2006-2010

207. Sarah K. Jarchow-Choy, Andrew T. Krueger, Haibo Liu, Jianmin Gao and Eric T. Kool,* Fluorescent xDNA Nucleotides as Efficient Substrates for a Template-independent Polymerase, Nucleic Acids Res., 2010, 39, 1586-1594.

206. Daniel J. Kleinbaum and Eric T. Kool,* Sandwich Probes: Two Simultaneous Reactions for Templated Nucleic Acid Detection, Chem. Comm., 2010, 46, 8154-8156.

205. Samuel S. Tan, Yin Nah Teo and Eric T. Kool,* Selective Sensor for Silver Ions Built from Polyfluorophores on a DNA Backbone, J. Org. Chem., 2010, 12, 4820-4823.

204. Hao Li, Raphael M. Franzini, Christopher Bruner and Eric T. Kool,* Templated Chemistry for Sequence-Specific Fluorogenic Detection of Duplex DNA, ChemBioChem, 2010, 11, 2132-2137.

203. Florent Samain, Samantak Ghosh, Yin Nah Teo and Eric T. Kool,* Polyfluorophores on a DNA Backbone: Sensors of Small Molecules in the Vapor Phase, Angew. Chem. Int. Ed.2010, 49, 7025-7029.

202. Tom Killelea, Samantak Ghosh, Samuel S. Tan, Pauline Heslop, Susan J. Firbank, Eric T. Kool and Bernard A. Connolly,* Probing the Interaction of Archaeal DNA Polymerases with Deaminated Bases Using X-ray Crystallography and Non-Hydrogen Bonding Isosteric Base Analogues, Biochemistry, 2010, 49, 5772-5781.

201. D.J. Kleinbaum, Gregory P. Miller and Eric T. Kool,* Double Displacement: An Improved Bioorthogonal Reaction Strategy for Templated Nucleic Acid Detection, Biocongj. Chem., 2010, 21, 1115-1120.

200. Haige Lu, Andrew T. Krueger, Jianmin Gao, Haibo Liu and Eric T. Kool,* Toward a designed genetic system with biochemical function: polymerase synthesis of single and multiple size-expanded DNA base pairs, Org. Biomol. Chem., 2010, 8, 2704-2710.

199. Nan Dai, Yin Nah Teo and Eric T. Kool,* DNA-Polyfluorophore Excimers as Sensitive Reporters for Esterases and Lipases, Chem. Commun., 2010, 46, 1221-1223.

198. Yin Nah Teo and Eric T. Kool,* Polyfluorophore excimers and exciplexes as FRET donors in DNA, Biocong. Chem., 2009, 20, 2371-2380.

197. Haige Lu, Stephen R. Lynch, Alex H. F. Lee and Eric T. Kool,* Structure and Replication of yDNA: A Novel Genetic Set Widened by Benzo-Homologation, ChemBioChem, 2009, 10, 2530-2538.

196. Yin Nah Teo, James N. Wilson and Eric T. Kool,* Polyfluorophore Labels on DNA: Dramatic Sequence Dependence of Quenching, Chem. Eur. J., 2009, 15, 11551-11558.

195. David Loakes, Jose Gallego, Vitor B. Pinheiro, Eric T. Kool and Philipp Holliger,* Evolving a Polymerase for Hydrophobic Base Analogues, J. Am. Chem. Soc. 2009, 131, 14827-14837.

194. Raphael M. Franzini and Eric T. Kool,* Efficient Nucleic Acid Detection by Templated Reductive Quencher Release, J. Am. Chem. Soc. 2009, 131, 16021-16023.

193. James C. Delaney, Jianmin Gao, Haibo Liu, Nidhi Shrivastav, John M. Essigmann and Eric T. Kool,* Efficient Replication Bypass of Size-Expanded DNA Base Pairs in Bacterial Cells, Angew. Chem. Int. Ed. 2009, 48, 4524-4527.

