Dissertation
Design and synthesis of novel antisense nucleopeptides and their biophysical evaluation
Washington State University
Doctor of Philosophy (PhD), Washington State University
12/2010
DOI:
https://doi.org/10.7273/000006170
Abstract
The ultimate aim of this research project is the development of a novel RNA-targeting nucleic acid surrogate that merges codified molecular recognition of nucleic acids with the ability of cell-penetrating peptides to translocate across cell membranes. Nucleobases are attached to side chains of amino acids at regular intervals on a cell-permeable backbone, which allows the sequence specific Watson-Crick base pairing. New surrogates were designed based on a cell-permeable polyprolyl peptide structures. An efficient modular synthesis in solution phase was successfully developed for homopolyprolyl nucleopeptides comprised of 15 and 30 prolines. A solid-supported segment coupling was also demonstrated to prepare an alternating nucleopeptide. The preliminary biophysical studies of the homopolyprolyl nucleopeptides with both ssDNA and RNA revealed that the proline-based nucleopeptides have a strong propensity to maintain an intrinsic PPII secondary structure, which is an unfavorable conformation that precludes Watson-Crick base pairing. The thermal denaturation studies of an alternating nucleopeptide, altHNP2, exhibited cooperative binding with both ssDNA and RNA. The affinity to RNA was higher than that of ssDNA. The altHNP2 forms a [RNA (altHNP2)2] triplex upon binding with both ssDNA and RNA. Each mismatch induced a penalty of 1 ~ 11 C in the observed melting temperature. Circular dichroism studies demonstrated that the secondary structure was a random coil, not a helical conformation. Hydroxyproline-based antisense agents were designed by modifications of altHNP2 and Micklefield's backbone extended pyrrolidine oligonucleotide mimic I (bePOM I). Theoretical studies by molecular mechanics revealed that the modified bePOM I has the lowest strain energy of the backbone, which forms a duplex with RNA. These studies provide the significant foundation for developing antisense nucleopeptides from readily available hydroxyproline moieties.
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Details
- Title
- Design and synthesis of novel antisense nucleopeptides and their biophysical evaluation
- Creators
- Chung-Min Park
- Contributors
- Philip P. Garner (Chair)Robert C Ronald (Committee Member) - Washington State University, Department of ChemistryJeffrey P Jones (Committee Member) - Washington State University, Department of ChemistryClifford Berkman (Committee Member) - Washington State University, Department of Chemistry
- Awarding Institution
- Washington State University
- Academic Unit
- Department of Chemistry
- Theses and Dissertations
- Doctor of Philosophy (PhD), Washington State University
- Publisher
- Washington State University
- Number of pages
- 271
- Identifiers
- 99901055025601842
- Language
- English
- Resource Type
- Dissertation