A High-Resolution High-Efficiency Force Spectroscopy for Measuring Drug-DNA Interactions

University Of Houston, Houston TX

Investigators

Abstract

The molecule-molecule bonds are the basis of molecular recognition and drug targeting in biology. However, this type of interactions remains difficult to quantify, mainly because of the lack of a suitable technique to provide a reliable and characteristic parameter. This proposal will develop a novel force spectroscopy that uses precisely controlled ultrasound to measure the binding forces to distinguish different molecular bonds. Tens of thousands of molecular bonds will be studied simultaneously and resolved based on their different binding forces. The technique, termed as ultrasound force-induced remnant magnetization spectroscopy (usFIRMS), will be a new scientific tool for studying molecular interactions, with high sensitivity, unprecedented resolution, and high detection efficiency. By overcoming the engineering challenges involved in the integration of ultrasound and the magnetic detector, the resulting instrument will be able to identify different molecular interactions precisely, reliably, and efficiently. The application scope of the new technique will focus on drug molecules binding with DNA duplexes to precisely reveal their binding forces and thermodynamics. The results will quantitatively identify the binding selectivity. Lack of selectivity has been a major setback for DNA-targeting drugs. Results obtained by the new technique are thus of high scientific merit. In addition to the engineering advancements and scientific values, the research activities in this proposal will provide excellent educational opportunities for students from a broad background, ranging from graduate students, undergraduates, and high school students. In particular, minority undergraduate students will be actively recruited for participation and ultimately leading a subset of the projects. This proposal aims at establishing the novel usFIRMS technique that uses acoustic radiation force generated by precisely attenuated ultrasound to selectively dissociate noncovalent bonds labeled with magnetically particles. The magnetic signal is monitored by an atomic magnetometer, which is the most sensitive device for magnetic detection. The proposed usFIRMS technique will open up a new field for characterizing noncovalent bonding, which is poorly understood but widely encountered in biochemistry and biology. On the technological front, this technique has three unique capabilities comparing with existing techniques. First, it possesses high force resolution that can clearly resolve molecular bonds with less than two pico-newton difference in the binding forces, which is one order of magnitude better than that of existing techniques. Second, it represents the first time that ultrasound is used for distinguishing molecular bonds. By integrating ultrasound components with an atomic magnetometer, the instrument allows for efficient and automated biochemical analysis that cannot be obtained with any other forms of mechanical forces. Third, the concept of broadband force spectroscopy will resolve different bonds in a single acquisition, instead of the time-consuming force sweeping. This revolutionary advancement will lead to high-throughput applications. On the fundamental science front, the application of usFIRMS in drug-DNA interactions will quantitatively identify the binding selectivity by establishing a new physicochemical parameter of differential binding force. It will serve as a new platform for drug optimization. The binding constants, free energy, and enthalpy can also be precisely determined because different molecular bonds are completely resolved to remove potential interference in measurements. Furthermore, the usFIRMS technique will find broad applications in biological research because of its unique combination of high resolution, high efficiency, and high applicability.