Year: 2022
Type: article
Abstract: The hybridization kinetic of an oligonucleotide to its template is a fundamental step in many biological processes such as replication arrest, CRISPR recognition, DNA sequencing, DNA origami, etc. Although single kinetic descriptions exist for special cases of this problem, there are no simple general prediction schemes. In this work, we have measured experimentally, with no fluorescent labelling, the displacement of an oligonucleotide from its substrate in two situations: one corresponding to oligonucleotide binding/unbinding on ssDNA and one in which the oligonucleotide is displaced by the refolding of a dsDNA fork. In this second situation, the fork is expelling the oligonucleotide thus significantly reducing its residence time. To account for our data in these two situations, we have constructed a mathematical model, based on the known nearest neighbour dinucleotide free energies, and provided a good estimate of the residence times of different oligonucleotides (DNA, RNA, LNA) of various lengths in different experimental conditions (force, temperature, buffer conditions, presence of mismatches, etc.). This study provides a foundation for the dynamics of oligonucleotide displacement, a process of importance in numerous biological and bioengineering contexts.
Source: Nucleic Acids Research
DOI: 10.1093/nar/gkac1113
Authors: Fangyuan Ding, Simona Cocco, Saurabh Raj, Maria Manosas, Thao Thi Thu Nguyen, Michelle M Spiering, David Bensimon, Jean-François Allemand, Vincent Croquette
Institutions: University of California, Irvine, Centre National de la Recherche Scientifique, Université Paris Cité, Université Paris Sciences et Lettres, École Normale Supérieure - PSL, Sorbonne Université, Laboratoire de Physique de l'Ecole Normale Supérieure, Indian Institute of Technology Delhi, Institut de Nanociència i Nanotecnologia de la Universitat de Barcelona, Universitat de Barcelona, Pennsylvania State University, Inserm, University of California, Los Angeles, Institut de Biologie de l'École Normale Supérieure, ESPCI Paris
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $3,876
Funders: Schlumberger Foundation, Human Frontier Science Program, Centre National de la Recherche Scientifique, Ministerio de Ciencia e Innovación, Fondation Pierre-Gilles de Gennes pour la recherche, National Institutes of Health, National Institute of General Medical Sciences, H2020 European Research Council
OpenAlex ID: W4310937913