Synthesis and Applications of Chemically-Modified Oligonucleotides

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Nucleic acids are the main building blocks of DNA and RNA, which are biomacromolecules with vast biological function. For example, nucleic acids contain the genetic blue print of the cell, and transfer of this genetic code to messenger RNA is necessary to direct the synthesis of unique proteins. Nucleic acids also have other biological functions including controlling the expression of particular genes. Since the discovery of the double helical structure of DNA 65 years ago, there have been significant advances in the nucleic acid field to improve its properties for biotechnological applications or for modern medicine. For instance, gene-silencing oligonucleotides are tools used to understand gene function. However, limitations continue due to the native structure of these molecules. Using organic chemistry, my research program develops synthetic analogs in order to improve its biological function. My research group then evaluates the biological impact of these synthetic analogs. The primary focus of my research group involves synthesizing novel chemically-modified oligonucleotides to use as gene-silencing oligonucleotides. First, we will explore the effect of expanding small molecules within a class of gene silencing molecules called short interfering RNAs (siRNAs). My lab has identified an area within siRNAs that is amenable to diverse chemical modification. As such, we will expand the scope and place molecules that can interact directly with different cellular biological components. When bound, these molecules may exhibit improved potency, cell-membrane permeability, and stability. Secondly, we will expand the scope of photoresponsive groups within siRNAs. Our lab has shown that the photoresponsive molecule, azobenzene, when placed within the core central region of siRNAs can be used to reversibly control the timing of gene silencing activity. Azobenzene can isomerize between a trans and cis form in the presence of visible and ultra-violet light, respectively. We will expand the scope of photoresponsive RNA groups, and explore functionalized azobenzene derivatives within siRNAs. This will allow us to fine-tune the activity of siRNAs, and allow us to better control its activity, and thus prevent off-target effects. Finally, my research group has expertise in developing novel backbone modifications for oligonucleotides. We will expand the scope of these modifications and explore their effect within the CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 editing system. The CRISPR/Cas9 system is an exciting, and relatively new system that has been shown to be amenable within a variety of biological systems. The multidisciplinary laboratory work is conducted by a talented team of undergraduate and graduate students who use a combination of solution-phase, solid-phase and biological techniques. As such, the trainees supervised from my lab are well prepared for a variety of professions including careers focused in chemistry and science.