Nucleic Acid Thermodynamics Derived from Mechanical Unzipping Experiments [PDF]
Life, 2022 Force-spectroscopy techniques have led to significant progress in studying the physicochemical properties of biomolecules that are not accessible in bulk assays. The application of piconewton forces with laser optical tweezers to single nucleic acids has
Paolo Rissone, Felix Ritort
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MeltR software provides facile determination of nucleic acid thermodynamics [PDF]
Biophysical Reports, 2023 Thermodenaturation (melting) curves of macromolecules are used to determine folding thermodynamic parameters. Notably, this insight into RNA and DNA stability underlies nearest neighbor theory and diverse structure prediction tools.
Jacob P. Sieg +3 more
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Optical melting measurements of nucleic acid thermodynamics. [PDF]
Methods Enzymol, 2009 Optical melting experiments provide measurements of thermodynamic parameters for nucleic acids. These thermodynamic parameters are widely used in RNA structure prediction programs and DNA primer design software. This review briefly summarizes the theory and underlying assumptions of the method and provides practical details for instrument calibration ...
Schroeder SJ, Turner DH.
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Native characterization of nucleic acid motif thermodynamics via non-covalent catalysis [PDF]
Nature Communications, 2016 DNA hybridisation thermodynamics parameters underlie rational design of oligonucleotides for diagnostics and nanotechnology. Here, the authors present an accurate method to measure the free energy of a given DNA structure at specific temperature and ...
Chunyan Wang, Jin H. Bae, David Yu Zhang
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Novel isoguanine derivative of unlocked nucleic acid-Investigations of thermodynamics and biological potential of modified thrombin binding aptamer. [PDF]
PLoS ONE, 2018 Thrombin binding aptamer (TBA), is a short DNA 15-mer that forms G-quadruplex structure and possesses anticoagulant properties. Some chemical modifications, including unlocked nucleic acids (UNA), 2'-deoxy-isoguanosine and 2'-deoxy-4-thiouridine were ...
Weronika Kotkowiak +2 more
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Thermodynamics of Nucleic Acid “Shape Readout” by an Aminosugar [PDF]
Biochemistry, 2011 Recognition of nucleic acids is important for our understanding of nucleic acid structure as well as for our understanding of nucleic acid-protein interactions.
Hongjuan Xi +5 more
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Thermodynamics of RNA duplexes modified with unlocked nucleic acid nucleotides [PDF]
Nucleic Acids Research, 2010 Thermodynamics provides insights into the influence of modified nucleotide residues on stability of nucleic acids and is crucial for designing duplexes with given properties.
Anna Pasternak, Jesper Wengel
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The Effect of Magnesium on the Thermodynamics of Nucleic Acid Tertiary Contact Formation [PDF]
Biophysical Journal, 2014 Functional RNAs fold into compact, well-defined tertiary structures despite strong electrostatic repulsion both within and between helices. To achieve these compact structures, many RNAs employ structural divalent cations, typically Mg2+. The simplest tertiary contact in nucleic acids is two helices, joined by some non-helical contact.
Herschel M. Watkins +4 more
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What Controls the Hybridization Thermodynamics of Spherical Nucleic Acids?* [PDF]
Journal of the American Chemical Society, 2020 The hybridization of free oligonucleotides to densely packed, oriented arrays of DNA modifying the surfaces of spherical nucleic acid (SNA)-gold nanoparticle conjugates occurs with negative cooperativity; i.e., each binding event destabilizes subsequent binding events. DNA hybridization is thus an ever-changing function of the number of strands already
Pratik S. Randeria +6 more
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Thermodynamics of force-dependent folding and unfolding of small protein and nucleic acid structures [PDF]
Integrative Biology, 2015 In this paper, we outline the theoretical framework for understanding the equilibrium force-dependent folding and unfolding transitions of protein domains and small nucleic acid structures, both having small rigid folded structures and highly flexible ...
Mingxi Yao, Hu Chen, Jie Yan
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