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Dynamics of molecules in torsional DNA exposed to microwave and possible impact on its deformation: stability analysis
In this work, we explore the dynamics of molecules in torsionally stressed DNA subjected to periodic external forces, specifically microwave...
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Nonlinear Dynamics of DNA Chain
Deoxyribonucleic acid (DNA) is found in all prokaryotic and eukaryotic cells and many viruses. This complex molecular structure is certainly one of...
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Dynamics of the HP1 Hinge Region with DNA Measured by Site-Directed Spin Labeling-EPR Spectroscopy
An epigenetic reader, heterochromatin protein 1 (HP1), possesses two conserved domains, the chromoshadow domain (CSD) and chromodomain (CD). The CD...
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“Flexible hinge” dynamics in mismatched DNA revealed by fluorescence correlation spectroscopy
Altered unwinding/bending fluctuations at DNA lesion sites are implicated as plausible mechanisms for damage sensing by DNA-repair proteins. These...
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Nonlinear Dynamics of DNA Chain with Long-Range Interactions
The present chapter is devoted to the investigation of the nonlinear dynamics of DNA molecules in the helicoidal Peyrard-Bishop DNA model with...
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Breathers-like rogue wave trains induced by nonlinear dynamics of DNA breathing
We introduce in the deoxyribonucleic acid (DNA) molecular chain at the first time the collective coordinates’ theory to measure the exact signature...
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Fluorescence Microscopy of Nanochannel-Confined DNA
Stretching of DNA in nanoscale confinement allows for several important studies. The genetic contents of the DNA can be visualized on the single DNA...
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DNA-Polyamine Interactions: Insight from Molecular Dynamics Simulations on the Sequence-Specific Binding of Spermidine3+
DNA is a polyanion stabilized in vivo by positively charged counterions, including metal ions and small organic molecules, e.g., putrescine2+,...
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Detecting DNA Loops Using Tethered Particle Motion
The range of motion of a micron-sized bead tethered by a single polymer provides a dynamic readout of the effective length of the polymer. The...
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Assessment of Dynamic Disorder in DNA Oligonucleotides Using Low-Frequency Raman Spectroscopy
AbstractThe degree of DNA compaction in various regions of the cell nucleus determines whether the corresponding genes should be expressed and other...
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Comparison of the Dynamics of DNA Damage in Blood Leukocytes and Survival Rate of Mice after Total Body Irradiation with Carbon Ions in the Bragg Peak or X-Rays
AbstractThe survival rate of mice irradiated with accelerated carbon ions (450 MeV/nucleon) at the Bragg peak or X-ray radiation at a dose of 6.5 Gy...
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Review of Mathematical Models Describing the Mechanical Motion in a DNA Molecule
AbstractSeveral mechanical models that reproduce the DNA structure were considered. Evolution was described in more detail for the mechanical model...
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DNA Origami-Based Single-Molecule Force Spectroscopy and Applications
Over the last years, single-molecule force spectroscopy provided insights into the intricate connection between mechanical stimuli and biochemical...
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Base flip** mechanism and binding strength of methyl-damaged DNA during the interaction with AGT
Methyl damage to DNA bases is common in the cell nucleus. O6-alkylguanine-DNA alkyl transferase (AGT) may be a promising candidate for direct damage...
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Single-Molecule FRET-Resolved Protein Dynamics – from Plasmid to Data in Six Steps
Single-molecule Förster resonance energy transfer (smFRET) is a powerful technique for the detection of conformational dynamics of biomolecules....
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Nonlinear Dynamics of Nanobiophysics
This book highlights important aspects of nonlinear dynamics of biophysical nanosystems, such as DNA, alpha helix, and microtubules. It presents the...
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Classical Molecular Dynamics Simulations of Biomolecules
Molecular dynamics simulations at atomic level have widely been used in studying macromolecular systems, such as protein, DNA and their complexes,...
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Electrostatics and hydrophobicity in the dynamics of intrinsically disordered proteins
Internal friction is a major contribution to the dynamics of intrinsically disordered proteins (IDPs). Yet, the molecular origin of internal friction...
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Connection number topological aspect for backbone DNA networks
AbstractThe present study investigates the complex topological characteristics of DNA networks, with a specific emphasis on the innovative metric...
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Storage of mechanical energy in DNA nanorobotics using molecular torsion springs
DNA nanostructures are increasingly used for the realization of mechanically active nanodevices and DNA-based nanorobots. A fundamental challenge in...
