TY - JOUR

T1 - QCM-based rupture force measurement as a tool to study DNA dehybridization and duplex stability

AU - Dultsev, Fedor N.

AU - Kolosovsky, Eugeny A.

AU - Lomzov, Alexander A.

AU - Pyshnyi, Dmitrii V.

N1 - Publisher Copyright: © 2016, Springer-Verlag Berlin Heidelberg.

PY - 2017/2

Y1 - 2017/2

N2 - The stability of double-stranded DNA (dsDNA) was assessed on the basis of unwinding force measurement. Unwinding force was measured directly with a quartz crystal microbalance (QCM). The amplitude of its surface oscillations was controlled by supplying variable alternate voltage. Under smoothly increasing amplitude of QCM surface oscillations, dsDNA fixed on QCM surface through one of its ends got unwound. This procedure allows reliable measurement of rupture force as small as 5-10 pN. It was demonstrated that oscillations of the surface, with dsDNA bound through one of its ends to this surface, at a frequency of 14 MHz, cause helix unwinding to form two complementary parts due to viscous forces of the liquid medium. Unwinding starts at the upper end. This was proven using oligonucleotide duplexes containing mismatches in different positions. For duplexes containing complementary 20 base pairs, the helix unwinding force is equal to 30-40 pN, which is in agreement with the data obtained by means of atomic-force microscopy (AFM) for the case of unzipping mode.

AB - The stability of double-stranded DNA (dsDNA) was assessed on the basis of unwinding force measurement. Unwinding force was measured directly with a quartz crystal microbalance (QCM). The amplitude of its surface oscillations was controlled by supplying variable alternate voltage. Under smoothly increasing amplitude of QCM surface oscillations, dsDNA fixed on QCM surface through one of its ends got unwound. This procedure allows reliable measurement of rupture force as small as 5-10 pN. It was demonstrated that oscillations of the surface, with dsDNA bound through one of its ends to this surface, at a frequency of 14 MHz, cause helix unwinding to form two complementary parts due to viscous forces of the liquid medium. Unwinding starts at the upper end. This was proven using oligonucleotide duplexes containing mismatches in different positions. For duplexes containing complementary 20 base pairs, the helix unwinding force is equal to 30-40 pN, which is in agreement with the data obtained by means of atomic-force microscopy (AFM) for the case of unzipping mode.

KW - Bond rupture

KW - DNA duplex

KW - QCM

KW - MECHANICAL STABILITY

KW - SINGLE

KW - SPECTROSCOPY

KW - SURFACE

KW - HYBRIDIZATION

KW - MELTING TEMPERATURES

KW - OLIGOMERS

KW - MOLECULES

KW - Viscosity

KW - Nucleic Acid Denaturation

KW - Nucleic Acid Hybridization

KW - Quartz Crystal Microbalance Techniques/methods

KW - DNA/chemistry

KW - Base Sequence

UR - http://www.scopus.com/inward/record.url?scp=84994787762&partnerID=8YFLogxK

U2 - 10.1007/s00216-016-0035-6

DO - 10.1007/s00216-016-0035-6

M3 - Article

C2 - 27838753

AN - SCOPUS:84994787762

VL - 409

SP - 891

EP - 901

JO - Analytical and Bioanalytical Chemistry

JF - Analytical and Bioanalytical Chemistry

SN - 1618-2642

IS - 4

ER -