192. Andrew T. Krueger and Eric T. Kool,* Redesigning the Architecture of the DNA Base Pair: Toward Biochemical and Biological Function of New Genetic Sets, Chem. Biol. 2009, 16, 242-248.

191. Sarah K. Jarchow-Choy, Elena Sjuvarsson, Herman O. Sintim, Staffan Eriksson and Eric T. Kool,* Nonpolar Nucleoside Mimics as Active Substrates for Human Thymidine Kinases, J. Am. Chem. Soc. 2009, 131, 5488-5494.

190. Yin Nah Teo, James N. Wilson and Eric T. Kool,* Polyfluorophores on a DNA Backbone: A Multicolor Set of Labels Excited at One Wavelength, J. Am. Chem. Soc. 2009, 131, 3923-3933.

189. Montse Terrazas and Eric T. Kool,* RNA Major Groove Modifications Improve siRNA Stability and Biological Activity, Nucleic Acids Res. 2009, 37, 346-353.

188. Andrew T. Krueger, Haige Lu, Torben Hojland, Haibo Liu, Jainmin Gao and Eric T. Kool,* Toward the Replication of xDNA, a Size-expanded Unnatural Genetic System, Nucleic Acids Symp. Ser. 2008, 52, 455-456.

187. Yin Nah Teo and Eric T. Kool,* Studies of Oligodeoxyfluorosides (ODFs) as FRET Probes for DNA Hybridization,Nucleic Acids Symp. Ser. 2008, 52, 233-234.

186. Raphael M. Franzini and Eric T. Kool,* 7-Azidomethoxy-Coumarins as Profluorophores for Templated Nucleic Acid Detection, ChemBioChem. 2008, 9, 2981-2988.

185. Jijumon Chelliserrykattil, Haige Lu, Alex H. F. Lee and Eric T. Kool,* Polymerase Amplification, Cloning, and Gene Expression of Benzohomolgous “yDNA” Base Pairs, ChemBioChem. 2008, 9, 2976-2980.

184. Alvaro Somoza, Adam P. Silverman, Rand M. Miller, Jijumon Chelliserrykattil and Eric T. Kool,* Steric Effects in RNA Interference: Probing the Influence of Nucleobase Size and Shape, Chem. Eur. J. 2008, 14, 7978-7987.

183. Andrea K. Pomerantz, Eric T. Kool,* and W. E. Moerner* Visualization of Long Telomere Mimics by Single-Molecule Fluorescence Imaging, J. Phys. Chem. B. 2008, 112, 13184-13187.

182. Adam P. Silverman, Hiroshi Abe and Eric T. Kool,* Quenched autoligation probes, Methods Mol. Biol. 2008,429, 161-170.

181. Alison L. Livingston, Valerie L. O’Shea, Taewoo Kim, Eric T. Kool, and Sheila S. David,* Unnatural Substrates Reveal the Importance of 8-oxoguanine for in vivo Mismatch Repair by MutY, Nat. Chem. Bio. 2008, 4, 51-58.

180. Rapheal M. Franzini and Eric T. Kool,* Organometallic Activation of a Fluorogen for Templated Nucleic Acid Detection, Org. Lett. 2008, 10, 2935-2938.

179. Harold R. Lee, Sandra A. Helquist, Eric T. Kool,* and Kenneth A. Johnson* Base Pair Hydrogen Bonds are Essential for Proofreading Selectivity by the Human Mitochondrial DNA Polymerase, J. Biol. Chem. 2008, 283, 14411-14416.

178. Harold R. Lee, Sandra A. Helquist, Eric T. Kool,* and Kenneth A. Johnson* Importance of Hydrogen Bonding for Efficiency and Specificity of the Human Mitochondrial DNA Polymerase, J. Biol. Chem. 2008, 283, 14402-14410.

177. Adam P. Silverman, Scott J. Garforth, Vinayaka R. Prasad, Eric T. Kool,* Probing the Active Site Steric Flexibility of HIV-1 Reverse Transcriptase: Different Constraints for DNA versus RNA-Templated Synthesis,Biochemistry 2008, 47, 4800-4807.

