1996-2000

83. L. Sun, M. Wang, E. T. Kool, J.-S. Taylor* Pyrene Nucleotide as a Mechanistic Probe: Evidence for a Transient Abasic Site-like Intermediate in the Bypass of Dipyrimidine Photoproducts by T7 DNA Polymerase, Biochemistry2000, 39, 14603-14610.

82. Juan C. Morales, Eric T. Kool,* A functional H-bonding map of the minor groove binding track of six DNA polymerases, Biochemistry 200039, 12979-12988.

81. Eric T. Kool, The roles of Watson-Crick and minor groove hydrogen bonds in DNA replication, Cold Spring Harbor Symp. Quant. Biol. 2000, 65, 93-102.

80. Eric T. Kool, Synthetically modified DNAs as substrates for polymerases, Curr. Opin. Chem. Biol.   20004, 602-608.

79. Yanzheng Xu and Eric T. Kool,* Rapid, selective selenium-mediated autoligation of DNA strands, J. Am. Chem. Soc. 2000122, 9040-9041.

78. Kevin M. Guckian, Thomas R. Krugh,* Eric T. Kool,* Solution structure of a nonpolar, non-hydrogen bonded base pair surrogate, J. Am. Chem. Soc. 2000122, 6841-6847.

77. Juan C. Morales, Eric T. Kool,* Varied molecular interactions in the active sites of several several DNA polymerases: Nonpolar nucleoside isosteres as probes, J. Am. Chem. Soc. 2000122, 1001-1007.

76. Juan C. Morales, Eric T. Kool,* The importance of terminal base pair hydrogen bonding in 3′ end proofreading by the Klenow fragment of E. coli DNA polymerase I, Biochemistry 200039, 2626-2632.

75. Kevin M. Guckian, B. A. Schweitzer, Rex X.-F. Ren, C. J. Sheils, Deborah C. Tahmassebi, Eric T. Kool,* Factors Contributing to Aromatic Stacking in Water: Evaluation in the context of DNA, J. Am. Chem. Soc. 2000122, 2213-2222.

74. Eric T. Kool,* Juan C. Morales, Kevin M. Guckian, Mimicking the Structures and Functions of DNA: Insights into DNA Stability and Replication, Angew. Chem. Int. Ed. 200039, 990-1009.

73. Tatsuo Ohmichi, Eric T. Kool,* The virtues of self-binding: High sequence specificity by self-processed hammerhead ribozymes, Nucleic Acids Res. 2000, 28, 776-783.

72. Christoph Strässler, Newton E. Davis, Eric T. Kool,* Novel nucleoside analogues with fluorophores replacing the DNA base, Helvetica Chimica Acta 199982, 2160-2171.

71. Peter T. Rowley,* Barbara A. Kosciolek, Eric T. Kool, Circular antisense oligonucleotides inhibit growth of chronic myeloid leukemia cells, Molecular Medicine 19995, 693-700.

70. Miriam Frieden, Enrique Pedroso,* Eric T. Kool,* Tightening the belt on polymerases: Evaluating the physical constraints on enzyme substrate size,   Angew. Chem. Int. Ed. 199938, 3654-3657.

69. Amy M. Diegelman and Eric T. Kool,* Mimicry of the hepatitis delta virus replication cycle mediated by synthetic circular oligodeoxynucleotides, Chemistry & Biology 19996, 569-576.

68. H. Hansma,* R. Golan, W. Hsieh, S. L. Daubendiek, E. T. Kool, Polymerase activities and RNA structures in the atomic force microscope. J. Struct. Biol. 1999127, 240-247.

67. Tracy J. Matray and Eric T. Kool*, A specific partner for abasic damage in DNA,  Nature 1999399, 704-708.

66. Daniel Barsky, Michael Colvin,* Eric T. Kool, Interaction and solvation energies of nonpolar DNA base analogues and their role in polymerase insertion fidelity, J. Biomol. Struct. Dyn. 199916, 1119-1134.

65. N. H. Thomson, B. L. Smith,* N. Almqvist, L. Schmitt, M. Kashlev, E. T. Kool, P. K. Hansma, Oriented, active Escherichia coli RNA polymerase: an atomic force microscope study, Biophys. J. 199976, 1024-1033.

