4.5 Article

Measuring Excess Heat Capacities of Deoxyribonucleic Acid (DNA) Folding at the Single-Molecule Level

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

Origin of heat capacity increment in DNA folding: The hydration effect

S. Hadzi et al.

Summary: The dehydration of DNA constituents is a major source contributing to the observed increase in heat capacity during DNA folding. Other potential sources of the overall change in heat capacity may compensate each other to a significant degree. The calculated hydration heat capacities for DNA structures align well with experimental values, while empirical parameters developed for proteins show poor predictions and should not be applied to DNA folding.

BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS (2021)

Article Chemistry, Physical

Pushing Camera-Based Single-Molecule Kinetic Measurements to the Frame Acquisition Limit with Stroboscopic smFRET

David A. Nicholson et al.

Summary: Single-molecule fluorescence resonance energy transfer experiments allow detailed examination of microscopic dynamics, but can be susceptible to systematic underestimation when rate constants are comparable to data acquisition rates. Stroboscopic illumination/detection can greatly reduce these errors, improving accuracy and dynamic range. This straightforward method offers a valuable addition to the smFRET toolkit, compatible with multiple trajectory analysis methods.

JOURNAL OF PHYSICAL CHEMISTRY B (2021)

Article Chemistry, Physical

Chirality-Dependent Amino Acid Modulation of RNA Folding

David A. Nicholson et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2020)

Article Chemistry, Physical

Single-molecule kinetic studies of DNA hybridization under extreme pressures

Hsuan-Lei Sung et al.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2020)

Article Biophysics

Thermodynamics of DNA: heat capacity changes on duplex unfolding

Anatoliy Dragan et al.

EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS (2019)

Review Biochemistry & Molecular Biology

Single-Molecule Kinetics in Living Cells

Johan Elf et al.

ANNUAL REVIEW OF BIOCHEMISTRY, VOL 88 (2019)

Article Chemistry, Physical

Amino Acid Stabilization of Nucleic Acid Secondary Structure: Kinetic Insights from Single-Molecule Studies

David A. Nicholson et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2018)

Article Biochemistry & Molecular Biology

Elasticity of the transition state for oligonucleotide hybridization

Kevin D. Whitley et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Chemistry, Multidisciplinary

Direct Measurement of Single-Molecule DNA Hybridization Dynamics with Single-Base Resolution

Gen He et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2016)

Review Chemistry, Physical

Biophysical Insights from Temperature-Dependent Single-Molecule Forster Resonance Energy Transfer

Erik D. Holmstrom et al.

ANNUAL REVIEW OF PHYSICAL CHEMISTRY, VOL 67 (2016)

Review Biochemistry & Molecular Biology

Insights into Protein-Ligand Interactions: Mechanisms, Models, and Methods

Xing Du et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2016)

Article Biochemistry & Molecular Biology

Cy3 and Cy5 dyes attached to oligonucleotide terminus stabilize DNA duplexes: Predictive thermodynamic model

Bernardo G. Moreira et al.

BIOPHYSICAL CHEMISTRY (2015)

Article Biochemistry & Molecular Biology

Taking the ruler to the jungle: single-molecule FRET for understanding biomolecular structure and dynamics in live cells

Marko Sustarsic et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2015)

Article Biochemical Research Methods

Confocal Single-Molecule FRET for Protein Conformational Dynamics

Yan-Wen Tan et al.

PROTEIN DYNAMICS: METHODS AND PROTOCOLS (2014)

Review Biochemistry & Molecular Biology

Differential scanning calorimetry as a tool for protein folding and stability

Christopher M. Johnson

ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS (2013)

Article Biochemistry & Molecular Biology

DNA hybridization kinetics: zippering, internal displacement and sequence dependence

Thomas E. Ouldridge et al.

NUCLEIC ACIDS RESEARCH (2013)

Review Chemistry, Multidisciplinary

Kinetics and Dynamics of DNA Hybridization

Yandong Yin et al.

ACCOUNTS OF CHEMICAL RESEARCH (2011)

Article Biophysics

Two methods of temperature control for single-molecule measurements

Matthew A. B. Baker et al.

EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS (2011)

Review Chemistry, Multidisciplinary

The application of atomic force spectroscopy to the study of biological complexes undergoing a biorecognition process

Anna Rita Bizzarri et al.

CHEMICAL SOCIETY REVIEWS (2010)

Article Multidisciplinary Sciences

Single-molecule derivation of salt dependent base-pair free energies in DNA

Josep M. Huguet et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Article Biophysics

Force-Driven Separation of Short Double-Stranded DNA

Dominik Ho et al.

BIOPHYSICAL JOURNAL (2009)

Review Biochemistry & Molecular Biology

Exploring RNA folding one molecule at a time

Elvin A. Aleman et al.

CURRENT OPINION IN CHEMICAL BIOLOGY (2008)

Article Chemistry, Multidisciplinary

Base-by-Base Dynamics in DNA Hybridization Probed by Fluorescence Correlation Spectroscopy

Xudong Chen et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2008)

Review Biochemical Research Methods

A practical guide to single-molecule FRET

Rahul Roy et al.

NATURE METHODS (2008)

Review Biochemistry & Molecular Biology

Heat capacity changes associated with nucleic acid folding

PJ Mikulecky et al.

BIOPOLYMERS (2006)

Article Biochemistry & Molecular Biology

Heat capacity changes associated with DNA duplex formation: Salt- and sequence-dependent effects

PJ Mikulecky et al.

BIOCHEMISTRY (2006)

Article Biochemistry & Molecular Biology

Length-dependent energetics of (CTG)(n) and (CAG)(n) trinucleotide repeats

S Amrane et al.

NUCLEIC ACIDS RESEARCH (2005)

Article Biochemistry & Molecular Biology

Thermodynamic stability of DNA tandem mismatches

BN Bourdélat-Parks et al.

BIOCHEMISTRY (2004)

Article Biochemistry & Molecular Biology

Hybridization kinetics and thermodynamics of molecular beacons

A Tsourkas et al.

NUCLEIC ACIDS RESEARCH (2003)

Article Multidisciplinary Sciences

Conformational energetics of stable and metastable states formed by DNA triplet repeat oligonucleotides:: Implications for triplet expansion diseases

J Völker et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)