Selected Publications

Chinnapen D.J.-F. and Sen D. (2004) A deoxyribozyme that harnesses light to repair thymine dimers in DNA.  Proceedings of the National Academy of Sciences U.S.A. 101: 65-9.

Lee, H.-W. Chinnapen, D.J.-F., and Sen, D. (2004) A Structure-Function Investigation of a Deoxyribozyme with Dual Chelatase and Peroxidase Activities. Pure and Applied Chemistry (in press)

Fahlman, R.P., Hsing, M., Sporer-Tuhten, C., and Sen, D. (2003) Duplex Pinching: A Structural Switch Suitable for Contractile DNA Nanoconstructions. Nano Letters (Am. Chem. Soc.) 3: 1073-1078.

Yu H.-Z., Luo C.-Y., Sankar C.G. and Sen, D.  (2003)  Voltammetric procedure for examining DNA-modified surfaces: quantitation, cationic binding activity, and electron-transfer kinetics.  Analytical Chemistry 75: 3902-7.

Sen, D. and Chinnapen, D.J.  (2003)  Deoxyribozymes that catalyze photochemistry: cofactor-dependent and -independent photorepair of thymine dimers.  Nucleic Acids Research Suppl. 3: 217-8.

Fahlman R.P., Sharma R.D. and Sen D.  (2002)  The charge conduction properties of DNA holliday junctions depend critically on the identity of the tethered photooxidant.  Journal of the American Chemical Society. 124: 12477-85.

Sen D.  (2002) Aptamer rivalry.  Chemistry & Biology.  8: 851-2.

Wang, D.Y., Lai, B.H.Y., and Sen, D. (2002) A General Strategy for Effector-mediated Control of RNA-cleaving Ribozymes and DNA Enzymes. Journal of Molecular Biology 318, 33-43.

Wang D.Y., Sen, D.  (2002)  Rationally designed allosteric variants of hammerhead ribozymes responsive to the HIV-1 Tat protein. Combinatorial Chemistry and High Throughput Screening. 5: 301-12.

Fahlman, R.P. and Sen, D. (2002) DNA Conformational Switches as Sensitive Electronic Sensors of Analytes. Journal of the American Chemical Society 124, 4610-4616.

Chinnapen, D.J.F. and Sen, D. (2002) Hemin-Stimulated Docking of Cytochrome c to a Hemin-DNA Aptamer Complex. Biochemistry 41, 5202-5212.

Wang, D.Y., Lai, B.H.Y., Feldman, A.R., and Sen, D. (2002) A general approach for the use of oligonucleotide effectors to regulate the catalysis of RNA-cleaving ribozymes and DNAzymes. Nucleic Acids Research 30, 1735-1742.

Feldman, A.R. and Sen, D. (2001) A New and Efficient DNA Enzyme for the Sequence-specific Cleavage of RNA. Journal of Molecular Biology 313, 283-294.

Witting, P.K., Travascio, P., Sen, D., and Mauk, A.G. (2001) A DNA Oligonucleotide-Hemin Complex Cleaves t-Butyl Hydroperoxide through a Homolytic Mechanism. Inorganic Chemistry 40, 5017-5023.

Wang, D.Y. and Sen, D. (2001) A Novel Mode of Regulation of an RNA-cleaving DNAzyme by Effectors that Bind to Both Enzyme and Substrate. Journal of Molecular Biology 310, 723-734.

Travascio, P., Witting, P.K., Mauk, A.G., and Sen, D. (2001) The Peroxidase Activity of a Hemin--DNA Oligonucleotide Complex: Free Radical Damage to Specific Guanine Bases of the DNA. Journal of the American Chemical Society 123, 1337-1347.

Geyer, C.R. and Sen, D. (2000) Use of Intrinsic Binding Energy for Catalysis by a Cofactor-independent DNA Enzyme. Journal of Molecular Biology 299, 1387-1398.

Fahlman, R.P. and Sen, D. (1999) “Synapsable” DNA Double Helices: Self-Selective Modules for Assembling DNA Superstructures. Journal of the American Chemical Society 121, 11079-11085.

Travascio, P., Bennet, A.J., Wang, D.Y., and Sen, D. (1999) A ribozyme and a catalytic DNA with peroxidase activity: active sites versus cofactor-binding sites. Chemistry & Biology 6, 779-787.

