DNA Renaturation at the Water-Phenol Interface [PDF]
, 2003 We study DNA adsorption and renaturation in a water-phenol two-phase system, with or without shaking. In very dilute solutions, single-stranded DNA is adsorbed at the interface in a salt-dependent manner.
121 +161 more
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Interaction of Nucleosides and Related Compounds with Nucleic Acids as Indicated by the Change of Helix-Coil Transition Temperature [PDF]
, 1962 A series of compounds has been tested for effectiveness in lowering the melting temperature of poly A and of thymus DNA. The order of increasing activity was found to be: adonitol, methyl riboside (both negligible) < cyclohexanol < phenol, pyrimidine ...
Helmkamp, G. K. +2 more
core +1 more source
A Theoretical Mechanism of Szilard Engine Function in Nucleic Acids and the Implications for Quantum Coherence in Biological Systems [PDF]
AIP Conf. Proc. 1316, July 2010, pp. 287-290, 2012 Nucleic acids theoretically possess a Szilard engine function that can convert the energy associated with the Shannon entropy of molecules for which they have coded recognition, into the useful work of geometric reconfiguration of the nucleic acid molecule.
arxiv +1 more source
Sequence- and structural-selective nucleic acid binding revealed by the melting of mixtures [PDF]
, 2006 A simple method for the detection of sequence- and structural-selective ligand binding to nucleic acids is described. The method is based on the commonly used thermal denaturation method in which ligand binding is registered as an elevation in the ...
Chaires, Jonathan B., Shi, Xiaochun
core +2 more sources
Molecular Dynamics Analysis of Biomolecular Systems Including Nucleic Acids [PDF]
arXiv, 2021 Along with recent progress in structural biology and genome biology, structural dynamics of molecular systems including nucleic acids has attracted attention in the context of gene regulation. Structure-function relationship is an important topic, where physicochemical properties of nucleotides are important as well as those of amino acids in proteins.
arxiv
Labeling of Unique Sequences in Double-Stranded DNA at Sites of Vicinal Nicks Generated by Nicking Endonucleases [PDF]
, 2008 We describe a new approach for labeling of unique sequences within dsDNA under nondenaturing conditions. The method is based on the site-specific formation of vicinal nicks, which are created by nicking endonucleases (NEases) at specified DNA sites on ...
Frank-Kamenetskii, Maxim D., Kuhn, Heiko
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Ab Initio Nucleic Acid Folding Simulations Using a Physics-Based Atomistic Free Energy Model [PDF]
, 2022 Performing full-resolution atomistic simulations of nucleic acid folding has remained a challenge for biomolecular modeling. Understanding how nucleic acids fold and how they transition between different folded structures as they unfold and refold has important implications for biology.
arxiv +1 more source
Rubredoxin Variant Folds without Iron [PDF]
, 1999 Pyroccocus furiosus rubredoxin (PFRD), like most studied hyperthermophilic proteins, does not undergo reversible folding. The irreversibility of folding is thought to involve PFRD’s iron-binding site.
Mayo, Stephen L., Strop, Pavel
core +1 more source
A pipeline for targeted metagenomics of environmental bacteria. [PDF]
, 2020 BackgroundMetagenomics and single cell genomics provide a window into the genetic repertoire of yet uncultivated microorganisms, but both methods are usually taxonomically untargeted.
Bowers, Robert M +7 more
core +2 more sources
Nanosecond chain dynamics of single-stranded nucleic acids [PDF]
arXiv, 2023 The conformational dynamics of single-stranded nucleic acids are fundamental for nucleic acid folding and function. However, their elementary chain dynamics have been difficult to resolve experimentally. Here we employ a combination of single-molecule F\"orster resonance energy transfer, nanosecond fluorescence correlation spectroscopy, fluorescence ...
arxiv