64. Juan C. Morales, Eric T. Kool,* Minor groove interactions between polymerase and DNA: More essential than Watson-Crick bonds?, J. Am. Chem. Soc. 1999121, 2723-2724.

63. Yanzheng Xu and Eric T. Kool,* High sequence fidelity in nonenzymatic autoligation of oligodeoxynucleotides, Nucleic Acids Res. 199927, 875-881.

62. Hecht, M. H., Hindsgaul, O., Eric T. Kool,* Biopolymers. Curr. Opin. Chem. Biol 19982, 673-674.

61. Kevin M. Guckian, Juan C. Morales, Eric T. Kool,* Structure and base pairing properties of a replicable nonpolar isostere for deoxyadenosine, J. Org. Chem. 199863, 9652-9656.

60. Kevin M. Guckian, Thomas R. Krugh,* Eric T. Kool,* Solution structure of a duplex DNA containing a replicable difluorotoluene-adenine pair, Nature Structural Biology 19985, 954-959.

59. Eric T. Kool, A mechanism for shape selection during DNA synthesis, Biopolymers (Nucleic Acid Sciences) 199848, 3-17.

58. Amy M. Diegelman, Eric T. Kool,* Methods for preparation of circular single-stranded DNAs, Current Protocols in Nucleic Acid Chemistry 1999.

57. Amy M. Diegelman, Sarah L. Daubendiek, Eric T. Kool,* Generation of RNA ladders by rolling circle transcription of small circular oligodeoxynucleotides, BioTechniques 199825, 754-758.

56. Juan C. Morales and Eric T. Kool,* Efficient replication of a DNA base pair between non-hydrogen-bonded nucleoside analogues, Biopolymers. 199848, 3-17.

55. Pamela L. Paris, Joseph Langenhan, Eric T. Kool,* Probing DNA sequences in solution with a monomer – excimer color change, Nucleic Acids Res. 199826, 3789-3793.

54. Yanzheng Xu and Eric T. Kool,* Chemical and enzymatic properties of 5′-bridging phosphorothioester linkages in DNA, Nucleic Acids Res. 199826, 3159-3164.

53. Tracy J. Matray and Eric T. Kool,* Selective and stable DNA base pairing without hydrogen bonds, J. Am. Chem. Soc. 1998120, 6191-6192.

52. Amy M. Diegelman and Eric T. Kool,* Generation of circular RNAs and catalytic RNAs by transcription of circular DNA oligonucleotides encoding hairpin ribozymes, Nucleic Acids Res. 199826, 3235-3241.

51. Eric T. Kool, Recognition of DNA, RNA, and proteins by circular oligonucleotides, Accounts Chem. Res. 199831, 502-510.

50. Kevin Ryan, Eric T. Kool,* Triplex-directed self-assembly of an artificial sliding clamp on duplex DNA, Chemistry & Biology 19985, 59-67.

49. Kevin M. Guckian, Eric T. Kool,* Highly precise shape mimicry by difluorotoluene deoxynucleoside, a replication-competent substitute for thymidine, Angew. Chem. Int. Ed. 199836, 2825-2828.

48. Eric T. Kool, “Topologically Modified DNA,” chapter in Comprehensive Natural Products Chemistry, vol.VII, Elsevier Press: Oxford, UK, 1998.

47. Dongyu Liu, Sean Moran, Eric T. Kool,* Bistranded, multisite replication of an unconventional difluorotoluene-adenine base pair and confirmation by “inverse” sequencing, Chemistry & Biology 19974, 919-926.

46. Sean Moran, Rex X.-F. Ren, Eric T. Kool,* A thymidine triphosphate shape mimic lacking Watson-Crick pairing ability is replicated with high specificity, Proc. Natl. Acad. Sci. USA 199794, 10506-10511.

45. W. Sun, S. Hattman*,   Eric Kool, Interaction of the bacteriophage Mu transcriptional activator protein, C, with its target site in the mom promoter,   J. Mol. Biol 1997273, 765-774.

44. Yanzheng Xu and Eric T. Kool,* A novel 5′-iodonucleoside allows efficient nonenzymatic ligation of single-stranded and duplex DNAs, Tetrahedron Lett. 199738, 5595-5598.

