Document Type

Student Research Paper


Summer 2021

Academic Department

Chemistry and Biochemistry

Faculty Advisor(s)

Dr. James MacKay


Research has uncovered previously unknown roles for non-coding RNA as enzymes, gene regulators, and post-transcriptional modifiers. However, additional undiscovered functions of non-coding RNA likely remain. To better understand the function of non-coding RNA, we design triplex-forming peptide nucleic acid (PNA), with modified nucleobases, that binds sequence-specifically to double-stranded RNA (dsRNA) and potentially inhibits the function of the dsRNA. PNA contains a neutral amide backbone that has favorable binding to negatively-charged dsRNA. Our modified nucleobases subsequently allow for sequence specific molecular recognition.

Here we report an extended nucleobase derived from isoorotic acid containing an amino group, that when protonated should exhibit favorable hydrogen bonding to the Hoogsteen face of the A-U base pair while also imparting cationic character to the PNA for increased binding affinity. The synthesis of the target nucleobase involves alkylation of isoorotic acid and protection of 2-aminobenzylamine. The alkylated isoorotic acid and protected aniline are coupled through amide bond formation, followed by hydrogenation to form a carboxylic acid for coupling with the PNA backbone. Upon synthesis of the extended nucleobase, we will incorporate it into PNA and determine the binding affinity and sequence selectivity of the nucleobase for the A-U base pair of dsRNA.


Scholarship, Creative Arts, and Research Project (SCARP)

Included in

Chemistry Commons



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