Literature Highlights Archive  Highlight Date Title Reference Link November 2008 Examining the ribonuclease H primer grip of HIV-1 reverse transcriptase by charge neutralization of RNA/DNA hybrids Chandravanu Dash, Brian J. Scarth, Christopher Badorrek, Matthias Götte, and Stuart F. J. Le Grice Nucleic Acids Res., Oct 2008; 10.1093/nar/gkn678 Nucleic Acids Res., Oct 2008; 10.1093/nar/gkn678 October 2008 Directed Evolution of Streptavidin Variants Using In Vitro Compartmentalization Matthew Levy and Andrew D. Ellington SAevol.pdf http://www.glenres.com/Literature/SAevol.pdf September 2008 The triple helix: 50 years later, the outcome Maria Duca, Pierre Vekhoff, Kahina Oussedik, Ludovic Halby, and Paola B. Arimondo Nucleic Acids Res. published 1 August 2008, 10.1093/nar/gkn493 Open Access http://nar.oxfordjournals.org/cgi/content/abstract/gkn493v1?ct=ct Pyrrolo-C as a molecular probe for monitoring conformations of the tRNA 3' end Chun-Mei Zhang, Cuiping Liu, Thomas Christian, Howard Gamper, Jef Rozenski, Dongli Pan, John B Randolph, Eric Wickstrom, Barry S Cooperman, and Ya-Ming Hou RNA 28 Aug 2008 http://highwire.stanford.edu/cgi/medline/pmid;18755841 August 2008 Four-color DNA sequencing with 3'-O-modified nucleotide reversible , terminators and chemically cleavable fluorescent dideoxynucleotides Jia Guo, Ning Xu, Zengmin Li, Shenglong Zhang, Jian Wu, Dae Hyun Kim, Mong Sano Marma, Qinglin Meng, Huanyan Cao, Xiaoxu Li, Shundi Shi, Lin , Yu, Sergey Kalachikov, James J. Russo, Nicholas J. Turro, and Jingyue , Ju PNAS. 2008; 105(27): p. 9145-9150 Open Access http://www.glenres.com/Literature/PNAS-2008-Guo-9145-50.pdf http://www.glenres.com/Literature/RNAS-2008-Guo-Support.pdf July 2008 Real-Time Reverse Transcription-PCR Assay for Comprehensive Detection of Human Rhinoviruses Xiaoyan Lu, Brian Holloway, Ryan K. Dare, Jane Kuypers, Shigeo Yagi, John V. Williams, Caroline B. Hall, and Dean D. Erdman J. Clin. Microbiol., Feb 2008; 46: 533 - 539 http://www.glenres.com/Literature/Lu_Holloway_JClinMicrob533.pdf June 2008 Formation of the double helix: a mutational study Mehrdad Majlessi and Michael M. Becker Nucleic Acids Res. 2008; 36(9): p. 2981-2989 Open Access http://nar.oxfordjournals.org/cgi/content/abstract/36/9/2981?ct=ct May 2008 Mismatch formation in solution and on DNA microarrays: how modified nucleosides can overcome shortcomings of imperfect hybridization caused by oligonucleotide composition and base pairing. Frank Seela and Simone Budow Mol Biosyst 2008, 4, (3), 232-245 http://www.rsc.org/publishing/journals/MB/article.asp?doi=b713259j April 2008 DNA binding shifts the redox potential of the transcription factor SoxR Alon A. Gorodetsky, Lars E. P. Dietrich, Paul E. Lee, Bruce Demple, Dianne K. Newman, and Jacqueline K. Barton PNAS. 2008; 105(10): p. 3684-3689 http://www.pnas.org/cgi/content/abstract/105/10/3684?ct=ct March 2008 Microarray analysis using disiloxyl 70mer oligonucleotides Marcus Gry Bjorklund, Christian Natanaelsson, Amelie Eriksson, Karlstrom, Yong Hao, and Joakim Lundeberg Nucleic Acids Res. 2008; 36(4): p. 1334-1342 Open Access http://nar.oxfordjournals.org/cgi/content/abstract/36/4/1334?ct=ct February 2008 Isoenergetic penta- and hexanucleotide microarray probing and chemical mapping provide a secondary structure model for an RNA element orchestrating R2 retrotransposon protein function Elzbieta Kierzek, Ryszard Kierzek, Walter N. Moss, Shawn M. Christensen, Thomas H. Eickbush, and Douglas H. Turner Nucleic Acids Res. published 5 February 2008, 10.1093/nar/gkm1085 Open Access http://nar.oxfordjournals.org/cgi/content/abstract/gkm1085v1?ct=ct January 2008 Three essential and conserved regions of the group II intron are proximal to the 5'-splice site Alexandre de Lencastre