43. Vineet Gupta and Eric T. Kool,* A self-cleaving DNA nucleoside, Chem. Commun. 1997, 1425-1426.

42. Sarah L. Daubendiek and Eric T. Kool,* Generation of catalytic RNAs by rolling transcription of synthetic DNA nanocircles, Nature Biotechnology 199715, 273-277.  

41. Sean Moran, Rex X.-F. Ren, Squire Rumney, Eric T. Kool,* Difluorotoluene, a nonpolar isostere of thymine, codes specifically and efficiently for adenine in DNA replication, J. Am. Chem. Soc. 1997119, 2056-2057.

40. Shaohui Wang, Yanzheng Xu, Eric T. Kool,* Recognition of RNA by triplex formation: Divergent effects of pyrimidine C-5 methylation, BioMed. Chem. 19975, 1043-1050.

39. Eric T. Kool,* Preorganization strategies for improving the recognition properties of DNA, Chem. Rev. 199797, 1473-1487.

38. Sandor Kasas, Neil H. Thomson, Bettye Smith, Helen G. Hansma, Xingshu Zhu, Martin Guthold, Carlos Bustamente, Eric T. Kool, Mikhail Kashlev, Paul K. Hansma,* E.Coli RNA polymerase structure and activity observed by atomic force microscopy, Biochemistry 199736, 461-468.

37. Eric T. Kool,* Design of oligonucleotides for binding DNA and RNA:   optimizing affinity and selectivity, New Journal of Chemistry 199721, 33-45.

36. Narayan C. Chaudhuri, Rex X.-F. Ren, Eric T. Kool,* C-nucleosides Derived from Simple Aromatic Hydrocarbons, SYNLETT 1997, 341-347.

35. Kevin Guckian, Barbara A. Schweitzer, Rex X.-F. Ren, Charles J. Sheils, Pamela L. Paris, Deborah C. Tahmassebi and Eric T. Kool,* Experimental measurement of aromatic stacking in the context of duplex DNA, J. Am. Chem. Soc. 1996118, 8182-8183.

34. Rex X.-F. Ren, Narayan C. Chaudhuri, P. L. Paris, S. Rumney IV, Eric T. Kool,* Naphthalene, Phenanthrene, and Pyrene as DNA base analogues:   Synthesis, Structure, and Fluorescence in DNA, J. Am. Chem. Soc. 1996118, 7671-7678.

33. Sean Moran, Rex X.-F. Ren, Charles J. Sheils, Squire Rumney IV, Eric T. Kool,* Synthetic Terminator Nucleosides Increase 3′ end Homogeneity in Enzymatic RNA/DNA Synthesis, Nucleic Acids Res. 199624, 2044-2052.

32. B. A. Schweitzer, C. J. Sheils, X.-F. Ren, N. C. Chaudhuri, Eric T. Kool,* Hydrophobic Nucleoside Isosteres as Biophysical Probes of Noncovalent Interactions:   Analysis of Structure and Electrostatics, in Biological Structure and Dynamics , vol. 2, R. H. Sarma, M. H. Sarma, Eds., Adenine Press: Albany, 1996, pp. 209-216.

31. Xiao-Feng Ren, Barbara A. Schweitzer, Charles J. Sheils, Eric T. Kool*, Stable DNA Loop Formation by Hydrophobic Nucleoside Isosteres, Angew. Chem. 1996108, 834-837; Angew. Chem. Int. Ed. Engl. 199635, 743-746.

30. Dongyu Liu, Sarah L. Daubendiek, Martin A. Zillmann, Kevin Ryan, Eric T. Kool,* Rolling Circle DNA Synthesis:   Small Circular Oligonucleotides as Efficient Templates for DNA Polymerases, J. Am. Chem. Soc. 199611, 1587-1594.

29. Eric T. Kool,* Topological Modification of Oligonucleotides as Potential Inhibitors of Gene Expression, Perspectives in Drug Discovery and Design 19964, 61-75.

28. Eric T. Kool,* Circular Oligonucleotides:   New Concepts in Oligonucleotide Design, Ann. Rev. Biophys. Biomol. Struct. 199625, 1-28.