The goal of the proposed program is to design, synthesize and implement new fluorescent nucleoside analogs as probes for nucleic acids structure, dynamics and recognition. The main criteria directing the proposed work are to maintain the highest possible structural similarity to the natural nucleobases, to shift the emission to longer wavelengths, and to retain adequate emission quantum efficiency.
The specific aims of this project are: (1) To design """"""""ideal"""""""" fluorescent nucleoside analog that will possess the following characteristics: (i) A high structural similarity to the native nucleobases to faithfully mimic their size and shape, as well as hybridization and recognition properties, (ii) A red shifted absorption spectrum to minimize overlap with the absorption of the natural bases, (iii) A respectable emission quantum efficiency and a long emission wavelength (preferably in the visible range);(2) To devise concise synthetic approaches to the desired nucleobase analogs;(3) To examine the photophysical characteristics of the new nucleosides;(4) To synthesize and characterize modified DNA and RNA oligonucleotides;(5) To biophysically and photophysically characterize the modified oligonucleotides;and (6) To implement the promising emissive analogs in biophysical and discovery assays. The increased appreciation for nucleic acids modifications and their impact on diseases, as well as the rapid emergence of resistant pathogens, necessitate the development of new tools for the effective study of nucleic acids, including their recognition properties and alteration by exogenous agents. The emissive nucleoside analogs will be implemented into novel fluorescence-based assays. These assays will facilitate: (i) the detection of DNA lesions (e.g., 8-oxoG), that play important roles in carcinogenesis, (ii) the discovery of new antibiotics targeting the bacterial ribosome, assisted by fluorescent A-site analogs, (iii) the discovery of novel anti-HIV agents, assisted by fluorescent DIS constructs, and (iv) the detection of protein toxins, such as ricin, via emissive probes that detect their depurinated RNA products. These investigations will advance the fundamental understanding of key biological processes related to disease development and will have long-term impact on improving human health by facilitating drug discovery.

Public Health Relevance

Nucleic acids (DNA and RNA) play central roles in biology and, as such, have immense impact on the development of diseases and, as such, on human health. Advancing effective fluorescence-based tools for exploring the modification of DNA and RNA or their interactions with potential therapeutic agents will advance new diagnostic approaches and will facilitate drug discovery.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM069773-08
Application #
8019535
Study Section
Synthetic and Biological Chemistry A Study Section (SBCA)
Program Officer
Fabian, Miles
Project Start
2004-01-01
Project End
2012-01-31
Budget Start
2011-02-01
Budget End
2012-01-31
Support Year
8
Fiscal Year
2011
Total Cost
$266,220
Indirect Cost
Name
University of California San Diego
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
804355790
City
La Jolla
State
CA
Country
United States
Zip Code
92093
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Kilin, Vasyl; Gavvala, Krishna; Barthes, Nicolas P F et al. (2017) Dynamics of Methylated Cytosine Flipping by UHRF1. J Am Chem Soc 139:2520-2528
Rovira, Alexander R; Fin, Andrea; Tor, Yitzhak (2017) Emissive Synthetic Cofactors: An Isomorphic, Isofunctional, and Responsive NAD+ Analogue. J Am Chem Soc 139:15556-15559
Liu, Wei; Shin, Dongwon; Ng, Martin et al. (2017) Stringent Nucleotide Recognition by the Ribosome at the Middle Codon Position. Molecules 22:
Hopkins, Patrycja A; McCoy, Lisa S; Tor, Yitzhak (2017) Enzymatic incorporation and utilization of an emissive 6-azauridine. Org Biomol Chem 15:684-690
Li, Yao; Fin, Andrea; McCoy, Lisa et al. (2017) Polymerase-Mediated Site-Specific Incorporation of a Synthetic Fluorescent Isomorphic G Surrogate into RNA. Angew Chem Int Ed Engl 56:1303-1307
Rovira, Alexander R; Tor, Yitzhak (2017) Synthesis of unique spirocyclic orthoester-type derivatives of isothiazolo[4,3-d]pyrimidine nucleosides. J Antibiot (Tokyo) :
Vranken, C; Fin, A; Tufar, P et al. (2016) Chemoenzymatic synthesis and utilization of a SAM analog with an isomorphic nucleobase. Org Biomol Chem 14:6189-92
Freeman, Noam S; Moore, Curtis E; Wilhelmsson, L Marcus et al. (2016) Chromophoric Nucleoside Analogues: Synthesis and Characterization of 6-Aminouracil-Based Nucleodyes. J Org Chem 81:4530-9
Sholokh, Marianna; Improta, Roberto; Mori, Mattia et al. (2016) Tautomers of a Fluorescent G Surrogate and Their Distinct Photophysics Provide Additional Information Channels. Angew Chem Int Ed Engl 55:7974-7978

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