and Anna Marie Pyle NA. 2007; 14(1): p. 11-24 Open Access http://www.rnajournal.org/cgi/content/abstract/14/1/11?ct=ct December 2007 High-throughput Generation of Synthetic Antibodies from Highly Functional Minimalist Phage-displayed Libraries Frederic A. Fellouse1, Kaori Esaki, Sara Birtalan, Demetrios Raptis, Vincenzo J. Cancasci, Akiko Koide, Parkash Jhurani, Mark Vasser Christian Wiesmann, Anthony A. Kossiakoff Shohei Koide and Sachdev S. Sidhu JMB_YSX.pdf JMB_YSX.pdf November 2007 Trans-lesion synthesis and RNaseH activity by reverse transcriptases on a true abasic RNA template Pascal A. Kupfer, Caroline Crey-Desbiolles, and Christian J. Leumann Nucleic Acids Res. 2007; 35(20): p. 6846-6853 Open Access http://nar.oxfordjournals.org/cgi/content/abstract/35/20/6846?ct=ct October 2007 DNA polymerase proofreading: active site switching catalyzed by the bacteriophage T4 DNA polymerase Elizabeth Fidalgo da Silva and Linda J. Reha-Krantz Nucleic Acids Res. 2007; 35(16): p. 5452-5463 Open Access http://nar.oxfordjournals.org/cgi/content/abstract/35/16/5452?ct=ct September 2007 Fluorescent nucleoside analogs: synthesis, properties and applications Guest editor: Yitzhak Tor Tetrahedron Vol. 63, No. 17, 2007 http://www.glenres.com/Literature/TET_2007_63_17.pdf August 2007 Synthesis and investigation of deoxyribonucleic acid/locked nucleic acid chimeric molecular beacons Chaoyong James Yang, Lin Wang, Yanrong Wu, Youngmi Kim, Colin D. Medley, Hui Lin,  and Weihong Tan Nucleic Acids Res. 2007;  35(12): p. 4030-4041 Open Access http://nar.oxfordjournals.org/cgi/content/abstract/35/12/4030?ct=ct July 2007 Enzymatic incorporation of a third nucleobase pair Zunyi Yang, A. Michael Sismour, Pinpin Sheng, Nyssa L. Puskar, and Steven A. Benner Nucleic Acids Res. published 18 June 2007, 10.1093/nar/gkm395 Open Access http://nar.oxfordjournals.org/cgi/content/abstract/gkm395v1?ct=ct June 2007 Nucleoside alpha-thiotriphosphates, polymerases and the exonuclease III analysis of oligonucleotides containing phosphorothioate linkages Zunyi Yang, A. Michael Sismour,  and Steven A. Benner Nucleic Acids Res. 2007;  35(9): p. 3118-3127 Open Access http://nar.oxfordjournals.org/cgi/content/abstract/35/9/3118?ct=ct May 2007 Tolerance of RNA Interference Toward Modifications of the 5' Antisense Phosphate of Small Interfering RNA Samit Shah, Simon H. Friedman Nucleic Acids Res. published 22 April 2007, 10.1093/nar/gkm234 Open Access http://www.liebertonline.com/doi/abs/10.1089/oli.2006.0067 OligoCalc: an online oligonucleotide properties calculator Warren A. Kibbe Nucleic Acids Res. 2006;  34(22): p. 6521-6529 Open Access http://nar.oxfordjournals.org/cgi/content/abstract/gkm234v1?ct=ct April 2007 Reversible site-specific tagging of enzymatically synthesized RNAs using aldehyde-hydrazine chemistry and protease-cleavable linkers Stephanie Pfander, Roberto Fiammengo, Srecko I. Kirin, Nils Metzler-Nolte, and Andres Jaschke Nucleic Acids Res. 2007; 35(4): p. e25 Open Access http://nar.oxfordjournals.org/cgi/content/abstract/35/4/e25?ct=ct March 2007 High-throughput Fluorescence Labelling of Full-length cDNA Products Based on a Reconstituted Translation System Yuko Kawahashi, Nobuhide Doi, Yo Oishi, Chizuru Tsuda, Hideaki  Takashima, Tomoya Baba, Hirotada Mori, Takashi Ito,  and Hiroshi Yanagawa J. Biochem. (Tokyo). 