With increasing knowledge about the structure of the human genome, information about the function is needed. We are particularly interested in small molecule drugs, as they offer potential therapeutic value by influencing the regulatory control of genes. While a number of small molecule drugs bind to specific DNA sequences, a higher degree of sequence recognition is needed, thus necessitating a more sound understanding of the factors that contribute to sequence recognition. We are using the osmotic stress approach that is based on the exclusion of solutes from the binding sites of macromolecules. Thus, osmotic pressure drives water from the DNA and its binding sites and perturbs the stability of complexes. We are now studying the sequence and drug dependence of water involvement. Figure adapted from http://www.cbs.umn.edu/~licata/os.html
Silver Nanocluster Synthesis using DNA
Manipulating the size and shape of matter on the nanometer scale offers exciting possibilities. For metals, the transition from bulk material to isolated atoms results in the separation of highly polarizable, continuous, plasmon-supporting bands into discrete energy levels. We are particularly interested in small metal nanoclusters (<10 atoms) and their unique optical and catalytic properties. For example, silver nanoclusters exhibit very strong absorption and emission and high photostability, making them nearly ideal fluorophores with applications in high-density optical data storage and biological labeling. In addition, metal nanoclusters have catalytic activity distinct from bulk metals. Biological molecules offer a route to produce chiral nanoclusters that could act as enantioselective catalysts. We are now studying the sequence dependence of nanocluster synthesis.
Petty, J. T.; Sengupta, B.; Story, S. P.; Degtyareva, N. N. "DNA Sensing by Amplifying the Number of Near-Infrared Emitting, Oligonucleotide-Encapsulated Silver Clusters.", Analytical Chemistry,2011, 83, 5957-5964.
Degtyareva, N. N.; Barber, C. A.; Reddish, M. J.; Petty, J. T. "Sequence length dictates repeated CAG folding in three-way junctions.", Biochemistry,2011, 50, 458-465.
Degtyareva, N. N.; Petty, J. T. "Non-B Conformations of CAG Repeats Using 2-Aminopurine", Methods in Enzymology,2011, 492, 213-231.
Petty, J. T.; Fan, C.; Story, S. P.; Sengupta, B.; Sartin, M.; Hsiang, J.-C.; Perry, J. W.; Dickson, R. M. "Optically Enhanced, Near-IR, Silver Cluster Emission Altered by Single Base Changes in the DNA Template", The Journal of Physical Chemistry B,2011, 24, 7996-8003.
Natalya Degtyareva, Courtney Barber, Bidisha Sengupta "Context Dependence of Trinucleotide Repeat Structures", Biochemistry,2010, 49, 3024-3030.
Kristine Loo, Natalya Degtyreva, Jihae Park, Bidisha Sengupta, Michaeal Reddish, Christopher Johnson, Andrea Bryant "Ag+-Mediated Assembly of 5′-Guanosine Monophosphate", Journal of Physical Chemistry C,2010, 114, 4320-4326.
Petty, J. T.; Fan, C.; Story, S. P.; Sengupta, B.; St. John Iyer, A.; Prudowsky, Z.; Dickson, R. M., DNA Encapsulation of 10 Silver Atoms Producing a Bright, Modulatable, Near-Infrared-Emitting Cluster. J. Phys. Chem. Lett. 2010, 1 (17), 2524-2529. "", The Journal of Physical Chemistry Letters,2010, 1, 2524-2529.
Natalya Degtyareva, Michaeal Reddish, Bidisha Sengupta, Jeff Petty "Structural Studies of a Trinucleotide Repeat Sequence Using 2-Aminopurine", Biochemistry,2009, 48, 2340–2346.
Bidisha Sengupta, Kerianne Springer, Jenna G. Buckman, Sandra P. Story, Oluwamuyiwa Henry Abe, Zahiyah W. Hasan, Zachary D. Prudowsky, Sheldon E. Rudisill, Natalya N. Degtyareva and Jeffrey T. Petty "DNA Templates for Fluorescent Silver Clusters and I-Motif Folding", Journal of Physical Chemistry C,2009, 113, 19518-19524.
Bidisha Sengupta, Caroline M. Ritchie, Jenna G. Buckman, Kenneth Johnsen, Peter M. Goodwin and Jeffrey T. Petty "Base-Directed Formation of Fluorescent Silver Clusters", Journal of Physical Chemistry C,2008, 112, 18776–18782.
