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TriLink Publications

TriLink prides itself on the preparation of publications to share with the scientific community. Our scientists contributed to the publications below.

Sriram Vaidyanathan, Krist T. Azizian, AKM Ashiqul Haque, Jordana M. Henderson, Ayal Hendel, Sabrina Shore, Justin S. Antony, Richard I. Hogrefe, Michael S.D. Kormann, Matthew H. Porteus, Anton P. McCaffrey Uridine Depletion and Chemical Modification Increase Cas9 mRNA Activity and Reduce Immunogenicity Without HPLC Purification. Mol Ther Nucleic Acids. 2018 June 22 10.1016/j.omtn.2018.06.010
Shore S, Henderson JM, Lebedev A, Salcedo MP, Zon G, McCaffrey AP, Natasha P, Hogrefe RI. Small RNA Library Preparation Method for Next-Generation Sequencing Using Chemical Modifications to Prevent Adapter Dimer Formation. PLoS One. 2016 Nov 22 11(11):e0167009
Roby RK, Sprouse M, Phillips N, Alicea-Centeno A, Shewale S, Shore S, Paul N. Mitochondrial genome interrogation for forensic casework and research studies. Curr Protoc Hum Genet. 2014 Apr 24;81:14.9.1-14.9.23
Snead NM, Escamilla-Powers JR, Rossi JJ, McCaffrey AP. 5' Unlocked Nucleic Acid Modification Improves siRNA Targeting. Mol Ther Nucleic Acids. 2013 Jul 2;2:e103.
Hogrefe RI, Midthune B, Lebedev A. Current Challenges in Nucleic Acid Synthesis. Isr. J. Chem., 2013; 53: 326–349.
Paul N, Adelfinskaya O, Hidalgo Ashrafi E, Le T, Shore S. Modified dNTPs: A Toolbox for Use in PCR. In: Nolan T, Bustin SA, eds. PCR Technology: Current Innovations. 3rd ed. New York, NY: CRC Press; 2013: 103-122.
Shore S, Hidalgo Ashrafi E, Paul N. (2012). Hot Start 7-Deaza-dGTP Improves Sanger Dideoxy Sequencing Data of GC-Rich Targets, DNA Sequencing - Methods and Applications, Dr. Anjana Munshi (Ed.), ISBN: 978-953-51-0564-0, InTech.
Shore S, Paul N. Robust PCR amplification of GC-rich targets with Hot Start 7-deaza-dGTP, BioTechniques 2010, 49(5): 841-843.
Paul N, Shum J, Le T. Hot Start PCR in Methods in Molecular Biology in RT-PCR Protocols, Springer Science+Business Media, LLC 2010, 630: 301-18.
Paul N., Yee J. PCR incorporation of modified dNTPs: the substrate properties of biotinylated dNTPs. BioTechniques 2010, 48(4): 333–334.
Hidalgo Ashrafi E, Yee J, Paul, N. Selective control of primer usage in multiplex one-step reverse transcription PCR. BMC Molecular Biology 2009, 10: 113.
Hidalgo Ashrafi E, Paul N. Heat Activatable Primers for Hot Start Primers for Hot Start PCR and Hot Start One-step RT-PCR - End Point and Real-Time Experiments in Current Protocols in Molecular Biology, Wiley Interscience 2009, 15.9.
Hidalgo Ashrafi E, Paul N. Improved PCR specificity with Hot Start PCR primers. BioTechniques 2009, 47(3): 789-90.
Koukhareva I, Lebedev A. 3’-Protected 2’-Deoxynucleoside 5’-Triphosphates as a Novel Tool for Heat-Triggered Activation of PCR. Analytical Chemistry 2009, 81(12): 4955–4962.
Le T, Hidalgo Ashrafi E, Paul N. Enhancing multiplex PCR efficiency using Hot Start dNTPs. BioTechniques 2009, 47(5): 972-3.
Le T, Paul N. Improved PCR flexibility with Hot Start dNTPs. BioTechniques 2009, 47(3): 789-90.
Lebedev A. Heat Activatable Primers for Hot Start PCR: Oligonucleotide Synthesis and Basic PCR Set-up in Current Protocols in Nucleic Acid Chemistry, Wiley Interscience 2009, 4.35.
Timoshchuk V, Hogrefe R. The “Corey Reagent”, 3,5-Di-tert-butyl-1,2-benzoquinone, as a Modifying Agent in the Synthesis of Fluorescent and Double-Headed Nucleotides. Nucleosides, Nucleotides and Nucleic Acids 2009, 28(5): 464-72.
Shum J, Paul N. Chemically modified primers for improved multiplex polymerase chain reaction. Analytical Biochemistry 2009, 388: 266-272.
Koukhareva I, Huang H, Yee J, Shum J, Paul N., Hogrefe R, Lebedev, A. Heat Activatable 3’-Modified dNTPs: Synthesis and Application for Hot Start PCR. Nucleic Acids Symposium Series 2008, Oxford University Press, No. 52: 259-260.
