(10a) Nucleic Acid Self-Assembly in Alternative Solvents

Research Interests: Control of nucleic acid self-assembly to build complex dynamic systems; Thermodynamics and kinetics of nucleic acid self-assembly

Teaching Interests: Chemical kinetics; Chemical thermodynamics; Biochemical engineering

 Abstract

Increased control of molecular self-assembly is important for the further development of nucleic acid-based technologies, with applications ranging from drug design and delivery to development of catalytic nucleic acid sequences. My research is guided by two main goals: understanding the fundamental chemical and physical properties which govern nucleic acid self-assembly, and utilizing nucleic acid self-assembly processes to build dynamic systems that solve specific problems.

My graduate work is focused on nucleic acid self-assembly in alternative solvents. While nucleic acid technology research has been carried out almost exclusively in aqueous buffer, alternative solvents could increase our ability to direct nucleic acid assembly. Deep eutectic solvents (DES), closely related to ionic liquids, are characterized by significantly lower melting points than their separate components. Recently, DES have been shown to preserve nucleic acid base pairing and duplex formation, offering a relatively unexplored medium for directing nucleic acid assembly.

I show that DES provide a highly effective means for tuning nucleic acid thermodynamics and kinetics. The power of alternative solvents to alter a nucleic acid assembly pathway is illustrated by our ability to circumvent the â??strand inhibition problemâ? by thermally cycling nucleic acids in a DES. Strand inhibition describes the propensity of a long nucleic acid polymer to form a duplex with its complementary strand rather than to serve as a template for assembly of oligonucleotides. This longstanding problem in the field of prebiotic chemistry has limited demonstration of a prebiotic nucleic acid replication mechanism. I address the problem of nucleic acid strand inhibition by employing highly viscous solvents to control the thermal stabilities and annealing rates nucleic acid polymers in a size-dependent manner. Based on these thermodynamic and kinetic effects, we show that thermal cycling in a viscous environment can be used to copy a gene-length region (over 300 nucleotides) of a longer mixed sequence template, using both DNA and RNA systems.