Natalya Degtyareva, Megan Fresia, Jeff Petty "DNA conformational effects on the interaction of netropsin with A-tract sequences", Biochemistry,2007, 46, 15136-43.
Natalya N. Degtyareva, Bret D. Wallace, Andrea R. Bryant, Kristine M. Loo, and Jeffrey T. Petty "Hydration Changes Accompanying the Binding of Minor Groove Ligands with DNA", Biophysical Journal,2007, 92, 959-965.
Caroline M. Ritchie, Kenneth R. Johnsen, John R. Kiser, Yasuko Antoku, Robert M. Dickson, and Jeffrey T. Petty "Ag Nanocluster Formation using a Cytosine Oligonucleotide Template ", Journal of Physical Chemistry C,2007, 111, 175-181.
Kiser, J. R.; Monk, R. W.; Smalls, R. L.; Petty, J. T. "Hydration Changes in the Association of Hoechst 33258 with DNA", Biochemistry,2005, 44, 16988-16997.
Petty, J.T.; Zheng, J.; Hud, N.V.; Dickson, R. M. "DNA-Templated Ag Nanocluster Formation", J. Am. Chem. Soc.,2004, 126, 5207.
Zheng, J.; Petty, J.T.; Dickson, R. "High Quantum Yield Blue Emission form Water-Soluble Au8 Nanodots", J. Am. Chem. Soc.,2003, 124, 13982.
Sovenyhazy, K. M.; Bordelon, J. A.; Petty, J. T. "Spectroscopic Studies of the Multiple Binding Modes of a Trimethine-Bridged Cyanine Dye with DNA", Nucleic Acids Res.,2003, 31, 2561.
J. A. Bordelon, K. J. Feierabend, S. A. Siddiqui, L. L. Wright, and J. T. Petty "Viscometry and Atomic Force Microscopy Studies of the Interactions of a Dimeric Cyanine Dye with DNA", J. Phys. Chem,2002, 106, 4838-4843.
Barker, K. D.; Benoit, B. R.; Bordelon, J. A.; Davis, R. J.; Delmas, A. S.; Mytykh, O. V.; Petty, J. T.; Wheeler, J. F.; Kane-Maguire, N. A. P. "Intercalative Binding and Photoredox Behavior of [(Cr(phen)2(dppz)]3+ with B-DNA", Inorg. Chim. Acta,2001, 127, 74.
Petty, J.T.; Bordelon, J. A.; Robertson, M.E. "Thermodynamic Characterization of the Association of Cyanine Dyes with DNA", J. Phys. Chem. B.,2000, 104, 7221.
Knight, L.B.; King, G.M.; Petty, J.T.; Matsushita, M.; Momose, T.; Shida, T. "ESR Studies of the Methane Radical Cations (12, 13CH4+, 12, 13CDH3+, 12CD2H2+, 12CD3H+, 12CD4H+) In Solid Neon Matrices Between 2.5 and 11K. Analysis of Tunneling. Part II.", J. Chem. Phys.,1995, 103, 3377-33895.
Lon B. Knight, Jr., S. T. Cobranchi and Jeff Petty "Electronic Ground State Assignment for O4+: Neon Matrix Electron-spin Resonance Investigation", J. Chem. Phys.,1989, 91, 4423.
Lon B. Knight, Jr., S.T. Cobranchi, Jeff Petty and D. P. Cobranchi "The Generation and ESR Characterization of 63,65Cu12CH2 and 63,65Cu13CH2 in Neon Matrices", J. Chem. Phys.,1989, 91, 4587.
Lon B. Knight, Jr., J. T. Petty, S. T. Cobranchi, David Feller and E. R. Davidson "The Generation of 12C31P and 13C31P by Reactive Laser Vaporization for Rare Gas Matrix Electron Spin Resonance Studies: Comparison with ab initio Theoretical Calculations", J. Chem. Phys.,1988, 88, 3441.
L. B. Knight, Jr. and J. T. Petty "Neon Matrix ESR Investigation of 69,71GaAs+ Generated by the Photoionization of Laser Vaporized GaAs(s)", J. Chem. Phys.,1988, 88, 481.