Complete unzipping and rezipping of lambda -phage double-stranded DNA is achieved by applying a constant force. A strong hysteresis is observed at all tested time scales and temperatures. Hysteresis also occurs for partial unzipping, indicating stability for the partially open state over a force range of 2- 5pN . Results are compared to nearest-neighbor model simulations, and reasonable agreement is found.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1103/PhysRevE.75.051908 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Nonequilibrium Thermodynamics of DNA Nanopore Unzipping.
Phys Rev Lett
January 2023
Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy.
Using theory and simulations, we carried out a first systematic characterization of DNA unzipping via nanopore translocation. Starting from partially unzipped states, we found three dynamical regimes depending on the applied force f: (i) heterogeneous DNA retraction and rezipping (f<17 pN), (ii) normal (17 pN
5-Methyl-cytosine stabilizes DNA but hinders DNA hybridization revealed by magnetic tweezers and simulations.
Nucleic Acids Res
November 2022
The Institute for Advanced Studies, College of Life Sciences, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China.
5-Methyl-cytosine (5mC) is one of the most important DNA modifications and plays versatile biological roles. It is well known that 5mC stabilizes DNA duplexes. However, it remains unclear how 5mC affects the kinetics of DNA melting and hybridization.
View Article and Find Full Text PDFStem-loop formation drives RNA folding in mechanical unzipping experiments.
Proc Natl Acad Sci U S A
January 2022
Small Biosystems Laboratory, Condensed Matter Physics Department, University of Barcelona, Barcelona 08028, Spain;
Accurate knowledge of RNA hybridization is essential for understanding RNA structure and function. Here we mechanically unzip and rezip a 2-kbp RNA hairpin and derive the 10 nearest-neighbor base pair (NNBP) RNA free energies in sodium and magnesium with 0.1 kcal/mol precision using optical tweezers.
View Article and Find Full Text PDFMeasuring Unzipping and Rezipping of Single Long DNA Molecules with Optical Tweezers.
Methods Mol Biol
March 2019
Department of Physics, University of California San Diego, La Jolla, CA, USA.
The unwinding of double-stranded DNA is a frequently occurring event during the cellular processes of DNA replication, repair, and transcription. To help further investigate properties of this fundamental process as well as to study proteins acting on unzipped DNA at the single molecule level, we describe a novel method for efficient preparation of long DNA constructs (arbitrary sequences of many kilobasepairs (kbp) in length) that can be forcibly unzipped and manipulated with optical tweezers or other single-molecule manipulation techniques. This method utilizes PCR, a nicking endonuclease, and strand displacement synthesis by the Klenow fragment of DNA polymerase I to introduce labeled nucleotides at appropriate positions to facilitate unzipping of the DNA by application of force.
View Article and Find Full Text PDFStochastic ratchet mechanisms for replacement of proteins bound to DNA.
Phys Rev Lett
June 2014
3Laboratoire de Physique Théorique de l'Ecole Normale Supérieure, CNRS and Université Pierre and Marie Curie, 75005 Paris, France.
Experiments indicate that unbinding rates of proteins from DNA can depend on the concentration of proteins in nearby solution. Here we present a theory of multistep replacement of DNA-bound proteins by solution-phase proteins. For four different kinetic scenarios we calculate the dependence of protein unbinding and replacement rates on solution protein concentration.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!