnamentioning

confidence: 99%

“…In the current manuscript, we extend the work study the effect of confinement on the thermal stability and the structural properties of duplex DNA. The present work is an extension of our previous research works [1,2]. For our study we have considered a 1 BNA chain that is confined in a cylindrical geometry.…”

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confidence: 99%

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Structural Analysis of DNA molecule in a confined shell

Maity¹,

Mathur²,

Imhof³

et al. 2022

Preprint

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Recent advances in operating and manipulating DNA have provided unique experimental possibilities in many fields of DNA research, especially in gene therapy. Researchers have deployed many techniques, experimental and theoretical, to study the DNA structure changes due to external perturbation. It is crucial to understand the structural and dynamical changes in the DNA molecules in a confined state to understand and control the self-assembly of DNA confined in a chamber or nano-channel for various applications. In the current manuscript, we extend the work study the effect of confinement on the thermal stability and the structural properties of duplex DNA. The present work is an extension of our previous research works [1,2]. For our study we have considered a 1 BNA chain that is confined in a cylindrical geometry. How the geometry of the confinement affects the opening and other structural parameters of DNA molecule is the objective of this manuscript. We have used a statistical model(PBD model) and Molecular dynamics simulations for our purpose.

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supporting

confidence: 92%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Melting Of 1 Bnamentioning

confidence: 99%

mentioning

confidence: 99%

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Structural Analysis of DNA molecule in a confined shell

Maity¹,

Mathur²,

Imhof³

et al. 2022

Preprint

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Discovering trends in the Lewis acidity of beryllium and magnesium hydrides and fluorides with increasing clusters size

Mó,

Montero‐Campillo,

Yáñez

et al. 2024

J Comput Chem

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We have reported in the last years the strong effect that Be‐ and Mg‐containing Lewis acids have on the intrinsic properties of typical bases, which become acids upon complexation. In an effort to investigate these changes when the Be and Mg derivatives form clusters of increasing size, we have examined the behavior of the (MX2)n (M = Be, Mg; X = H, F; n = 1, 2, 3) clusters when they interact with ammonia, methanimine, hydrogen cyanide and pyridine, and with their corresponding deprotonated forms. The complexes obtained at the M06‐2X/aug‐cc‐pVTZ level were analyzed using the MBIE energy decomposition formalism, in parallel with QTAIM, ELF, NCIPLOT and AdNDP analyses of their electron density. For n = 1 the interaction enthalpy for the different families of monomers, Be (Mg) hydrides and Be (Mg) fluorides, follows the same trend as the intrinsic basicity of the base that interacts with them. This interaction is greatly reinforced after the deprotonation of the base, resulting in a significant enhancement of the intrinsic acidity of the corresponding MX2–Base complex. For (MX2)2 clusters a further reinforcement of the interaction with the base is observed, this reinforcement being again larger for the deprotonated complexes. However, the concomitant increase of their intrinsic acidity is one order of magnitude larger for hydrides than for fluorides. Unexpectedly, the cyclic conformers (MX2)3, which are more unstable than the linear ones, become the global minima after association with the base and the same is true for the deprotonated complex. Accordingly, a further increase of the intrinsic acidity of the (MX2)3–Base complexes with respect to the (MX2)2–Base ones is observed. This effect is maximum for (MgF2)3 clusters, to the point that the (MgF2)3–Base complexes become more acidic than nitric acid, the extreme case being the cluster (MgF2)3–NCH, whose acidity is higher than that of perchloric acid.

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