Glen Report 29.1

CDPI₃ MGB™-Oligonucleotide conjugates and their applications

This article by Eugene Lukhtanov of ELITechGroup Molecular Diagnostics introduces the tripeptide of dihydropyrroloindole-carboxylate (CDPI₃), which is a minor groove binding (MGB) moiety derived from the natural product CC-1065 and exhibits strong DNA binding properties. Synthetic oligonucleotides with covalently-attached CDPI3 moieties have enhanced DNA affinity and have improved the hybridization properties of sequence-specific DNA probes. Short CDPI₃-oligonucleotides hybridize with single-stranded DNA to give more stable DNA duplexes than unmodified oligonucleotides of similar length. The author describes the general properties of CDPI₃ MGB-oligonucleotide conjugates in detail, along with some specific applications:

Arrest of primer extension and PCR blockers
Short and fluorogenic PCR primers
Real-time PCR probes
miRNA Inhibitors

CDPI₃ MGB products are sold under licensing arrangements between ELITechGroup Inc. and Glen Research.

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5'-CDPI3 MGB™ Phosphoramidite and 3'-CDPI3 MGB™ CPG

DNA probes with conjugated MGB groups form extremely stable duplexes with single-stranded DNA targets, allowing shorter probes to be used for hybridization based assays. In comparison with unmodified DNA, MGB probes have higher melting temperature (T_m) and increased specificity, especially when a mismatch is in the MGB region of the duplex. MGB probes, therefore, can be significantly shorter than traditional probes, providing better sequence discrimination and flexibility to accommodate more targets.

The simplest approach to MGB probe design is to use an MGB support, add a quencher molecule as the first addition and complete the synthesis with a 5'-fluorophore. Alternatively, a fluorophore support could be used with the 5' terminus containing a quencher molecule followed by a final MGB addition at the 5' terminus.

In this article, we introduce 5'-CDPI₃ MGB™ Phosphoramidite and 3'-CDPI₃ MGB™ CPG. Specific instructions are provided for the use of these products and the procedures are illustrated using HPLC and MS data. Details of a melting study using a CDPI₃ MGB-oligonucleotide conjugate are presented.

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Studying DNA Repair Pathways Using Site-Specifically Modified Oligonucleotides

In this review article, Young K. Cheun & Orlando D. Schärer of the Center for Genomic Integrity, Institute for Basic Science, Ulsan National Institute of Science and Technology discuss why research into DNA damage and repair is facilitated by the availability of monomers containing ‘damaged’ bases.

DNA is an inherently unstable molecule that can react with both endogenous (water, reactive oxygen species) and exogenous agents (UV light, environmental mutagens, antitumor agents). Errors during replication of damaged sites in DNA leads to mutations in genes and eventually cancer. More recently, it has become clear that persistent DNA lesions are associated with many additional pathologies including premature aging and neurodegeneration Fortunately, a variety of pathways exist to repair DNA to counteract this threat but mutations in DNA repair genes can lead to debilitating inherited disorders and contribute to disease predisposition.

The authors note that the detailed studies of the molecular mechanisms of DNA repair pathways were made possible by using site-specifically modified oligonucleotides and that the availability of phosphoramidites to synthesize oligonucleotides with DNA lesions has contributed to the field. They illustrate the article using primarily structural studies in the following examples:

DNA polymerases and glycosylases interacting with thymine glycol
Recognition of 8-Oxoguanine
Cyclobutane pyrimidine dimer (CPD) – the most important exogenous DNA adduct

Phosphoramidites that allow the generation of oligonucleotides containing site-specific lesions have been vital components for studying the mechanism of DNA repair. New DNA lesions are still being discovered and the study of their biological consequences will require their site-specific incorporation into oligonucleotides. The authors conclude that the increased availability of phosphoramidites for the synthesis of lesion-containing oligonucleotides should facilitate many future discoveries in the broad area of DNA damage and repair.

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N-Acetylgalactosamine (GalNAc) Oligonucleotide Conjugates

A directed approach to the delivery of therapeutic oligonucleotides specifically to the liver has been to target the asialoglycoprotein receptor (ASGPR) using a suitable glycoconjugate. Indeed, ASGPR is the ideal target for delivery of therapeutic oligonucleotides to the liver since it combines tissue specificity, high expression levels and rapid internalization and turnover. The use of oligonucleotide glycoconjugates has led to significant advances in therapeutic delivery as evidenced by the work of Alnylam Pharmaceuticals and Ionis Pharmaceuticals using multivalent N-acetylgalactosamine (GalNAc) oligonucleotide conjugates.

Glen Research is delighted to introduce a GalNAc modification strategy using a monomeric GalNAc support and the equivalent GalNAc phosphoramidite. Our experimental work has shown that these products are fully compatible with regular oligonucleotide synthesis and deprotection. Oligonucleotides containing GalNAc can be deprotected using standard procedures during which the acetyl protecting groups on the GalNAc group are removed. Glen Research offers these GalNAc C3 products under an agreement with AM Chemicals LLC.

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Sequence Modification using Glen Research's 5-Modified dU Family

In this article, we review a variety of sequence modifiers that might be useful in the design of MGB probes containing a fluorophore, quencher, etc., attached to the 5 position of dU. Familial subsets designed for modification, fluorescent labelling, quenchers and click chemistry are covered.

Modification - This section covers our products for derivatizing oligonucleotides with amino, carboxy and thiol groups for subsequent post synthesis labelling.
Labelling - For direct labelling of oligonucleotides, we offer dU analogues containing biotin, fluorescein, TAMRA, dabcyl, SIMA (HEX), EDTA and Ferrocene.
Quenchers - Molecules that can be used as quenchers are also available as dU analogues - TAMRA, dabcyl, BHQ-1™, BHQ-2™ and BBQ-650®.
Click Chemistry - We support the use of copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) reactions between azides and alkynes . This strategy allows the use of the vast library of azide tags to be used in oligonucleotide labelling. To realize efficient click-chemistry labelling of alkyne modified oligonucleotides, our dT analogues use a 5-(octa-1,7-diynyl) side chain but labelling closer to the base can be done using 5-ethynyl-dU. In addition, DBCO-dT can be used for copper free click coupling with an azide.

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Literature Highlight

Highlight Date	Title	Reference	Link
June 2016	Synthesis of chemically modified DNA	Arun Shivalingam, Tom Brown Biochemical Society Transactions Jun 09, 2016, 44 (3) 709-715; DOI: 10.1042/BST20160051/p>	http://www.glenresearch.com/Literature/709.full.pdf http://www.biochemsoctrans.org/content/44/3/709
February 2016	RNA epigenetics?	Chuan He Nature Chemical Biology VOL 6, DECEMBER 2010	http://www.nature.com/nchembio/journal/v6/n12/pdf/nchembio.482.pdf
August 2015	In Vitro Fluorogenic Real-Time Assay of the Repair of Oxidative DNA Damage	Sarah K. Edwards, Toshikazu Ono, Shenliang Wang, Wei Jiang, Raphael M. Franzini, Jong Wha Jung, Ke Min Chan, and Eric T. Kool ChemBioChem Volume 16, Issue 11, pages 1637–1646, July 27, 2015	http://www.glenresearch.com/Literature/Edwards_etal_2015_ChemBioChem.pdf http://onlinelibrary.wiley.com/doi/10.1002/cbic.201500184/abstract
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)
January 2010	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
September 2008	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
May 2007	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
January 2007	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
October 2006	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
August 2006	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
June 2006	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
March 2006	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