176. Andrew T. Krueger and Eric T. Kool,* Fluorescence of Size-Expanded DNA Bases: Reporting on DNA Sequence and Structure with an Unnatural Genetic Set, J. Am. Chem. Soc. 2008, 130, 3989-3999.

175. James N. Wilson, Younjin Cho, Samuel S. Tan, Andrea Cuppoletti, Eric T. Kool,* Quenching of fluorescent nucleobases by neigboring DNA: The “Insulator” concept, ChemBioChem 2008, 2, 279-285.

174. Gregory P. Miller, Adam P. Silverman and Eric T. Kool,* New, Stronger Nucleophiles for Nucleic Acid-Templated Chemistry: Synthesis and Application in Fluorescence Detection of Cellular RNA, Bioorg. Med. Chem. 2008, 16, 56-64.

173. James N. Wilson, Jianmin Gao, Eric T. Kool,* Oligodeoxyfluorosides: Strong Sequence Dependence of Fluorescence Emission, Tetrahedron 2007, 63, 3427-3433.

172. Andrew T. Krueger and Eric T. Kool,* Model Systems for Understanding DNA Base Pairing, Curr. Op. Chem. Biol. 2007, 11, 588-594.

171. James N. Wilson, Yin Nah Teo, and Eric T. Kool,* Efficient Quenching of Oligomeric Fluorophores on a DNA Backbone, J. Am. Chem. Soc. 2007, 129, 15426-15427.

170. Adam P. Silverman, Qingfei Jiang, Myron F. Goodman,* and Eric T. Kool,* Steric and Electrostatic Effects in DNA Synthesis by the SOS-Induced Polymerase II and IV of Escherichia Coli, Biochemistry 2007, 46, 13874-13881.

169. Adam P. Silverman and Eric T. Kool,* RNA Probes of Steric Effects in Active Sites: High Flexibility of HIV-1 Reverse Transcriptase, J. Am. Chem. Soc. 2007, 129, 10626-10627.

168. Yosuke Taniguchi and Eric T. Kool,* Synthesis and properties of low-polarity mimics of 8-oxopurines, Nucleic Acids Symp. Ser. 2007, 51, 217-218.

167. Yosuke Taniguchi and Eric T. Kool,* Nonpolar Isosteres of Damaged DNA Bases: Effective Mimicry of Mutagenic Properties of 8-Oxopurines, J. Am. Chem. Soc. 2007, 129, 8836-8844.

166. Eric T. Kool and Marcy L. Waters, The Model Student: What Chemical Model Systems Can Teach Us About Biology, Nat. Chem. Bio. 2007, 3, 70-73.

165. Scott J. Garforth, Tae Woo Kim, Michael A. Parniak, Eric T. Kool* and Vinayaka R. Prasad,* Site-Directed Mutagenesis in the Fingers Subdomain of HIV-1 Reverse Transcriptase Reveals a Specific Role for the b3-b4 Hairpin Loop in dNTP Selection, J. Mol. Bio. 2007, 365, 38-49.

164. Adam P. Silverman and Eric T. Kool,* Oligonucleotide Probes for RNA-Targeted Fluorescence In Situ Hybridization, Adv. Clin. Chem. 2007, 43, 79-115.

163. Andrew T. Krueger, Haige Lu, Alex H.F. Lee and Eric T. Kool,* Synthesis and Properties of Size-Expanded DNAs: Toward Designed, Functional Genetic Systems, Acc. Chem. Res. 2007, 40, 141-150.

162. James N. Wilson and Eric T. Kool,* Fluorescent DNA Base Replacements: Reporters and Sensors for Biological Systems, Org. Biomol. Chem. 2006, 4, 4265-4274.

161. Eric T. Kool,* Haige Lu, Su Jeong Kim, Samuel Tan, James N. Wilson, Jianmin Gao, and Haibo Liu; New Designs for DNA Bases: Expanded DNAs and Oligofluorosides, Nucleic Acids Symp. Ser. 2006, 50, 15-16.

