DNA/RNA Quadruplexes: Structure, Stability, Interactions

Summary

Principal Investigator: RICHARD SHAFER
Abstract: [unreadable] DESCRIPTION (provided by applicant): This project focuses on the unusual nucleic acid conformation of quadruplexes, built upon the guanine quartet. Evidence for the presence of these structures in biological systems, and their functional roles, has been mounting over the past five years: for example, quadruplex structures have been proposed to play a role in regulating telomerase activity, in initiation of transcription, in translational repression, and in binding specifically to a substantial number of proteins. Furthermore, applications have been described for quadruplexes as a folding motif for protein recognition, and as diagnostic agents, in addition to antiviral and anticancer chemotherapeutic agents. Structures based on guanine quartets are unique among nucleic acids in their dependence on specific binding of certain stabilizing cations. Our long term goal is an enhanced understanding of the thermodynamics, structure and interactions of this class of nucleic acids, in particular, in terms of the specific nature of cation binding, the properties of folded RNA quadruplexes and their differences with respect to DNA quadruplexes, and their interactions with other molecules of biological interest. In particular, we propose thermodynamic analyses of a series of biologically significant guanine-rich sequences, both in DNA and RNA forms, structural analyses of these sequences, development of methods to assess the molecularity of quadruplex forms and a detailed investigation of a catalytic DNA construct and its interactions with hemin. Experimental techniques to be employed in this goal include UV/CD spectroscopy, isothermal titration calorimetry, NMR, and fluorescence, and equilibrium sedimentation. This combination of approaches will afford a detailed examination of the conformation and interaction properties of the very important nucleic acid species. [unreadable] [unreadable]
Funding Period: 2003-06-01 - 2009-05-31
more information: NIH RePORT

Top Publications

  1. pmc Covalent ligation studies on the human telomere quadruplex
    Jianying Qi
    Department of Pharmaceutical Chemistry, School of Pharmacy, University of California San Francisco, CA 94143 0446, USA
    Nucleic Acids Res 33:3185-92. 2005
  2. ncbi Characterization of an unusual folding pattern in a catalytically active guanine quadruplex structure
    Pinaki R Majhi
    University of California San Francisco, Department of Pharmaceutical Chemistry, San Francisco, CA 94143 0446, USA
    Biopolymers 82:558-69. 2006
  3. pmc Engineering the quadruplex fold: nucleoside conformation determines both folding topology and molecularity in guanine quadruplexes
    Chung Fei Tang
    Department of Pharmaceutical Chemistry, School of Pharmacy and Graduate Group in Chemistry and Chemical Biology, University of California, San Francisco, California 94143 0446, USA
    J Am Chem Soc 128:5966-73. 2006
  4. ncbi Electrostatics dominate quadruplex stability
    Ivan V Smirnov
    Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94143 0446, USA
    Biopolymers 85:91-101. 2007
  5. ncbi Human telomere quadruplex: refolding and selection of individual conformers via RNA/DNA chimeric editing
    Jianying Qi
    Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, San Francisco, California 94143 0446, USA
    Biochemistry 46:7599-606. 2007
  6. ncbi Heat capacity changes associated with guanine quadruplex formation: an isothermal titration calorimetry study
    Pinaki R Majhi
    Department of Pharmaceutical Chemistry and Graduate Program in Chemistry and Chemical Biology, University of California, San Francisco, CA 94143, USA
    Biopolymers 89:302-9. 2008

Scientific Experts

Detail Information

Publications6

  1. pmc Covalent ligation studies on the human telomere quadruplex
    Jianying Qi
    Department of Pharmaceutical Chemistry, School of Pharmacy, University of California San Francisco, CA 94143 0446, USA
    Nucleic Acids Res 33:3185-92. 2005
    ..Circular dichroism spectra showed that the ligation product was derived from an antiparallel, single-stranded guanine quadruplex rather than a parallel single-stranded guanine quadruplex structure...
  2. ncbi Characterization of an unusual folding pattern in a catalytically active guanine quadruplex structure
    Pinaki R Majhi
    University of California San Francisco, Department of Pharmaceutical Chemistry, San Francisco, CA 94143 0446, USA
    Biopolymers 82:558-69. 2006
    ..These results suggest that the catalytically active form, studied in the presence of K+, may be a parallel, multistranded quadruplex rather than an antiparallel, unimolecular quadruplex...
  3. pmc Engineering the quadruplex fold: nucleoside conformation determines both folding topology and molecularity in guanine quadruplexes
    Chung Fei Tang
    Department of Pharmaceutical Chemistry, School of Pharmacy and Graduate Group in Chemistry and Chemical Biology, University of California, San Francisco, California 94143 0446, USA
    J Am Chem Soc 128:5966-73. 2006
    ..These results demonstrate how conformational properties of guanine nucleosides govern not only the quadruplex folding topology but also impact quadruplex molecularity and provide a means to control these properties...
  4. ncbi Electrostatics dominate quadruplex stability
    Ivan V Smirnov
    Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94143 0446, USA
    Biopolymers 85:91-101. 2007
    ..Nonetheless, many cosolvents and small molecules, such as ethanol, dimethylformamide, and betaine, stabilize the quadruplex conformation in sharp distinction to their destabilization of DNA duplexes...
  5. ncbi Human telomere quadruplex: refolding and selection of individual conformers via RNA/DNA chimeric editing
    Jianying Qi
    Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, San Francisco, California 94143 0446, USA
    Biochemistry 46:7599-606. 2007
    ..The ability to engineer and control quadruplex folding motifs illustrated here with HT may prove useful more generally for a variety of quadruplex-forming sequences...
  6. ncbi Heat capacity changes associated with guanine quadruplex formation: an isothermal titration calorimetry study
    Pinaki R Majhi
    Department of Pharmaceutical Chemistry and Graduate Program in Chemistry and Chemical Biology, University of California, San Francisco, CA 94143, USA
    Biopolymers 89:302-9. 2008
    ..For all sequences studied, quadruplex formation was exothermic but with an increasing magnitude with increasing temperature. These results are discussed in terms of the change in heat capacity associated with quadruplex formation...