Li, Y. and Sen, D. (1998) A Small and Efficient DNA Enzyme.  Structure, Motion, Interaction and Expression of Biological Macromolecules and Function, Volume 1 (Adenine Press): 139-150.

Sen, D.  (1998)  DNA Selection and Amplification. Comprehensive Natural Products Chemistry (eds. D.R. Barton and K. Nakanishi, Elsevier Press) 7: 615-642.

Sen, D. and Geyer, C.R. (1998) DNA enzymes. Current Opinion in Chemical Biology 2, 680-687.

Travascio, P., Li, Y., and Sen, D. (1998) DNA-enhanced peroxidase activity of a DNA-aptamer-hemin complex. Chemistry & Biology 5, 505-517.

Fahlman, R.P. and Sen, D. (1998) Cation-regulated Self-association of "Synapsable" DNA Duplexes. Journal of Molecular Biology 280, 237-244.

Li, Y. and Sen, D. (1998) The modus operandi of a DNA enzyme: enhancement of substrate basicity. Chemistry & Biology 5, 1-12.

Geyer, C,R, and Sen, D. (1998) Lanthanide Probes for a Phosphodiester-cleaving, Lead-dependent, DNAzyme. Journal of Molecular Biology 275, 483-489.

Geyer, C.R. and Sen, D. (1997) Evidence for the metal-cofactor independence of an RNA phosphodiester-cleaving DNA enzyme. Chemistry & Biology 4, 579-593.

Li, Y. and Sen, D. (1997) Toward an Efficient DNAzyme. Biochemistry 36, 5589-5599.

Wellinger, R.J. and Sen, D. (1997) The DNA Structures at the Ends of Eukaryotic Chromosomes. European Journal of Cancer 33, 735-749.

Li, Y. and Sen, D. (1996) A catalytic DNA for porphyrin metallation. Nature Structural Biology 3, 743-747.

Li, Y., Geyer, C.R., and Sen, D. (1996) Recognition of Anionic Porphyrins by DNA Aptamers. Biochemistry 35, 6911-6922.

Venczel, E.A. and Sen, D. (1996) Synapsable DNA. Journal of Molecular Biology 257, 219-224.

Awang, G. and Sen, D. (1993) Mode of dimerization of HIV-1 genomic RNA. Biochemistry 32, 11453-11457.

Venczel, E.A. and Sen, D. (1993) Parallel and antiparallel G-DNA structures from a complex telomeric sequence. Biochemistry 32, 6220-6228.

Sen, D and Gilbert, W.  (1992)  Cationic Switches in the Formation of DNA Structures containing Guanine-Quartets.  Structure and Function, Volume 1 (Adenine Press): 43-51.

Sen, D. and Gilbert, W. (1992) Novel DNA superstructures formed by telomere-like oligomers. Biochemistry 31, 65-70.

Sen, D. and Gilbert, W. (1992) Guanine quartet structures. Methods in Enzymology 211, 191-199.

Wu, C.J., Karttunen, J.T., Chin, D.H., Sen, D., and Gilbert, W. (1991)  Murine Memory B Cells are Multi-Isotype Expressors.  Immunology 72, 48-55.

Sen, D. and Gilbert, W.  (1991) The structure of telomeric DNA: DNA Quadruplex Formation.  Current Opinion in Structural Biology 1, 435-438.

Sen, D. and Gilbert, W. (1990) A sodium-potassium switch in the formation of four-stranded G4-DNA. Nature 344, 410-414.

Sen, D. and Gilbert, W. (1988) Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and its implications for meiosis. Nature 334, 364-366.

Sen, D., Mitra S., and Crothers, D.M.  (1986)  Higher order structure of chromatin: evidence from photochemically detected linear dichroism.  Biochemistry  25: 3441-7.

Sen, D. and Crothers, D.M.   (1986)  Condensation of chromatin: role of multivalent cations.  Biochemistry  25: 1495-503.

Sen, D. and Crothers, D.M.  (1986)  Influence of DNA-binding drugs on chromatin condensation.  Biochemistry  25: 1503-9.

Mitra, S., Sen, D., and Crothers, D.M.  (1984)  Orientation of nucleosomes and linker DNA in calf thymus chromatin determined by photochemical dichroism.  Nature 308: 247-50.