Research Projects

Modified nucleotides and their derivatives are useful for monitoring cellular activities and therapeutics, but access to them is limited due to complex chemical procedures. Modified oligonucleotides are typically obtained through solid phase synthesis or limited chemo-enzymatic methods. A site-selective method for alkylating the N2 position of guanine in DNA and RNA oligonucleotides using reductive amination is being developed to address this issue. The researchers will examine the reductive amination reaction mechanism to understand its molecular basis of selectivity towards guanine. They will test several guanine monophosphate (GMP) analogues and guanine triphosphate (GTP) to determine how functional group changes affect selectivity. The product obtained will have applications in polymerase-mediated synthesis of modified DNA/RNA, eliminating the need for phosphoramidite analogs for solid phase synthesis. Based on the understanding of mechanism and selectivity, they plan to develop a site-specific version of alkylation of guanine. They will optimize electrophile and solvents during the reductive amination reaction to selectively label a single-stranded oligonucleotide while leaving the double-stranded oligonucleotide intact. This differential reactivity is possible through bulky electrophiles, which may not access the Watson-Crick H-bonded face in double-stranded DNA. The researchers propose using site-selective labeling of guanine in single-stranded nucleic acids as a probe of secondary structure. As nucleic acids play diverse structural and functional roles, it is crucial to have independent methods for investigating RNA structure. Their method will allow probing of RNA secondary structure and help delineate the structure-function relationship in RNA and other nucleic acids.