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Issue 20, 2019
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Kinetics and equilibrium constants of oligonucleotides at low concentrations. Hybridization and melting study

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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.

Graphical abstract: Kinetics and equilibrium constants of oligonucleotides at low concentrations. Hybridization and melting study

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Publication details

The article was received on 11 Mar 2019, accepted on 08 May 2019 and first published on 08 May 2019


Article type: Paper
DOI: 10.1039/C9CP01295H
Phys. Chem. Chem. Phys., 2019,21, 10798-10807

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    Kinetics and equilibrium constants of oligonucleotides at low concentrations. Hybridization and melting study

    K. Bielec, K. Sozanski, M. Seynen, Z. Dziekan, P. R. ten Wolde and R. Holyst, Phys. Chem. Chem. Phys., 2019, 21, 10798
    DOI: 10.1039/C9CP01295H

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