2007;  141(1): p. 19-24 Paper Abstract (http://jb.oxfordjournals.org/cgi/content/abstract/141/1/19?ct=ct) February 2007 Novel DNA probes with low background and high hybridization-triggered fluorescence Eugeny A. Lukhtanov, Sergey G. Lokhov, Vladimir V. Gorn, Mikhail A. Podyminogin, and Walt Mahoney Nucleic Acids Res. 2007; 35(5): p. e30 Open Access http://nar.oxfordjournals.org/cgi/content/abstract/35/5/e30?ct=ct January 2007 The chemical stability of abasic RNA compared to abasic DNA Pascal A. Kupfer and Christian J. Leumann Nucleic Acids Res. 2007 35: 58-68 http://nar.oxfordjournals.org/cgi/content/abstract/35/1/58?etoc Sequence-dependent formation of intrastrand crosslink products from the UVB irradiation of duplex DNA containing a 5-bromo-2'-deoxyuridine or 5-bromo-2'-deoxycytidine Yu Zeng and Yinsheng Wang Nucleic Acids Res. 2006;  34(22): p. 6521-6529 Open Access http://nar.oxfordjournals.org/cgi/content/abstract/34/22/6521?ct=ct December 2006 Mimicking damaged DNA with a small molecule inhibitor of human UNG2 Daniel J. Krosky, Mario A. Bianchet, Lauren Seiple, Suhman Chung, L., Mario Amzel, and James T. Stivers Nucleic Acids Res. 2006; 34(20): p. 5872-5879 Open Acces http://nar.oxfordjournals.org/cgi/content/abstract/34/20/5872?ct=ct November 2006 Solid-phase translation and RNA protein fusion: a novel approach for folding quality control and direct immobilization of proteins using anchored mRNA Manish Biyani, Yuzuru Husimi and Naoto Nemoto Nucleic Acids Research, 2006, Vol. 00, No. 00 http://nar.oxfordjournals.org/cgi/content/abstract/gkl771v1Ê October 2006 Dynamic assembly of primers on nucleic acid templates Nicole A. Leal, Makoto Sukeda,Ê and Steven A. Benner Nucleic Acids Res. published 28 September 2006, 10.1093/nar/gkl625 Open Access http://nar.oxfordjournals.org/cgi/content/abstract/gkl625v2?ct=ct Controlling activation of the RNA-dependent protein kinase by siRNAs using site-specific chemical modification Sujiet Puthenveetil, Landon Whitby, Jin Ren, Kevin Kelnar, Joseph F. Krebs, and Peter A. Beal Nucleic Acids Res. published 18 September 2006, 10.1093/nar/gkl464 Open Access http://nar.oxfordjournals.org/cgi/content/abstract/gkl464v1?ct=ct September 2006 Chemical synthesis of oligodeoxyribonucleotides containing the Dewar valence isomer of the (6-4) photoproduct and their use in (6-4) photolyase studies Junpei Yamamoto, Kenichi Hitomi, Takeshi Todo,¾and Shigenori Iwai Nucleic Acids Res. published 26 August 2006, 10.1093/nar/gkl572 Open Access http://nar.oxfordjournals.org/cgi/content/abstract/gkl572v1?ct=ct August 2006 IPyrene binary probes for unambiguous detection of mRNA using time-resolvedû fluorescence spectroscop Angel A. Marti, Xiaoxu Li, Steffen Jockusch, Zengmin Li, BinduûRaveendra, Sergey Kalachikov, James J. Russo, Irina Morozova, Sathyanarayanan V. Puthanveettil, Jingyue Ju, and Nicholas J. Turro Nucleic Acids Res. 2006;û 34(10): p. 3161-3168 Open Access http://nar.oxfordjournals.org/cgi/content/full/34/10/3161 Widespread siRNA "off-target" transcript silencing mediated by seed region sequence complementarity Aimee L. Jackson, Julja Burchard, Janell Schelter, B. Nelson Chau, Michele Cleary, Lee Lim, and Peter S. Linsley RNA. 2006;û 12(7): p. 1179-1187 Open Access http://www.rnajournal.org/cgi/content/short/rna.25706v1 July 2006 Formation of N-branched oligonucleotides as by-products in solid-phase oligonucleotide synthesis Cazenave C, Bathany K, Rayner B Oligonucleotides 16 (2): 181-185 2006 http://www.liebertonline.com/doi/abs/10.1089/oli.2006.16.181 (PDF) June 2006 Improvement of an Unusual Twin-Arginine Transporter Leader Peptide by a Codon-Based Randomization Approach Olga Monroy-Lagos, Xavier Soberon, Paul Gaytan, and Joel Osuna Appl. Envir. Microbiol. 