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Literature Highlights Archive

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Title

Reference

Link

July 2014

2'-OMe-Phosphorodithioate-Modified siRNAs Show Increased Loading Into The RISC Complex And Enhanced Anti-tumour Activity

Sherry Y. Wu, Xianbin Yang, Kshipra M. Gharpure, Hiroto Hatakeyama, Martin Egli, Michael H. McGuire, Archana S. Nagaraja, Takahito M. Miyake, Rajesha Rupaimoole, Chad V. Pecot, Morgan Taylor, Sunila Pradeep, Malgorzata Sierant, Cristian Rodriguez-Aguayo, Hyun J. Choi, Rebecca A. Previs, Guillermo N. Armaiz-Pena, Li Huang, Carlos Martinez, Tom Hassell, Cristina Ivan, Vasudha Sehgal, Richa Singhania, Hee-Dong Han, Chang Su, Ji Hoon Kim, Heather J. Dalton, Chandra Kovvali, Khandan Keyomarsi, Nigel A.J. McMillan, Willem W. Overwijk, Jinsong Liu, Ju-Seog Lee, Keith A. Baggerly, Gabriel Lopez-Berestein, Prahlad T. Ram, Barbara Nawrot & Anil K. Sood

Nature Communications
S.Y. Wu, et al., Nature Communications, 2014, 5, 3459-3459.

http://www.glenresearch.com/Literature/NatureCommunication2014.pdf

http://www.nature.com/ncomms/2014/140312/ncomms4459/full/ncomms4459.html

May 2014

Novel Photodynamic Effect of a Psoralen-Conjugated Oligonucleotide for the Discrimination of the Methylation of Cytosine in DNA

Asako Yamayosh, Yohei Matsuyama, Mikihiko Kushida, Akio Kobori and Akira Murakami

Photochemistry and Photobiology
Volume 90, Issue 3, pages 716–722, May/June 2014

http://onlinelibrary.wiley.com/doi/10.1111/php.12232/abstract

May 2014

Combined nucleobase and backbone modifications enhance DNA duplex stability and preserve biocompatibility

Afaf H. El-Saghee and Tom Brown

Chem. Sci.,2014, 5, 253-259

http://pubs.rsc.org/en/content/articlehtml/2014/sc/c3sc51753e

November 2013

Directed evolution of genetic parts and circuits by compartmentalized partnered replication

Jared W Ellefson, Adam J Meyer, Randall A Hughes, Joe R Cannon, Jennifer S Brodbelt & Andrew D Ellington

Nature Biotechnology (2013) doi:10.1038/nbt.2714

http://www.glenresearch.com/Literature/Ellefson et al. NBT 2013.pdf

http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2714.html

August 2013

Monitoring eukaryotic and bacterial UDG repair activity with DNA-multifluorophore sensors

Toshikazu Ono, Sarah K. Edwards, Shenliang Wang, Wei Jiang, and Eric T. Kool

Nucleic Acids Res. published 3 May 2013, 10.1093/nar/gkt309

http://nar.oxfordjournals.org/content/early/2013/05/03/nar.gkt309.full.pdf+html

May 2013

Generation of high-affinity DNA aptamers using an expanded genetic alphabet

Michiko Kimoto, Rie Yamashige, Ken-ichiro Matsunaga, Shigeyuki Yokoyama & Ichiro Hirao

Nature Biotechnology (2013) doi:10.1038/nbt.2556

http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2556.html

December 2012

Conjugating Phosphospermines to siRNAs for Improved Stability in Serum, Intracellular Delivery and RNAi-Mediated Gene Silencing

Clément Paris, Valérie Moreau, Gaëlle Deglane, Loukmane Karim, Bernard Couturier, Marie-Elise Bonnet, Valérie Kedinger, Mélanie Messmer, Anne-Laure Bolcato-Bellemin, Jean-Paul Behr, Patrick Erbacher, and Nathalie Lenne-Samuel

Mol. Pharmaceutics, 2012, 9 (12), pp 3464-3475 DOI: 10.1021/mp300278b

http://pubs.acs.org/doi/abs/10.1021/mp300278b
http://www.glenresearch.com/Literature/Paris_etal_2012.pdf

Supplemental Information

August 2012

Assessing the biocompatibility of click-linked DNA in Escherichia coli

A. Pia Sanzone, Afaf H. El-Sagheer, Tom Brown, and Ali Tavassoli

Nucleic Acids Res. published 16 August 2012, 10.1093/nar/gks756

http://nar.oxfordjournals.org/content/early/2012/08/14/nar.gks756.full

June 2012

Thermodynamics of the multi-stage DNA lesion recognition and repair by formamidopyrimidine-DNA glycosylase using pyrrolocytosine fluorescence-stopped-flow pre-steady-state kinetics

