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

Abstract

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.

Determination of the Thermodynamic Parameters of DNA Double Helix Unwinding with the Help of Mechanical Methods

“…In the present work, we continue to develop the procedure proposed by us previously. − It was demonstrated that unwinding of the DNA double helix may be carried out with the help of quartz crystal microbalance (QCM). In particular, temperature dependence was studied previously . In the present work, we made an attempt to determine the height of the energy barrier.…”

“…In particular, temperature dependence was studied previously. 20 In the present work, we made an attempt to determine the height of the energy barrier. To compare our data with the data available from literature and to verify our approach, we carried out parallel AFM-based measurements with our oligonucleotides.…”

Assembly of a miRNA‐modified QCM sensor for miRNA recognition through response patterns

“…Probe hybridization techniques include northern blotting, in situ hybridization, and microarrays are well established but often require a large quantity of samples. Amplification technologies, including real‐time fluorescent quantitative polymerase chain reaction (RT‐PCR) and rolling circle amplification (RCA), are often time‐consuming and complicated to operate. Recently, the quartz crystal microbalance (QCM) mass sensor has the characteristics of high sensitivity, label‐free and, real‐time analysis, and it has been widely used in biosensors .…”

“…Amplification technologies, including real‐time fluorescent quantitative polymerase chain reaction (RT‐PCR) and rolling circle amplification (RCA), are often time‐consuming and complicated to operate. Recently, the quartz crystal microbalance (QCM) mass sensor has the characteristics of high sensitivity, label‐free and, real‐time analysis, and it has been widely used in biosensors . Many studies have shown that DNA‐modified QCM biosensors can be applied to detect such processes as DNA hybridization and single base mismatch of DNA .…”

“…Recently, the quartz crystal microbalance (QCM) mass sensor has the characteristics of high sensitivity, label-free and, real-time analysis, and it has been widely used in biosensors. [20][21][22][23][24][25] Many studies have shown that DNA-modified QCM biosensors can be applied to detect such processes as DNA hybridization 26 and single base mismatch of DNA. 27 However, studies on QCM biosensor for miRNA detection has been still limited.…”