Quantitative Determination of Size and Shape of Surface-Bound DNA Using an Acoustic Wave Sensor

Abstract

DNA bending plays a significant role in many biological processes, such as gene regulation, DNA replication, and chromosomal packing. Understanding how such processes take place and how they can, in turn, be regulated by artificial agents for individual oriented therapies is of importance to both biology and medicine. In this work, we describe the application of an acoustic wave device for characterizing the conformation of DNA molecules tethered to the device surface via a biotin-neutravidin interaction. The acoustic energy dissipation per unit mass observed upon DNA binding is directly related to DNA intrinsic viscosity, providing quantitative information on the size and shape of the tethered molecules. The validity of the above approach was verified by showing that the predesigned geometries of model double-stranded and triple-helix DNA molecules could be quantitatively distinguished: the resolution of the acoustic measurements is sufficient to allow discrimination between same size DNA carrying a bent at different positions along the chain. Furthermore, the significance of this analysis to the study of biologically relevant systems is shown during the evaluation of DNA conformational change upon protein (histone) binding.

High-frequency phase shift measurement greatly enhances the sensitivity of QCM immunosensors

“…cause changes in both phase (Δφ) and amplitude (ΔA): Δφ corresponds to the amount of bound mass and ΔA to conformation of the bound biomolecules or viscoelastic properties at the sensor-liquid interface (Mitsakakis and Gizeli, 2011).The amplitude change to phase change ratio (ΔA/Δφ) provides an insight on viscosity changes occurring at the sensor-liquid interface. Some researchers concluded that experimental high ΔA/Δφ ratios are reliable indicators of viscous interactions, whereas small ratios indicate a rigid layer (Tsortos et al, 2008), as desirable for reliable microgravimetric measurements (Kanazawa and Gordon, 1985). Taking For 100 MHz QCM immunosensors, carbaryl was also used as a model analyte.…”

Diamond‐based DNA sensors: surface functionalization and read‐out strategies

“…In a recent study by Tsortos et al, acoustic quartz sensors have been used to investigate the conformation of dsDNA molecules [134]. Although this type of read-out would in principle work even better with diamond, no actual results of diamondbased prototype devices have been reported in literature yet.…”

PAME: Plasmonic Assay Modeling Environment

“…Ultimately, 45.56% of the surface sites were covered in gold, and 18.64% in silver. NeutrAvidin was modeled as a 6nm sphere (Tsortos et al, 2008) of dispersive refractive index, n ≈ 1.5 (Sarid and Challener, 2010), filling a 6nm-wide shell on the nanoparticles from 0 to 95% coverage (617 proteins per AuNP and 363 per AgNP), as shown in Fig. (7).…”