Kinetics and equilibrium constants of oligonucleotides at low concentrations. Hybridization and melting study
Literature Information
Publication Date
2019-05-08
DOI
10.1039/C9CP01295H
Impact Factor
3.676
Authors
Krzysztof Bielec, Krzysztof Sozanski, Marco Seynen, Zofia Dziekan, Pieter Rein ten Wolde, Robert Holyst
View Original
Abstract
Although DNA hybridization/melting is one of the most important biochemical reactions, the non-trivial kinetics of the process is not yet fully understood. In this work, we use Förster resonance energy transfer (FRET) to investigate the influence of temperature, ionic strength, and oligonucleotide length on the kinetic and equilibrium constants of DNA oligonucleotide binding and dissociation. We show that at low reagent concentrations and ionic strength, the time needed to establish equilibrium between single and double strand forms may be of the order of days, even for simple oligonucleotides of a length of 20 base pairs or less. We also identify and discuss the possible artifacts related to fluorescence-based experiments conducted in extremely dilute solutions. The results should prove useful for the judicious design of technologies based on DNA-matching, including sensors, DNA multiplication, sequencing, and gene manipulation.
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Source Journal
Physical Chemistry Chemical Physics
CiteScore:
5.5
Self-citation Rate:
10.3%
Articles per Year:
3036
Physical Chemistry Chemical Physics (PCCP) is an international journal co-owned by 19 physical chemistry and physics societies from around the world. This journal publishes original, cutting-edge research in physical chemistry, chemical physics and biophysical chemistry. To be suitable for publication in PCCP, articles must include significant innovation and/or insight into physical chemistry; this is the most important criterion that reviewers and Editors will judge against when evaluating submissions. The journal has a broad scope and welcomes contributions spanning experiment, theory, computation and data science. Topical coverage includes spectroscopy, dynamics, kinetics, statistical mechanics, thermodynamics, electrochemistry, catalysis, surface science, quantum mechanics, quantum computing and machine learning. Interdisciplinary research areas such as polymers and soft matter, materials, nanoscience, energy, surfaces/interfaces, and biophysical chemistry are welcomed if they demonstrate significant innovation and/or insight into physical chemistry. Joined experimental/theoretical studies are particularly appreciated when complementary and based on up-to-date approaches.
Recommended Compounds
![9H-Fluoren-9-ylmethyl {15-[(2,5-dioxo-1-pyrrolidinyl)oxy]-15-oxo-3,6,9,12-tetraoxapentadec-1-yl}carbamate structure](https://static.chemtradehub.com/structs/131/1314378-14-7-4316.webp "9H-Fluoren-9-ylmethyl {15-[(2,5-dioxo-1-pyrrolidinyl)oxy]-15-oxo-3,6,9,12-tetraoxapentadec-1-yl}carbamate structure")
9H-Fluoren-9-ylmethyl {15-[(2,5-dioxo-1-pyrrolidinyl)oxy]-15-oxo-3,6,9,12-tetraoxapentadec-1-yl}carbamate
CAS Number:
1314378-14-7
Molecular Formula:
C30H36N2O10
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