Fluctuations in the DNA double helix: A critical review
A critical overview of the extensive literature on fluctuations in the DNA double helix is
presented. Both theory and experiment are comprehensively reviewed and analyzed …
presented. Both theory and experiment are comprehensively reviewed and analyzed …
Physics of base-pairing dynamics in DNA
As a key molecule of life, Deoxyribo-Nucleic Acid (DNA) is the focus of numbers of
investigations with the help of biological, chemical and physical techniques. From a physical …
investigations with the help of biological, chemical and physical techniques. From a physical …
DNA breathing integration with deep learning foundational model advances genome-wide binding prediction of human transcription factors
It was previously shown that DNA breathing, thermodynamic stability, as well as
transcriptional activity and transcription factor (TF) bindings are functionally correlated. To …
transcriptional activity and transcription factor (TF) bindings are functionally correlated. To …
Specificity and heterogeneity of terahertz radiation effect on gene expression in mouse mesenchymal stem cells
We report that terahertz (THz) irradiation of mouse mesenchymal stem cells (mMSCs) with a
single-frequency (SF) 2.52 THz laser or pulsed broadband (centered at 10 THz) source …
single-frequency (SF) 2.52 THz laser or pulsed broadband (centered at 10 THz) source …
Elucidation of leak-resistance DNA hybridization chain reaction with universality and extensibility
S Li, P Li, M Ge, H Wang, Y Cheng, G Li… - Nucleic Acids …, 2020 - academic.oup.com
Hybridization chain reaction (HCR) was a significant discovery for the development of
nanoscale materials and devices. One key challenge for HCR is the vulnerability to …
nanoscale materials and devices. One key challenge for HCR is the vulnerability to …
DNA dynamics play a role as a basal transcription factor in the positioning and regulation of gene transcription initiation
We assess the role of DNA breathing dynamics as a determinant of promoter strength and
transcription start site (TSS) location. We compare DNA Langevin dynamic profiles of …
transcription start site (TSS) location. We compare DNA Langevin dynamic profiles of …
A nonlinear dynamic model of DNA with a sequence-dependent stacking term
No simple model exists that accurately describes the melting behavior and breathing
dynamics of double-stranded DNA as a function of nucleotide sequence. This is especially …
dynamics of double-stranded DNA as a function of nucleotide sequence. This is especially …
Distributions of bubble lifetimes and bubble lengths in DNA
We investigate the distribution of bubble lifetimes and bubble lengths in DNA at
physiological temperature, by performing extensive molecular dynamics simulations with the …
physiological temperature, by performing extensive molecular dynamics simulations with the …
Examining DNA breathing with pyDNA-EPBD
Motivation The two strands of the DNA double helix locally and spontaneously separate and
recombine in living cells due to the inherent thermal DNA motion. This dynamics results in …
recombine in living cells due to the inherent thermal DNA motion. This dynamics results in …
Influence of a single deuterium substitution for protium on the frequency generation of different-size bubbles in IFNA17
A Basov, A Dorohova, V Malyshko, A Moiseev… - International Journal of …, 2023 - mdpi.com
The influence of a single 2H/1H replacement on the frequency generation of different-size
bubbles in the human interferon alpha-17 gene (IFNA17) under various energies was …
bubbles in the human interferon alpha-17 gene (IFNA17) under various energies was …