2006;û 72(5): p. 3797-3801 http://aem.asm.org/cgi/content/abstract/72/5/3797 Electron trap for DNA-bound repair enzymes: A strategy for DNA-mediated signaling Eylon Yavin, Eric D. A. Stemp, Valerie L. OShea, Sheila S. David, and Jacqueline K. Barton PNAS; March 7, 2006; vol. 103; no. 10; 3610-3614û http://www.pnas.org/cgi/content/abstract/103/10/3610 May 2006 Tumor Targeting by an Aptamer Arian J. Hicke, Andrew W. Stephens, Ty Gould, Ying-Fon Chang, Cynthia K. Lynott, James Heil, Sandra Borkowski, Christoph-Stephan Hilger, Gary Cook, Stephen Warren, and Paul G. Schmidt J Nucl Med. 2006;û 47(4): p. 668-678 http://jnm.snmjournals.org/cgi/content/abstract/47/4/668?ck=nck April 2006 Molecular beacons with intrinsically fluorescent nucleotides Angel A. Marti, Steffen Jockusch, Zengmin Li, Jingyue Ju, and Nicholas J. Turro Nucleic Acids Res. 2006; 34(6): p. e50 http://nar.oxfordjournals.org/cgi/content/abstract/34/6/e50?ct March 2006 Pyrrolo-C as a fluorescent probe for monitoring RNA secondary structure formation Rebecca A. Tinsley and Nils G. Walter RNA, DOI: 10.1261/rna.2165806 http://www.rnajournal.org/cgi/content/abstract/rna.2165806v1 Novel thermostable Y-family polymerases: applications for the PCR amplification of damaged or ancient DNAs John P. McDonald, Ashley Hall, Didier Gasparutto, Jean Cadet, Jack Ballantyne, and Roger Woodgate Nucleic Acids Res. 2006;û 34(4): p. 1102-1111 http://nar.oxfordjournals.org/cgi/content/full/34/4/1102 February 2006 Examining Ty3 Polypurine Tract Structure and Function by Nucleoside Analog Interference Chandravanu Dash, John P. Marino, and Stuart F. J. Le Grice Pedersen J. Biol. Chem. 2006; 281(5): p. 2773-2783 http://www.jbc.org/cgi/content/abstract/281/5/2773?ct January 2006 Easily denaturing nucleic acids derived from intercalating nucleic acids: thermal stability studies, dual duplex invasion and inhibition of transcription start Vyacheslav V. Filichev, Birte Vester, Lykke H. Hansen, and Erik B. Pedersen Nucl. Acids Res. 2005 33: 7129-7137. http://nar.oxfordjournals.org/cgi/content/abstract/33/22/7129?etoc December 2005 Color-blind fluorescence detection for four-color DNA sequencing Ernest K. Lewis, Wade C. Haaland, Freddy Nguyen, Daniel A. Heller, Matthew J. Allen, Robert R. MacGregor, C. Scott Berger, Britain Willingham, Lori A. Burns, Graham B. I. Scott, Carter Kittrell, Bruce R. Johnson, Robert F. Curl and Michael L. Metzker PNAS, April 12,2005, vol.102, no. 15,5346-535 http://www.pnas.org/cgi/content/full/102/15/5346 November 2005 Recognition of CG inversions in DNA triple helices by methylated 3H-pyrrolo[2,3-d]pyrimidin-2(7H)-one nucleoside analogues. Rohan T. Ranasinghe, David A. Rusling, Vicki E. C. Powers, Keith R. Fox and Tom Brown Chemical Communications, 2005,û(20),û2555 - 2557. http://www.rsc.org/publishing/journals/CC/article.asp?doi=b502325d October 2005 Triplex-induced recombination and repair in the pyrimidine motif. Jennifer M. Kalish, Michael M. Seidman, Daniel L. Weeks, and Peter M. Glazer Nucl. Acids Res. 2005 33: 3492-3502. http://nar.oxfordjournals.org/cgi/reprint/33/11/3492 September 2005 Direct selection of trans-acting ligase ribozymes by in vitro compartmentalization. M. Levy, K.E. Griswold, and A.D. Ellington RNA, 2005, rna.2121705 http://www.rnajournal.org/cgi/content/abstract/rna.2121705v1 August 2005 tRNA-linked molecular beacons for imaging mRNAs in the cytoplasm of living cells Musa M. Mhlanga1, Diana Y. Vargas, Cindy W. Fung, Fred Russell Kramer and Sanjay Tyagi 1902-1912 Nucleic Acids Research, 2005, Vol. 33, No. 6 http://nar.oxfordjournals.org/cgi/reprint/33/6/1902 July 2005 DNA microarrays on a dendron-modified surface improve significantly the detection of single nucleotide variations in the p53 gene Soon Jin Oh, et al Nucl. Acids Res. 2005 33: e90. http://nar.oxfordjournals.org/cgi/reprint/33/10/e90 June 2005 Investigating HIV-1 Polypurine Tract Geometry via Targeted Insertion of Abasic Lesions in the(-)-DNA Template and (+)-RNA Primer Hye Young Yi-Brunozzi and Stuart F. J. Le Grice J. Biol. Chem. 2005; 280(20): p. 20154-20162   http://www.jbc.org/cgi/content/abstract/280/20/20154?ct
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