Date of Award

Spring 5-10-2014

Degree Type


Degree Name

Doctor of Philosophy (PhD)



First Advisor

Zhen Huang

Second Advisor

Binghe Wang

Third Advisor

Donald Hamelberg


Nucleic acids, as one of the most important macromolecules in living systems, play critical roles in storing, transferring, regulating genetic information, directing proteins synthesis, and catalysis. Understanding the structure of nucleic acid can bring us valuable information for mechanistic study and for drug discovery as well. Among all experimental methods, X-ray crystallography is the most powerful tool in structural biology study to reveal the 3D structure of macromolecules, which has provided over 80% of the highly detailed structural information to date. However, this great technology comes with two disturbing features, crystallization and phasing. The covalent selenium modification of nucleic acids has been proven to be a powerful tool to address both issues in nucleic acid crystallography. First part of this dissertation focuses on the development of novel selenium-modified nucleic acids (SeNA) for crystallization and phasing of B-form DNA containing structures. The novel 2’-SeMeANA modification is the first and currently the only selenium modification, which is fully compatible with X-ray crystallographic study of B-form DNA. Since selenium derivatization at 2’-arabino position dose not affect the B-type 2’-endo sugar conformation, this strategy is suitable for incorporating selenium into DNA for structural studies of B-DNA, DNA-protein complexes, and DNA-drug complexes.

Specific base pairing is essential to many biological processes, including replication, transcription, and translation. It is crucial to NA (nucleic acid) sequence-based diagnostic and therapeutic applications as well. By utilizing the unique steric and electronic property of selenium, we designed, synthesized the novel 2-Se-U RNA modification, and demonstrated its highly specific base-pairing property by both biophysical and crystallographic methods. Our studies of 2-Se-U-containing RNAs suggest that this single-atom replacement can largely improve base pairing fidelity against U/G wobble pair, without significant impact on U/A pair.