This proposal addresses the need for new reagents targeted toward specific sequences of DNA and RNA. Such reagents would have potential use in both diagnostic and therapeutic applications. The reagents described (in the proposal) are peptide nucleic acid (PNA) oligomers, which are synthetic analogs of DNA and RNA in which the sugar-phosphodiester backbone is replaced by a polyamide. PNAs hybridize to complementary single-stranded DNA and RNA with high affinity and sequence selectivity. Most applications of PNA will require hybridization to a target sequence that is part of a folded structure that could impose significant barriers to binding by sterically blocking access to the target site. PNA can bind to duplex DNA by strand invasion but only certain sequences can be targeted. The growing awareness of the importance on nonduplex DNA secondary structures and the rich variety of secondary and tertiary structures exhibited by RNA have prompted us to initiate studies on the ability of PNA to target these structures, both in simple model systems and within the context of a large, folded RNA molecule. We will use a variety of spectroscopic, calorimetric and gel electrophoretic methods to study the thermodynamics and kinetic factors controlling PNA hybridization to these targets. The principal aim of this proposal is to broadly examine the scope of PNA hybridization to structured targets to better evaluate the potential utility of PNA in diagnostic and therapeutic applications. The following Specific Aims will allow us to achieve this goal: * Examine binding of PNA to DNA and RNA hairpin motifs. * Study binding of homopyrimidine PNA to single- and double-stranded RNA sequences * Evaluate PNA-DNA and PNA-RNA hybridization kinetics. * Effect of RNA tertiary structure on PNA hybridization.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM058547-03
Application #
6519936
Study Section
Bio-Organic and Natural Products Chemistry Study Section (BNP)
Program Officer
Lewis, Catherine D
Project Start
2000-04-01
Project End
2005-03-31
Budget Start
2002-04-01
Budget End
2003-03-31
Support Year
3
Fiscal Year
2002
Total Cost
$142,903
Indirect Cost
Name
Carnegie-Mellon University
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
052184116
City
Pittsburgh
State
PA
Country
United States
Zip Code
15213
Gupta, Anisha; Lee, Ling-Ling; Roy, Subhadeep et al. (2013) Strand invasion of DNA quadruplexes by PNA: comparison of homologous and complementary hybridization. Chembiochem 14:1476-84
Roy, Subhadeep; Zanotti, Kimberly J; Murphy, Connor T et al. (2011) Kinetic discrimination in recognition of DNA quadruplex targets by guanine-rich heteroquadruplex-forming PNA probes. Chem Commun (Camb) 47:8524-6
Lusvarghi, Sabrina; Murphy, Connor T; Roy, Subhadeep et al. (2009) Loop and backbone modifications of peptide nucleic acid improve g-quadruplex binding selectivity. J Am Chem Soc 131:18415-24
Roy, Subhadeep; Tanious, Farial A; Wilson, W David et al. (2007) High-affinity homologous peptide nucleic acid probes for targeting a quadruplex-forming sequence from a MYC promoter element. Biochemistry 46:10433-43
Marin, Violeta L; Armitage, Bruce A (2006) Hybridization of complementary and homologous peptide nucleic acid oligomers to a guanine quadruplex-forming RNA. Biochemistry 45:1745-54
Datta, Bhaskar; Bier, Mark E; Roy, Subhadeep et al. (2005) Quadruplex formation by a guanine-rich PNA oligomer. J Am Chem Soc 127:4199-207
Marin, Violeta L; Armitage, Bruce A (2005) RNA guanine quadruplex invasion by complementary and homologous PNA probes. J Am Chem Soc 127:8032-3
Marin, V; Hansen, H F; Koch, T et al. (2004) Effect of LNA modifications on small molecule binding to nucleic acids. J Biomol Struct Dyn 21:841-50
Datta, Bhaskar; Schmitt, Christoph; Armitage, Bruce A (2003) Formation of a PNA2-DNA2 hybrid quadruplex. J Am Chem Soc 125:4111-8
Kushon, S A; Jordan, J P; Seifert, J L et al. (2001) Effect of secondary structure on the thermodynamics and kinetics of PNA hybridization to DNA hairpins. J Am Chem Soc 123:10805-13

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