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.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Synthetic and Biological Chemistry A Study Section (SBCA)
Program Officer
Fabian, Miles
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of California San Diego
Schools of Arts and Sciences
La Jolla
United States
Zip Code
Li, Yao; Fin, Andrea; McCoy, Lisa et al. (2016) Polymerase-Mediated Site-Specific Incorporation of a Synthetic Fluorescent Isomorphic G Surrogate into RNA. Angew Chem Int Ed Engl :
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
Rudek, Michelle A; Dasari, Arvind; Laheru, Daniel et al. (2016) Phase 1 Study of ABT-751 in Combination With CAPIRI (Capecitabine and Irinotecan) and Bevacizumab in Patients With Advanced Colorectal Cancer. J Clin Pharmacol 56:966-73
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 55:7974-8
Sholokh, Marianna; Sharma, Rajhans; Shin, Dongwon et al. (2015) Conquering 2-aminopurine's deficiencies: highly emissive isomorphic guanosine surrogate faithfully monitors guanosine conformation and dynamics in DNA. J Am Chem Soc 137:3185-8
Rios, Andro C; Yu, Hiu T; Tor, Yitzhak (2015) Hydrolytic Fitness of N-glycosyl Bonds: Comparing the Deglycosylation Kinetics of Modified, Alternative and Native Nucleosides. J Phys Org Chem 28:173-180
Mizrahi, Rena A; Shin, Dongwon; Sinkeldam, Renatus W et al. (2015) A Fluorescent Adenosine Analogue as a Substrate for an A-to-I RNA Editing Enzyme. Angew Chem Int Ed Engl 54:8713-6
Rovira, Alexander R; Fin, Andrea; Tor, Yitzhak (2015) Chemical Mutagenesis of an Emissive RNA Alphabet. J Am Chem Soc 137:14602-5
Shin, Dongwon; Lönn, Peter; Dowdy, Steven F et al. (2015) Cellular activity of siRNA oligonucleotides containing synthetic isomorphic nucleoside surrogates. Chem Commun (Camb) 51:1662-5
McCoy, Lisa S; Shin, Dongwon; Tor, Yitzhak (2014) Isomorphic emissive GTP surrogate facilitates initiation and elongation of in vitro transcription reactions. J Am Chem Soc 136:15176-84

Showing the most recent 10 out of 58 publications