Date of Award


Document Type

Open Access Dissertation

Degree Name

Doctor of Philosophy in Chemistry (PhD)

Administrative Home Department

Department of Chemistry

Advisor 1

Shiyue Fang

Committee Member 1

Christo Christov

Committee Member 2

Lanrong Bi

Committee Member 3

Smitha Rao


Oligonucleotide cross-linking agents are expected to become a new class of antisense drugs. They function by first hybridizing with a complementary mRNA and then form a covalent bond to permanently link the mRNA to the oligonucleotide agent. Because of covalent cross-linking, this new class of antisense drugs are expected to have much higher potency than existing ones.

Some oligonucleotide cross-linking agents have appeared in the literature, but they have various drawbacks, which include slow cross-linking rate and reversible cross-linking. To address these problems, we designed a series of new cross-linking oligonucleotides with a range of different reactivities. These oligonucleotides were expected to react with complementary mRNA with higher rates and selectivity. To synthesize this new class of cross-linking agents, we used the Dmoc oligonucleotide synthesis technology recently developed in our laboratory. Using this new technology, oligonucleotide deprotection and cleavage were achieved under mild conditions, under which the cross-linking functions in our agents were kept intact. In contrast, if known oligonucleotide synthesis technologies had been used, the cross-linking functions would not have survived. After successful synthesis of the new class of cross-linking oligonucleotides, they were subjected to hybridization with complementary oligonucleotides under various conditions. The progress of the hybridizations was monitored and analyzed with RP-HPLC and MALDI-TOF. At the current stage of the project, the properties of the cross-linking oligonucleotides were found to be less than ideal. However, successful synthesis of potential cross-liking oligonucleotides, development of key procedures and protocols for cross-linking experiments and development of analytical techniques to detect cross-linked products have paved the foundation for us to design and screen a series of similar oligonucleotides. Because as long as we can place the cross-linking function at proximity to a reactive site of complementary oligonucleotide, the two oligonucleotides will be forced to react, we believe that screening a series of oligonucleotides will provide desired cross-linking agents.