There are growing demands for 3D structure determination of nucleic acids and their protein complexes for understanding disease molecule-level mechanisms and discovering innovative drugs. X-ray crystallography is one of the most direct and powerful tools for structure determination of these macromolecules and complexes. However, the crystallization and phase determination (two long-standing and bottle-neck problems) have largely slowed down structural determination of new structures and folds. Therefore, it is of tremendous value to develop novel technologies that allow the crystallization facilitation and phase determination. Recently, the PI's group has pioneered and successfully demonstrated a novel derivatization strategy via replacement of oxygen of nucleic acids with selenium (Se). Their research is based on their central hypothesis that since oxygen and selenium are in the same elemental family, selenium can be used to stably replace oxygen of nucleic acids atom-specifically without causing significant perturbation. We have successfully demonstrated that their Se-derivatized nucleic acids (SeNA) can be used to solve the phase problem. Furthermore, we have discovered that the atom-specific Se-derivatization can largely facilitate crystallization of DNAs, RNAs and their complexes with proteins. Therefore, the SeNA strategy has great potential to provide novel and rational solutions to these two long-standing problems, leading to valuable products and services. Though we have already synthesized several Se-derivatized phosphoramidites and triphosphates (the Se-building block reagents), the relatively-low synthetic scales and inefficient purification protocols limit them to synthesizea small number and quantity of the Se-RNAs and Se-DNAs (the Se-oligonucleotide/nucleic acid reagents) for crystallization, phase determination, and structure & function characterizations. The synthesis scales largely limit applications of the novel reagents and technologies, though we have successfully completed STTR Phase I project. In this Phase II research project, we plan to increase the Se- phosphoramidite synthesis to tens of grams in scale (50 gram each) and the Se-triphosphate synthesis to gram scale (1 gram each). These are 20-30 times larger than their current synthetic scales. Our primary objectives are to achieve larger-scale synthesis of the Se-building blocks and Se-DNAs & Se-RNAs and to facilitate crystallization and phase & structure determination of nucleic acids and their protein complexes via the Se- derivatizations. Ample preliminary results strongly support feasibility of the proposed work, and the team has extensive expertise in the proposed research areas. Our long-term goal is to fully establish standard and convenient strategies for rational crystallization facilitation and phase & structure determination of nucleic acids via the Se-derivatizations. Our novel Se-technologies will service the customers in structure determination of nucleic acids and their complexes with proteins and small molecules for discovering new drugs and biology.
| Vandavasi, Venu Gopal; Blakeley, Matthew P; Keen, David A et al. (2018) Temperature-Induced Replacement of Phosphate Proton with Metal Ion Captured in Neutron Structures of A-DNA. Structure 26:1645-1650.e3 |
| Chen, Yiqing; Zhang, Jing; Liu, Hehua et al. (2017) Unique 5'-P recognition and basis for dG:dGTP misincorporation of ASFV DNA polymerase X. PLoS Biol 15:e1002599 |
| Liu, Hehua; Yu, Xiang; Chen, Yiqing et al. (2017) Crystal structure of an RNA-cleaving DNAzyme. Nat Commun 8:2006 |
