Development of functional and responsive nucleic acid systems for applications in biotechnology

点击翻译按钮获取中文摘要

My research program aims at developing biotechnology using nucleic acid polymers. By introducing well-defined chemical modifications into DNA/RNA scaffolds, we will develop probes and tools to investigate biochemical processes ranging from redox reactions to genome repair pathways. This research area will advance our understanding of nucleic acids in ways well-beyond their widely known role in modern biology as information carriers. The proposed research aims to find chemical triggers to activate or silence functional nucleic acid materials. Much effort has been devoted to identifying nucleic acid sequences (such as DNA/RNA) with function such as catalysis (ribozymes) and molecular recognition (aptamers). Ribozymes catalyze various chemical transformations, which can be harnessed to control gene expression. On the other hand, aptamers are short single-stranded nucleic acid sequences that can selectively bind to a specific target (including proteins, peptides, and small molecules such as toxins). The proposed strategy involves modulating nucleic acid function via an external stimulus. Switching function on (or off) will be possible by embedding site-specific chemical modifications in the nucleic acid sequence, that intrinsically respond to specific stimuli. An oxidative desulfurization strategy will serve as an initial platform to this research program. Thiolated nucleotide units within RNA strands, such as 2-thiouridine or 2-thiocytidine (2sU / 2sC), are susceptible to oxidative desulfurization reactions with various oxidants. Interestingly, the desulfurized products have a dramatic shift in the base-pairing preferences; for instance, 2sU pairs more strongly with A compared to U, whereas U is more promiscuous in forming a pair with G (in addition to A). Desulfurization chemistry can thus be used to fine tune structure and functionality of RNA-based technology, such as ribozymes (DNAzymes), riboswitches and aptasensors. Given that the presence of 2sU (or 2sC) can disrupt critical base pairs necessary for RNA activity, a novel redox switching mechanism will be explored to either silence or activate functional RNA sequences. Thio modifications within RNA has precedence in the literature, making this avenue promising for in vivo applications. The approach outlined here will pave the way to utilizing redox-sensitive nucleic acid probes in a unique fashion. In addition to desulfurization, this program will be expanded to other types of biocompatible triggers. For instance, the introduction of certain alkyl groups within nucleic acid-based technologies can be corrected by cellular repair mechanisms. In doing so, a similar activation/silencing mechanism can be summoned. The proposed research will introduce an additional gate to modulate the specific function of defined nucleic acid sequences, and enhance the capabilities of current biotechnology.