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Dipankar Sen - Selected Publications

  • Sen, D. and Poon, L. (2011). RNA and DNA complexes with hemin [Fe(III) heme] are efficient peroxidases and peroxygenases: how do they do it and what does it mean? Crit. Rev. Biochem. Mol. Biol. 46: 478-492.
  • Poon, L., Methot, S., Morabi-Pazooki, W., Pio, F., Bennet, A. J., and Sen, D. (2011) Guanine-rich RNAs and DNAs that bind heme robustly catalyze oxygen transfer reactions. J. Am. Chem. Soc. 133: 1877-1884.
  • Sen, D. and Leung, E. K.-Y. (2010). The use of charge flow and quenching (CFQ) to probe Nucleic Acid folds and folding. Methods 52:141-149.
  • Poon, L., Zandberg, W., Hsiao, D., Erno, Z., Sen, D., Gates, B. D. and Branda, N. R. (2010) Photothermal Release of Single-Stranded DNA from the Surface of Gold Nanoparticles Through Controlled Denaturating and Au-S Bond Breaking. ACS Nano 4:6395-6403.
  • Sekhon, G.S. and Sen, D. (2010). A Stereochemical Glimpse of the Active Site of the 8-17 Deoxyribozyme from Iodine-Mediated Crosslinks Formed with the Substrate's Scissile Site. Biochemistry 49:9072-9077.
  • Ge, B., Huang, Y. C., Sen, D., and Yu, H.-Z. (2010). A Robust Electronic Switch Made of Immobilized Duplex/Quadruplex DNA. Angewandte Chemie 49:9965-9967.
  • Liu, Y. and Sen, D. (2010). Local rather than global folding enables the lead-dependent activity of the 8-17 Deoxyribozyme: Evidence from contact photocrosslinking. J. Mol. Biol. 395:234-241.
  • Huang, Y. C. and Sen, D. (2010). A contractile electronic switch made of DNA. J. Am. Chem. Soc. 132:2663-2671. [Highlighted in the Feb 15, 2010 issue of Chemical & Engineering News, the mouthpiece of the American Chemical Society.]
  • Sekhon, G.S. and Sen, D. (2009). Unusual DNA-DNA Crosslinks Between a Photolyase Deoxyribozyme, UV1C, and its Bound Oligonucleotide Substrate. Biochemistry 48:6335-47.
  • Thorne, R., Chinnapen, D., Sekhon, G., and Sen, D. (2009). A Deoxyribozyme, Sero1C, uses Light and Serotonin to Repair Diverse Pyrimidine Dimers in DNA. J. Mol. Biol. 388:21-29.
  • Huang, Y. C., Cheng, A., Yu, H.-Z., and Sen, D. (2009). The charge conduction properties of a parallel stranded DNA G-quadruplex: Implications for chromosomal oxidative damage. Biochemistry 48:6794-6804.
  • Huang, Y. C., Ge, B., Sen, D., and Yu, H. (2008) "Immobilized DNA switches as electronic sensors for picomolar detection of plasma proteins. J. Am. Chem. Soc. 130:8023-8029.
  • Bergeron, L. J., Sen, K., and Sen, D. (2008) A Guanine-Linked End-Effect is a Sensitive Reporter of Charge Flow in DNA and RNA Double Helices. Biochimie 90:1064-1073.
  • Liu, Y. and Sen, D. (2008) A contact photo-cross-linking investigation of the active site of the 8-17 deoxyribozyme. J. Mol. Biol. 381:845-859.
  • Leung, E.K. and Sen, D. (2007) Electron hole flow patterns through the RNA-cleaving 8-17 deoxyribozyme yield unusual information about its structure and folding. Chemistry & Biology 14: 41-51.
  • Lee, H.-W., Robinson, S.G, Bandyopadhyay, S., Mitchell, R.H., and Sen, D. (2007) Reversible Photo-Regulation of a Hammerhead Ribozyme using a Diffusible Effector. J. Mol. Biol. 371: 1163-1173.
  • Chinnapen D.J. and Sen D. (2007) Towards Elucidation of the Mechanism of UV1C, a Deoxyribozyme with Photolyase Activity. J Mol Biol. 2:1326-1336.
  • Feldman, A. R., Leung, K. Y., Bennet, A. J., and Sen, D. (2006) The RNA-Cleaving Bipartite DNAzyme is a Distinctive Metalloenzyme. Chembiochem 7: 98-105.
  • Travascio, P, Sen, D., and Bennet, A.J. (2006) DNA and RNA enzymes with peroxidase activity-- an investigation into the mechanism of action. Can. J. Chem. 84:613-619.
  • Su, L., Sen, D., and Yu, H.Z. (2006) Voltammetric study of the ion-exchange binding of nonelectroactive metal cations to DNA-modified surfaces. Analyst 131:317-322.