Nikita A. Kuznetsov, Yuri N. Vorobjev, Lev N. Krasnoperov, and Olga S. Fedorova

Nucleic Acids Res. published 14 May 2012, 10.1093/nar/gks423

http://nar.oxfordjournals.org/content/early/2012/05/14/nar.gks423.full

January 2012

Amplified microRNA detection by templated chemistry

Emily M. Harcourt and Eric T. Kool

Nucleic Acids Res. published 25 January 2012, 10.1093/nar/gkr1313

http://nar.oxfordjournals.org/content/early/2012/01/24/nar.gkr1313.full

November 2011

Highly specific unnatural base pair systems as a third base pair for PCR amplification

Rie Yamashige, Michiko Kimoto, Yusuke Takezawa, Akira Sato, Tsuneo Mitsui, Shigeyuki Yokoyama, and Ichiro Hirao

Nucleic Acids Res. published 24 November 2011, 10.1093/nar/gkr1068

http://nar.oxfordjournals.org/content/early/2011/11/24/nar.gkr1068.full

September 2011

Thymine DNA Glycosylase Can Rapidly Excise 5-Formylcytosine and 5-Carboxylcytosine

POTENTIAL IMPLICATIONS FOR ACTIVE DEMETHYLATION OF CpG SITES

Yatanu Maiti and Alexander C. Drohat

The Journal of Biological Chemistry, 286, 35334-35338.5

http://www.glenresearch.com/Literature/J.Biol.Chem.-2011-Maiti-35334-8.pdf

http://www.jbc.org/content/286/41/35334.abstract

August 2011

5-Hydroxy-5-methylhydantoin DNA lesion, a molecular trap for DNA glycosylases

Yann-Vaï Le Bihan, Maria Angeles Izquierdo, Franck Coste, Pierre Aller, Francoise Culard, Tim H. Gehrke, Kadija Essalhi, Thomas Carell and Bertrand Castaing

Nucleic Acids Research, 2011, Vol. 39, No. 14 6277-6290 doi:10.1093/nar/gkr215

http://nar.oxfordjournals.org/content/39/14/6277.full-text-lowres.pdf

OR
http://www.glenresearch.com/Literature/LBihan-6277-90.pdf

June 2011

A universal code for RNA recognition by PUF proteins

Aleksandra Filipovska, Muhammad F M Razif, Karoline K A Nygård & Oliver Rackham

Nature Chemical Biology Published OnLIne:15 May 2011 | DOI: 10.1038/NCHEMBIO.577

http://www.glenresearch.com/Literature/nchembio_577_s.pdf

April 2011

Induced cross-linking reactions to target genes using modified oligonucleotides

F. Nagatsugi and S. Imoto

Organic & Biomolecular Chemistry, 2011, 9, 2579-2585.

http://www.glenresearch.com/Literature/April2011.pdf

March 2011

Positional photocleavage control of DNA-based nanoswitches

Allen K. Mok, Nancy A. Kedzierski, Paul N. Chung and Philip S. Lukeman

Chem. Commun., 2011, Advance Article

http://pubs.rsc.org/en/Content/ArticleLanding/2011/CC/C1CC10292C

Deember 2010

A multivalent DNA aptamer specific for the B-cell receptor on human lymphoma and leukemia

Prabodhika R. Mallikaratchy, Alessandro Ruggiero, Jeffrey R. Gardner, Vitaly Kuryavyi, William F. Maguire, Mark L. Heaney, Michael R. McDevitt, Dinshaw J. Patel and David A. Scheinberg,

Nucleic Acids Res. First published online October 28, 2010, 10.1093/nar/gkq996 Open Access

http://nar.oxfordjournals.org/cgi/content/abstract/gkq855v1?ct=ct

October 2010

Photosensitized [2 + 2] cycloaddition of N-acetylated cytosine affords stereoselective formation of cyclobutane pyrimidine dimer

Junpei Yamamoto, Kosuke Nishiguchi, Koichiro Manabe, Chikahide Masutani, Fumio Hanaoka, and Shigenori Iwai

Nucleic Acids Res. published 29 September 2010, 10.1093/nar/gkq855 Open Access

http://nar.oxfordjournals.org/cgi/content/abstract/gkq855v1?ct=ct

August 2010

Deep sequencing analysis of mutations resulting from the incorporation of dNTP analogs

Katherine L. Petrie and Gerald F. Joyce

Nucleic Acids Res. published 6 August 2010, 10.1093/nar/gkq68

http://nar.oxfordjournals.org/cgi/content/full/gkq685

July 2010

Intracellular delivery of an antisense oligonucleotide via endocytosis of a G protein-coupled receptor

