Di Liu

Nucleic acids are highly programmable molecules: they have well-defined helical geometries and enable predictable recognition via base pairings (or complementarity). DNA/RNA nanotechnology, taking advantage of both aspects of the programmability of nucleic acids, enables the construction of sophisticated nanoscale architectures. My group is interested in employing the rational design principles developed in the field of DNA/RNA nanotechnology for solving fundamental and urgent problems in biological and pharmaceutical research. Specifically, we will (i) identify potential drugs targeting type IA topoisomerase, which hold the promise of broad-spectrum antibiotics; (ii) determine high-resolution RNA structures (such as bacterial regulatory RNAs or structured motifs from viral RNAs), which will enable the development of RNA-targeting drugs; and (iii) design improved mRNA vaccines or medicines for disease prevention or treatment.

(i) Synthetic DNA topology and search for type IA topoisomerase inhibitors. DNA topology defines the structural and functional principles of DNA and plays a profound role in almost every major DNA-related process. Most previous studies of DNA topology relied on the naturally occurring negatively supercoiled plasmids. We reason that synthetic DNA constructs of naturally inaccessible topologies would reveal unexplored mechanistic aspects of DNA topology and elucidate how cells tackle the DNA topology problems. In living cells, DNA topology is regulated by DNA topoisomerases (a Nobel Prize-worthy discovery). Because DNA topoisomerases are essential for cell viability, topoisomerase inhibitors are among the most effective and most commonly used anticancer and antibacterial drugs. Though drugs targeting type IB and IIA topoisomerases are in current clinical use, there is presently no clinical drug targeting any type IA topoisomerase. The fact that every bacterial pathogen has at least one type IA topoisomerase makes inhibitors of this kind of topoisomerase potential broad-spectrum antibiotics for combating antimicrobial resistance. We are interested in utilizing the synthetic DNA topological structures for the identification of type IA topoisomerase inhibitors.

(ii) Nanoarchitectural engineering of RNA for cryo-EM structural determination. Many functional RNAs fold into intricate 3D architectures and high-resolution structures are necessary for understanding their underlying mechanisms. However, the research of RNA structural biology is difficult and significantly lagging (e.g., RNA structures deposited in the PDB is less than 1% of protein structures). Single-particle cryogenic electron microscopy (cryo-EM; 2017 Nobel Prize in Chemistry), which dispenses with the need for procuring crystals and solving phase problem, is gaining increasing popularity, and its obtained resolution is now beginning to rival that of X-ray crystallography. Though recent two years have witnessed increased interests in RNA cryo-EM structures, cryo-EM has not been well explored in RNA structural determination. The first sub-3 Å cryo-EM structure of an RNA-only construct (a Tetrahymena group I intron) has been yielded via our method of ROCK (RNA oligomerization-enabled cryo-EM via installing kissing-loops). ROCK addresses two primary challenges of RNA cryo-EM structural determination—structural flexibility and small molecular weight. Built on the preliminary success of ROCK, we aim to develop methods to improve or complement ROCK to further unleash the largely unexplored potential of cryo-EM in RNA structural studies for elucidating the mechanisms of functional RNAs and facilitating the invention of RNA-targeting therapeutics.

(iii) Improving the efficiency and selectivity of mRNA therapeutics. In the backdrop of the successful and timely mRNA vaccine development for responding to the COVID-19 pandemic, mRNA therapeutics (2023 Nobel Prize in Physiology or Medicine) have sparked enormous interests in both fundamental and translational research. The efficacy of mRNA has been boosted by the past decades’ technological innovations in base modifications and delivery. However, two fundamental limitations of mRNA may impede its more widespread translational success. First, the intracellular stability of mRNA is relatively low, limiting its utility in applications requiring high and durable protein expression. Second, mRNA’s intrinsic lack of selectivity prohibits its targeted expression in specific organ or cell type because any cell with the complete translation machinery is capable of translating the transfected mRNA. Thus, we aim to address these two limitations by programming the structures of the mRNA molecules.