TY - JOUR

T1 - A QCM-based rupture event scanning technique as a simple and reliable approach to study the kinetics of DNA duplex dissociation

AU - Kurus, N. N.

AU - Dultsev, F. N.

AU - Golyshev, V. M.

AU - Nekrasov, D. V.

AU - Pyshnyi, D. V.

AU - Lomzov, A. A.

PY - 2020/8/14

Y1 - 2020/8/14

N2 - Rupture Event Scanning (REVS) is applied for the first time within an approach based on dynamic force spectroscopy. Using model DNA duplexes containing 20 pairs of oligonucleotides including those containing single mismatches, we demonstrated the possibility of reliable determination of the kinetic parameters of dissociation of biomolecular complexes: barrier positions, the rate constants of dissociation, and the lifetime of complexes. Within this approach, mechanical dissociation of DNA duplexes occurs according to a mechanism similar to unzipping. It is shown that this process takes place by overcoming a single energy barrier. In the case where a mismatch is located at the farthest duplex end from the QCM surface, a substantial decrease in the position of the barrier between the bound and unbound states is observed. We suppose that this is due to the formation of an initiation complex containing 3-4 pairs of bases, and this is sufficient for starting duplex unzipping. This journal is

AB - Rupture Event Scanning (REVS) is applied for the first time within an approach based on dynamic force spectroscopy. Using model DNA duplexes containing 20 pairs of oligonucleotides including those containing single mismatches, we demonstrated the possibility of reliable determination of the kinetic parameters of dissociation of biomolecular complexes: barrier positions, the rate constants of dissociation, and the lifetime of complexes. Within this approach, mechanical dissociation of DNA duplexes occurs according to a mechanism similar to unzipping. It is shown that this process takes place by overcoming a single energy barrier. In the case where a mismatch is located at the farthest duplex end from the QCM surface, a substantial decrease in the position of the barrier between the bound and unbound states is observed. We suppose that this is due to the formation of an initiation complex containing 3-4 pairs of bases, and this is sufficient for starting duplex unzipping. This journal is

KW - DYNAMIC FORCE SPECTROSCOPY

KW - OPTICAL TWEEZERS

KW - BINDING FORCES

KW - SINGLE

KW - ADHESION

KW - THERMODYNAMICS

KW - TRANSITION

KW - STRENGTH

KW - MODELS

KW - VIRUS

UR - http://www.scopus.com/inward/record.url?scp=85095916266&partnerID=8YFLogxK

U2 - 10.1039/d0ay00613k

DO - 10.1039/d0ay00613k

M3 - Article

C2 - 32716423

AN - SCOPUS:85095916266

VL - 12

SP - 3771

EP - 3777

JO - Analytical Methods

JF - Analytical Methods

SN - 1759-9660

IS - 30

ER -