Xin Ming, Md Rowshon Alam, Michael Fisher, Yongjun Yan, Xiaoyuan Chen, and Rudolph L. Juliano

Nucleic Acids Res. published 15 June 2010, 10.1093/nar/gkq534

http://nar.oxfordjournals.org/cgi/content/full/gkq534

June 2010

Solid-Phase Synthesis of Oligodeoxyribonucleotides without Base Protection Utilizing O-Selective Reaction of Oxazaphospholidine Derivatives

N. Oka, Y. Maizuru, M. Shimizu, and T. Wada

Nucleosides, Nucleotides and Nucleic Acids, Volume 29, Issue 2 February 2010 , pages 144 - 154

http://www.informaworld.com/smpp/content~db=all~content=a919499271~frm=abslink

May 2010

Zip nucleic acids are potent hydrolysis probes for quantitative PCR.

Clément Paris, Valérie Moreau, Gaëlle Deglane, Emilie Voirin, Patrick Erbacher and Nathalie Lenne-Samuel

Nucleic Acids Res. published 22 March 2010, 10.1093/nar/gkq163

http://nar.oxfordjournals.org/cgi/content/full/38/7/e95

April 2010

Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process.

Emily M. LeProust, Bill J. Peck, Konstantin Spirin, Heather Brummel McCuen, Bridget Moore, Eugeni Namsaraev, and Marvin H. Caruthers

Nucleic Acids Res. published 22 March 2010, 10.1093/nar/gkq163

http://nar.oxfordjournals.org/cgi/content/full/gkq163

March 2010

Straightforward carbamoylation of nucleophilic compounds employing organic azides, phosphines, and aqueous trialkylammonium hydrogen carbonate.

Andrey Yagodkin, Kerstin Löschcke, Janne Weisell and Alex Azhayev

Tetrahedron,Volume 66, Issue 12, 20 March 2010, Pages 2210-2221

http://www.sciencedirect.com/science/

(PDF)

February 2010

Fluorescent probes for the analysis of DNA strand scission in base excision repair.

Naoyuki Matsumoto, Tatsuya Toga, Ryosuke Hayashi, Kaoru Sugasawa, Katsuo Katayanagi, Hiroshi Ide, Isao Kuraoka, and Shigenori Iwai

Nucleic Acids Res. published 27 January 2010, 10.1093/nar/gkq022

http://nar.oxfordjournals.org/cgi/content/full/gkq022

January 2010

Nanoparticle-based bio-barcode assay redefines "undetectable" PSA and biochemical recurrence after radical prostatectomy

C. Shad Thaxton, Robert Elghanian, Audrey D. Thomas, Savka I. Stoeva, Jae-Seung Lee, Norm D. Smith, Anthony J. Schaeffer, Helmut Klocker, Wolfgang Horninger, Georg Bartsch, and Chad A. Mirkin

PNAS October 19, 2009 doi: 10.1073/pnas.0904719106

http://www.pnas.org/content/early/2009/10/16/0904719106.abstract

(pdf version)

New approach to real-time nucleic acids detection: folding polymerase chain reaction amplicons into a secondary structure to improve cleavage of Förster resonance energy transfer probes in 5'-nuclease assays.

Igor V. Kutyavin

Nucleic Acids Res. published 7 December 2009, 10.1093/nar/gkp1138

http://nar.oxfordjournals.org/cgi/content/abstract/gkp1138

December 2009

High Fidelity Base Pairing at the 3′-Terminus

Amritraj Patra and Clemens Richert

J. Am. Chem. Soc., 2009, 131 (35), pp 12671–12681

http://pubs.acs.org/doi/abs/10.1021/ja9033654

November 2009

Biochemical properties and base excision repair complex formation of apurinic/apyrimidinic endonuclease from Pyrococcus furiosus

Shinichi Kiyonari, Saki Tahara, Tsuyoshi Shirai, Shigenori Iwai, Sonoko Ishino, and Yoshizumi Ishino

Nucleic Acids Res. 2009; 37(19): p. 6439-6453 Open Access

http://nar.oxfordjournals.org/cgi/content/abstract/37/19/6439?ct=ct

October 2009

Redox signaling between DNA repair proteins for efficient lesion detection

Amie K. Boal, Joseph C. Genereux, Pamela A. Sontz, Jeffrey A. Gralnick, Dianne K. Newman, and Jacqueline K. Barton