  • Liu, Y. and Sen, D. (2004) Light-Regulated Catalysis by an RNA-Cleaving Deoxyribozyme. J. Mol. Biol. 341: 887-892.
  • Su, L, Sankar, C. G., Sen, D. and Yu, H.-Z. (2004) Kinetics of Ion-Exchange Binding of Redox Metal Cations to Thiolate-DNA Monolayers on Gold. Analytical Chem (Am. Chem. Soc.) 76: 5953-5959.
  • Bechhoefer, J. and Sen, D. (2004) Comment on "Insulating behavior of lambda-DNA on the micron scale". Phys. Rev. Lett. 93: 239801.
  • 聽 (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) 聽 A Structure-Function Investigation of a Deoxyribozyme with Dual Chelatase and Peroxidase Activities. Pure and Applied Chemistry (in press)
  • (2003) Duplex Pinching: 聽 A Structural Switch Suitable for Contractile DNA Nanoconstructions. 聽 Nano Letters (Am. Chem. Soc.) 聽 3: 1073-1078.
  • (2003)  Voltammetric procedure for examining DNA-modified surfaces: quantitation, cationic binding activity, and electron-transfer kinetics.  Analytical Chemistry  75: 3902-7.
  •  (2003)  Deoxyribozymes that catalyze photochemistry: cofactor-dependent and -independent photorepair of thymine dimers.  Nucleic Acids Research Suppl.  3: 217-8.
  •  (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.
  •  (2002) Aptamer rivalry.  Chemistry & Biology.  8: 851-2.
  • (2002) A General Strategy for Effector-mediated Control of RNA-cleaving Ribozymes and DNA Enzymes. Journal of Molecular Biology 318, 33-43.
  •  (2002)  Rationally designed allosteric variants of hammerhead ribozymes responsive to the HIV-1 Tat protein. 聽 Combinatorial Chemistry and High Throughput Screening. 5: 301-12.
  • (2002) DNA Conformational Switches as Sensitive Electronic Sensors of Analytes. Journal of the American Chemical Society 124, 4610-4616.
  • (2002) Hemin-Stimulated Docking of Cytochrome c to a Hemin-DNA Aptamer Complex. Biochemistry 41, 5202-5212.
  • (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.
  • (2001) A New and Efficient DNA Enzyme for the Sequence-specific Cleavage of RNA. Journal of Molecular Biology 313, 283-294.
  • (2001) A DNA Oligonucleotide-Hemin Complex Cleaves t-Butyl Hydroperoxide through a Homolytic Mechanism. Inorganic Chemistry 40, 5017-5023.
  • (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.
  • (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.
  • (2000) Use of Intrinsic Binding Energy for Catalysis by a Cofactor-independent DNA Enzyme. Journal of Molecular Biology 299, 1387-1398.
  • (1999) 鈥淪ynapsable鈥� DNA Double Helices: Self-Selective Modules for Assembling DNA Superstructures. Journal of the American Chemical Society 121, 11079-11085.
  • (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.
  • (1998) DNA enzymes. Current Opinion in Chemical Biology 2, 680-687.
  • (1998) DNA-enhanced peroxidase activity of a DNA-aptamer-hemin complex. Chemistry & Biology 5, 505-517.
  • (1998) Cation-regulated Self-association of "Synapsable" DNA Duplexes. Journal of Molecular Biology 280, 237-244.
  • (1998) The modus operandi of a DNA enzyme: enhancement of substrate basicity. Chemistry & Biology 5, 1-12.
  • (1998) Lanthanide Probes for a Phosphodiester-cleaving, Lead-dependent, DNAzyme. Journal of Molecular Biology 275, 483-489.
  • (1997) Evidence for the metal-cofactor independence of an RNA phosphodiester-cleaving DNA enzyme. Chemistry & Biology 4, 579-593.
  • (1997) Toward an Efficient DNAzyme. Biochemistry 36, 5589-5599.
  • (1997) The DNA Structures at the Ends of Eukaryotic Chromosomes. European Journal of Cancer 33, 735-749.
  • (1996) A catalytic DNA for porphyrin metallation. Nature Structural Biology 3, 743-747.
  • (1996) Recognition of Anionic Porphyrins by DNA Aptamers. Biochemistry 35, 6911-6922.
  • (1996) Synapsable DNA. Journal of Molecular Biology 257, 219-224.
  • (1993) Mode of dimerization of HIV-1 genomic RNA. Biochemistry 32, 11453-11457.
  • (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.
  • (1992) Novel DNA superstructures formed by telomere-like oligomers. Biochemistry 31, 65-70.
  • (1992) Guanine quartet structures. Methods in Enzymology 211, 191-199.
  •  (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.
  • (1990) A sodium-potassium switch in the formation of four-stranded G4-DNA. Nature 344, 410-414.
  • (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.