Author ORCID Identifier

0000-0002-6883-9369

Date of Award

Spring 2-26-2020

Degree Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Department

Chemistry

First Advisor

Jun Yin

Abstract

Nucleic acid X-ray crystallography faces crystallization as well as phasing challenge. The Phasing problem could be rationally solved by incorporation of selenium into the DNA or RNA oligonucleotides, while the crystallization of nucleic acid is still challenging. To address these challenges without structural perturbation, we decided to explore the atom-specific incorporation and place a selenium atom on the 2’-beta position to control B-form DNA formation during crystallization process. Herein we report the first synthesis of the β-2’-MeSe-thymidine (2’SeT) phosphoramidite and Se-DNAs. We found that the Se-DNAs and Se-DNA-protein complexes formed crystals most of time with higher quality and diffraction resolution than the non-modified ones. Surprisingly, the Se-DNA can form crystals up to 600 microns in size, which were frequently hundreds of times larger in volume than the corresponding native. Moreover, we discovered that the high-quality Se-DNA crystals offered the diffraction resolution up to 1.15 Å and the Se-derivatized structure was virtually identical to the native one. In the meanwhile, we synthesized the β-2’-MeSe-cytidine (2’SeC) phosphoramidite and its DNA oligos. To our surprise, the selenium modification greatly facilitate crystallization when the modified cytidine was placed at the terminals of the oligo. The crystal of the Se-DNA formed within a few hours, where the corresponding native crystalized over 1 week.

Furthermore, we describe the first synthesis of 2’-MeSe-arabinouridine (2’SeU) phosphoramidite and its DNAs to investigate the structure of DNAs containing the uracil. The Se-derivatized DNA X-ray crystal structure (1.25 Å) was virtually identical to the native one. Interestingly, during the Se incorporation step, we also found that the MeSe group attack the C-4 of the uracil generating a oxazolinyl-selenolester when the N-3 was protected with tert-butyloxycarbonyl (Boc) group which may activate the C-4 position through a n-π* interaction.

Besides the structure studies, we also synthesized the 5-phenylselenium and 5-phenyltelenium modified deoxyuridine and incorporated them into DNA oligos to investigate their charge transport properties. The conductance and current-voltage (I-V) characteristics measurement indicates that the Te modification more effectively manipulate the electronic structure of the DNA compared to the Se modification and the corresponding native.

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