PNAS. 2009; 106:15237-15242

http://www.pnas.org/content/106/36/15237.abstract

September 2009

Kinetics of deamination and Cu(II)/H2O2/Ascorbate-induced formation of 5-methylcytosine glycol at CpG sites in duplex DNA

Huachuan Cao, Yong Jiang, and Yinsheng Wang

Nucleic Acids Res. published 25 August 2009, 10.1093/nar/gkp615

http://nar.oxfordjournals.org/cgi/content/full/gkp615

August 2009

Using photons to manipulate enzyme inhibition by an azobenzene-modified nucleic acid probe

Youngmi Kima, Joseph A. Phillips, Haipeng Liua, Huaizhi Kanga, and Weihong Tan

PNAS April 21, 2009 vol. 106 no. 16 6489-6494

http://www.pnas.org/content/106/16/6489.abstract?sid=b48a43ba-f5e6-4f0d-8209-bc106310f73c

July 2009

Molecular Recognition and Self-Assembly Special Feature: Assembly and organization processes in DNA-directed colloidal crystallization

Robert J. Macfarlane, Byeongdu Lee, Haley D. Hill, Andrew J. Senesi, Soenke Seifert, and Chad A. Mirkin

PNAS. 2009; 106:10493-10498

http://www.pnas.org/content/early/2009/06/18/0900630106.abstract

June 2009

Direct observation of the hole protonation state
and hole localization site in DNA-oligomers

Amitava Adhikary, Deepti Khanduri, and Michael D. Sevilla

J. Am. Chem. Soc., 2009, 10.1021/ja9014869

J. Am. Chem. Soc., 2009, 10.1021/ja9014869
http://www.glenres.com/Literature/ja9014869.pdf (PDF)
http://www.glenres.com/Literature/Literature/ja9014869_si_001.pdf (Supporting Information)

May 2009

Aptamer Switch Probe Based on Intramolecular Displacement

Zhiwen Tang, Prabodhika Mallikaratchy, Ronghua Yang, Youngmi Kim, Zhi Zhu, Hui Wang and Weihong Tan

J. Am. Chem. Soc., 2008, 130 (34), pp 11268–11269

http://pubs.acs.org/doi/abs/10.1021/ja804119s

April 2009

Use of Sloppy Molecular Beacon Probes for Identification of Mycobacterial Species

Hiyam H. El-Hajj, Salvatore A. E. Marras, Sanjay Tyagi, Elena Shashkina, Mini Kamboj, Timothy E. Kiehn, Michael S. Glickman, Fred Russell Kramer, and David Alland
Journal of Clinical Microbiology, April 2009, p. 1190-1198, Vol. 47, No. 4.

http://jcm.asm.org/cgi/content/full/47/4/1190


(pdf Version)

March 2009

RNA major groove modifications improve siRNA stability and biological activity

Montserrat Terrazas and Eric T. Kool
346–353 Nucleic Acids Research, 2009, Vol. 37, No. 2

http://nar.oxfordjournals.org/cgi/content/full/37/2/346

February 2009

Human Nei-like protein NEIL3 has AP lyase activity specific for single-stranded DNA and confers oxidative stress resistance in Escherichia coli mutant

Masashi Takao, Yoshitsugu Oohata, Kengo Kitadokoro, Kumiko Kobayashi, Shigenori Iwai, Akira Yasui, Shuji Yonei and Qiu-Mei Zhang
Takao 2009 Genes Cells 261-270 NEIL3 dna repair ox damages.pdf

Takao 2009 Genes Cells 261-270 NEIL3 dna repair ox damages.pdf

January 2009

Detection of DNA damage: effect of thymidine glycol residues on the thermodynamic, substrate and interfacial acoustic properties of oligonucleotide duplexes.

Yang, F.; Romanova, E.; Kubareva, E.; Dolinnaya, N.; Gajdos, V.; Burenina, O.; Fedotova, E.; Ellis, J. S.; Oretskaya, T.; Hianik, T.; Thompson, M.
Analyst 2009, 134, (1), 41-51

http://www.glenres.com/Literature/DNADamage.pdf

December 2008

Hot Start PCR with heat-activatable primers: a novel approach for improved PCR performance

Alexandre V. Lebedev, Natasha Paul, Joyclyn Yee, Victor A. Timoshchuk, Jonathan Shum, Kei Miyagi, Jack Kellum, Richard I. Hogrefe, and Gerald Zon
Nucleic Acids Res. published 16 September 2008, 10.1093/nar/gkn575 Open Access

http://nar.oxfordjournals.org/cgi/content/full/36/20/e131

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

http://nar.oxfordjournals.org/cgi/content/abstract/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 (http://www.glenresearch.com/Literature/March2007.pdf
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,and 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. OShea, 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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