Koukhareva I, Huang H, Yee J, Paul N, Hogrefe R., Lebedev, A. A new Approach to Improved Hot Start PCR: Nucleoside 5’-Triphosphates with Thermolabile 3’-Protecting Group. Collection Symposium Series 2008, Academy of Sciences of the Czech Republic, 10: 259-263.
Lahoud G, Timoshchuk V, Lebedev A, De Vega M, Salas M, Arar K, Hou Y, Gamper H. Enzymatic Synthesis of Structure-Free DNA with Pseudo-Complementary Properties. Nucleic Acids Research 2008, 36: 3409-3419.
Lahoud G, Timoshchuk V, Lebedev A, Arar K, Hou Y, Gamper H. Properties of pseudo-complementary DNA substituted with weakly pairing analogs of guanine or cytosine. Nucleic Acids Research 2008, 36: 6999-7008.
Lebedev A, Paul N, Yee J, Timoshchuk V, Shum J, Miyagi K, Kellum J, Hogrefe R, Zon G. Hot start PCR with heat-activatable primers: a novel approach for improved PCR performance. Nucleic Acids Research 2008, 36(20): 131.
Nawrot B, Paul N, Rebowska B, Stec J. Significance of stereochemistry of 3'-terminal phosphorothioate-modified primer in DNA polymerase mediated chain extension. Molecular Biotechnology 2008, 40(2): 119-126.
Lebedev A, Combs D, Hogrefe R. Preactivated Carboxyl Linker for the Rapid Conjugation of Alkylamines to Oligonucleotides on Solid Support. Bioconjugate Chemistry 2007, 18: 1530-1536.
Pirollo K, Rait A, Zhou Q, Hwang S, Dagata J, Zon G, Hogrefe R, Palchik G, Chang E. Materializing the Potential of Small Interfering RNA via a Tumor-Targeting Nanodelivery System. Cancer Research 2007, 67(7): 2938-2943.
Hogrefe R, Lebedev A, Zon G, Pirollo K, Rait A, Zhou O, Yu W, Chang E. Chemically modified short interfering hybrids (siHYBRIDS): Nanoimmunoliposome delivery in vitro and in vivo for RNAi of HER-2. Nucleosides, Nucleotides & Nucleic Acids 2006, 25: 889-907.
Hussein Y, Anderson N, Lian T, Abdou I, Strekowski L, Timoshchuk V, Vaghefi M, Netzel T. Solvent and Linker Influences on AQ(*-)/dA(*+) Charge-Transfer State Energetics and Dynamics in Anthraquinonyl-Linker-Deoxyadenosine Conjugates. Journal of Physical Chemistry A. 2006, 110: 4320-4328.
Pirollo K, Zon G, Rait A, Zhou Q, Yu W, Hogrefe R, Chang E. Tumor-Targeting Nanoimmunoliposome Complex for Short Interfering RNA Delivery. Human Gene Therapy 2006, 17: 117-124.
Timoshchuk V. Functionalization of Pyrimidine and Purine Nucleosides at C4 and C6: C-Nucleophilic Substitution of Their C4- and C6-(1,2,4-Triazol-1-yl) Derivatives. Nucleosides, Nucleotides and Nucleic Acids 2005, 24: 1043-1046.
Koukhareva I, Vaghefe M, Lebedev A. Synthesis and properties of NTP analogs with modified triphosphate chains in Nucleoside triphosphates: Chemistry, Biotechnology and Biological Applications, Taylor and Francis 2005: 39-104.
Koukhareva I, Lebedev A. Chemical route to the capped RNAs. Nucleosides, Nucleotides & Nucleic Acids 2004, 23(10): 1667- 1680.
Timoshchuk V, Hogrefe R, Vaghefi M. Improved and Reliable Synthesis of 3' - Azido-2',3'-dideoxyguanosine Derivatives. Nucleosides, Nucleotides & Nucleic Acids 2004, 23(1-2): 171-181.
Wang K, Li J, Fang X, Schuster S, Vicens M, Kelley S, Lou H, Li J, Beck T, Hogrefe R, Tan W. Novel Fluorescent Molecular Beacon DNA Probes for Biomolecular Recognition. Biomedical Photonics Handbook 2003, 57: 1-23.
Fang X, Cao Z, Beck T, Tan, W. Molecular Aptamer for Real-time Oncoprotein latelet-derived Growth Factor Monitoring by Fluorescence Anisotropy. Journal of the American Chemical Society 2001, 73(23): 5752-5757.
Lebedev A, Koukhareva I, Beck T, Vaghefi, M. Preparation of oligodeoxynucleotide 5’-triphosphates using solid support approach. Nucleosides Nucleotides Nucleic Acids. 2001 Apr-Jul;20(4-7):1403-9.
Zhang P, Beck T, Tan W. Design of a Molecular Beacon DNA Probe with Two Fluorophores. Angew Chem Int Ed Engl. 2001 Jan 19;40(2):402-405.
Hogrefe R. An Antisense Oligonucleotide Primer. Antisense Nucleic Acid Drug Dev. 1999 Aug;9(4):351-7.

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