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

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. Graphical Abstract Rupture force depending on mismatch position in dsDNA.

QCM-based measurement of bond rupture forces in DNA double helices for complementarity sensing.

After fixing the DNA molecule in the form of a double helix on the surface of a thickness shear mode resonator (QCM), mechanical oscillations at increasing amplitude cause detorsion of the helix. The force necessary for detorsion can be determined from the voltage applied to the QCM at the rupture moment. The high sensitivity of this method is due to the fact that measurements are carried out in the frequency region around the QCM resonance, where any (even very weak) distortions of the consistent oscillating system cause noticeable distortions of the amplitude-frequency dependence, and these distortions are used to fix the rupture moment. The measured rupture forces were within 30-40 pN, and the sensitivity was 10(8) molecules. It was demonstrated that the proposed procedure allows one to determine the factors that affect the stability of the DNA double helix. This procedure can be the basis for the development of a new method of rapid DNA analysis. Experiments performed with model DNA showed that it is possible to reveal complementarity between two DNA samples.

New procedure to record the rupture of bonds between macromolecules and the surface of the quartz crystal microbalance (QCM).

It is shown that an increase in the amplitude of QCM shear oscillations during frequency scanning around the resonance frequency is accompanied (at a definite voltage) by distortions in the amplitude-frequency dependence for QCM. We demonstrated that these distortions are connected to the rupture of macromolecules from the QCM surface. It is shown that the identification of the rupture of particles and macromolecules from the QCM surface can be carried out by relying on the analysis of these distortions of the amplitude-frequency dependence. The distortions were distinguished as a signal. The number of broken bonds can be estimated from the value of this distortion signal, and the threshold voltage applied to the system can be used to estimate the rupture force to high accuracy. Using the proposed method, we estimated the strength of a physical bond, which was 3 pN. This procedure can be useful for studying biological objects and represents an advanced step in the development of the REVS (rupture event scanning) technique.

QCM operating in threshold mode as a gas sensor.

Application of the threshold mode allowed us to use the quartz resonator (quartz crystal microbalance, QCM) as a highly sensitive gas sensor measuring the forces of the rupture of adsorbed gas components from the resonator surface oscillating with increasing amplitude. This procedure allows one to analyze different gas components using the same surface modification, just varying the rupture threshold by varying the amplitude of shear oscillations. The sensitivity of the threshold measurements is 2 to 3 orders of magnitude higher than for the gravimetric procedure. It is demonstrated that the QCM operating as an active element can be used as a gas sensor. This procedure seems to be promising in investigating the reactivity of the surface or the interactions of gaseous components with the surface containing various functional groups, thus contributing to the surface chemistry.