160. Adam P. Silverman, Ellen J. Baron, Eric T. Kool,* RNA-Templated Chemistry in Cells: Discrimination of Escherichia, Shigella, and Salmonella Bacterial Strains With a New Two-Color FRET Strategy, ChemBioChem 2006,7, 1890-1894.

159. Lyudmila Yakovleva, Jacob S. Lai, Eric T. Kool,* and Stewart Shuman,* Nonpolar Nucleobase Analogs Illuminate Requirements for Site-Specific DNA Cleavage by Vaccinia Topoisomerase, J. Biol. Chem. 2006, 281,35914-35921.

158. Herman O. Sintim and Eric T. Kool,* The Difluorotoluene Debate–A Decade Later, Chem. Comm. 2006, 35,3665-3675.

157. Adam P. Silverman and Eric T. Kool,* Detecting DNA and RNA with Templated Chemical Reactions, Chem. Rev.2006, 106, 3775-3789.

156. Stephen R. Lynch, Haibo Lu, Jianmin Gao and Eric T. Kool,* Toward a Designed, Functioning Genetic System with Expanded-Size Base Pairs: Solution Structure of the Eight-Base xDNA Double Helix, J. Am Chem. Soc. 2006128, 14704-14711.

155. Alvaro Somoza, Jijumon Chelliserrykattil and Eric T. Kool,* The Roles of Hydrogen Bonding and Sterics in RNA Interference, Angew. Chem. Int. Ed. 200645, 4994-4997.

154. Alex H. F. Lee and Eric T. Kool,* Exploring the Limits of DNA Size: Naphtho-Homologated DNA Bases and Pairs, J. Am Chem. Soc. 2006128, 9219-9230.

153. Su Jeong Kim and Eric T. Kool,* Sensing Metal Ions with DNA Building Blocks: Fluorescent Pyridobenzimidazole Nucleosides, J. Am Chem. Soc. 2006128, 6164-6171.

152. C. Hariharan, L. B. Bloom, S. A. Helquist, E. T. Kool, L. J. Reha-Krantz,* Dynamics of Nucleotide Incorporation:   Snapshots Revealed by 2-Aminopurine Fluorescence Studies, Biochemistry 200645, 2836-2844.

151. Herman O. Sintim and Eric T. Kool,* Remarkable Sensitivity to DNA Base Shape in the DNA Polymerase Active Site, Angew. Chem. Int. Ed. 200645, 1974-1979.

150. Shin Mizukami, Tae W . Kim, Sandra A. Helquist, Eric T. Kool,* Varying DNA Base Pair Size in Sub-Angstrom Increments:   Evidence for a Loose, Not Large, Active Site in Low-fidelity Dpo4 Polymerase, Biochemistry 200645, 2772-2778.

149. Y. Cho, Eric T. Kool,* Enzymatic synthesis of fluorescent oligomers assembled on a DNA backbone,ChemBioChem 20067, 669-672.

148. Herman O. Sintim and Eric T. Kool,* Enhanced Base Pairing and Replication Efficiency of Thiothymidines, Expanded-size Variants of Thymidine, J. Am. Chem. Soc. 2006128, 396-397.

147. Hiroshi Abe and Eric T. Kool,* Flow cytometric detection of specific RNAs in native human cells with quenched autoligating FRET probes, Proc. Natl. Acad. Sci. USA 2006103, 263-268.

146. Tae Woo Kim, Luis G. Brieba, Tom Ellenberger , Eric T. Kool,* Functional evidence for a small and rigid active site in a high-fidelity DNA polymerase:   Probing T7 DNA Pol with variable-sized base pairs, J. Biol. Chem. 2006281, 2289-2295.

145. Olga Potapova, C. Chan, Angela M. DeLucia, Sandra A. Helquist, Eric T. Kool, Nigel D. F. Grindley and Catherine M. Joyce* DNA polymerase catalysis in the absence of Watson-Crick hydrogen bonds: analysis by single-turnover kinetics, Biochemistry 200645, 890-898.