PON, RICHARD T. - University of Calgary - Department of Biochemistry & Molecular Biology

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The two Pon laboratories (DNA/RNA Synthesis and DNA Sequencing) are primarily involved in the provision of core laboratory services as part of the UCDNA Services facility. These services are provided to a broad base of users, both internal and external, on a fee-for-service basis. Synthetic oligonucleotides containing either DNA, RNA, or modified structures are produced by solid-phase synthesis. DNA sequencing and genotyping is conducted using fluorescently labeled dideoxy-terminators (Sanger sequencing) and automated capillary gel electrophoresis (ABI 3730 48 capillary sequencer). DNA plasmid preparation (for sequencing) via TempliPhi amplification is also available. Details on these services can be found at http://www.ucalgary.ca/dnalab/ . Although no graduate students are involved, research is conducted into novel or improved methods of solid-phase oligonucleotide synthesis. Recent projects have developed novel linker arms, solid-phase supports, or synthetic strategies for reusing solid-phase supports. Currently, improved methods for RNA production, particularly double-stranded RNAi synthesis via tandem synthesis, and new RNA conjugates are being investigated.

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An Algorithm Measuring Donor Cell-Free DNA in Plasma of Cellular and Solid Organ Transplant Recipients That Does Not Require Donor or Recipient Genotyping.Gordon PM, Khan A, Sajid U, Chang N, Suresh V, Dimnik L, Lamont RE, Parboosingh JS, Martin SR, Pon RT, Weatherhead J, Wegener S, Isaac D, Greenway SC.Front Cardiovasc Med. 2016 Sep 22;3:33. An siRNA-based functional genomics screen for the identification of regulators of ciliogenesis and ciliopathy genes.Wheway G, Schmidts M, Mans DA, Szymanska K, Nguyen TM, Racher H, Phelps IG, Toedt G, Kennedy J, Wunderlich KA, Sorusch N, Abdelhamed ZA, Natarajan S, Herridge W, van Reeuwijk J, Horn N, Boldt K, Parry DA, Letteboer SJ, Roosing S, Adams M, Bell SM, Bond J, Higgins J, Morrison EE, Tomlinson DC, Slaats GG, van Dam TJ, Huang L, Kessler K, Giessl A, Logan CV, Boyle EA, Shendure J, Anazi S, Aldahmesh M, Al Hazzaa S, Hegele RA, Ober C, Frosk P, Mhanni AA, Chodirker BN, Chudley AE, Lamont R, Bernier FP, Beaulieu CL, Gordon P, Pon RT, Donahue C, Barkovich AJ, Wolf L, Toomes C, Thiel CT, Boycott KM, McKibbin M, Inglehearn CF; UK10K Consortium.; University of Washington Center for Mendelian Genomics., Stewart F, Omran H, Huynen MA, Sergouniotis PI, Alkuraya FS, Parboosingh JS, Innes AM, Willoughby CE, Giles RH, Webster AR, Ueffing M, Blacque O, Gleeson JG, Wolfrum U, Beales PL, Gibson T, Doherty D, Mitchison HM, Roepman R, Johnson CA.Nat Cell Biol. 2015 Aug;17(8):1074-87. doi: 10.1038/ncb3201. Attachment of nucleosides and other linkers to solid-phase supports for oligonucleotide synthesis.Guzaev AP, Pon RT.Curr Protoc Nucleic Acid Chem. 2013 Mar;Chapter 3:Unit 3.2. doi: 10.1002/0471142700.nc0302s52. Nucleoside phosphoramidites containing cleavable linkers.Pon RT.Curr Protoc Nucleic Acid Chem. 2006 Jan;Chapter 3:Unit 3.12. doi: 10.1002/0471142700.nc0312s23. Attachment of nucleosides to solid-phase supports.Pon RT.Curr Protoc Nucleic Acid Chem. 2001 May;Chapter 3:Unit 3.2. doi: 10.1002/0471142700.nc0302s00. Solid-phase supports for oligonucleotide synthesis.Pon RT.Curr Protoc Nucleic Acid Chem. 2001 May;Chapter 3:Unit 3.1. doi: 10.1002/0471142700.nc0301s00. Large-scale synthesis of "Cpep" RNA monomers and their application in automated RNA synthesis.Pon RT, Yu S, Prabhavalkar T, Mishra T, Kulkarni B, Sanghvi YS.Nucleosides Nucleotides Nucleic Acids. 2005;24(5-7):777-81. Tandem oligonucleotide synthesis using linker phosphoramidites.Pon RT, Yu S.Nucleic Acids Res. 2005 Apr 6;33(6):1940-8. Solution structure of a DNA duplex containing an alpha-anomeric adenosine: insights into substrate recognition by endonuclease IV.Aramini JM, Cleaver SH, Pon RT, Cunningham RP, Germann MW.J Mol Biol. 2004 Apr 16;338(1):77-91. Linker phosphoramidite reagents for the attachment of the first nucleoside to underivatized solid-phase supports.Pon RT, Yu S.Nucleic Acids Res. 2004 Jan 29;32(2):623-31. Structural basis for topoisomerase I inhibition by nucleoside analogs.Gmeiner WH, Yu S, Pon RT, Pourquier P, Pommier Y.Nucleosides Nucleotides Nucleic Acids. 2003 May-Aug;22(5-8):653-8. Review. Tandem oligonucleotide synthesis using linker (First Base) phosphoramidites.Pon RT, Yu S.Nucleic Acids Res Suppl. 2002;(2):1-2. Gemcitabine (2',2'-difluoro-2'-deoxycytidine), an antimetabolite that poisons topoisomerase I.Pourquier P, Gioffre C, Kohlhagen G, Urasaki Y, Goldwasser F, Hertel LW, Yu S, Pon RT, Gmeiner WH, Pommier Y.Clin Cancer Res. 2002 Aug;8(8):2499-504. Tandem oligonucleotide synthesis on solid-phase supports for the production of multiple oligonucleotides.Pon RT, Yu S, Sanghvi YS.J Org Chem. 2002 Feb 8;67(3):856-64. Solution structure of an arabinonucleic acid (ANA)/RNA duplex in a chimeric hairpin: comparison with 2'-fluoro-ANA/RNA and DNA/RNA hybrids.Denisov AY, Noronha AM, Wilds CJ, Trempe JF, Pon RT, Gehring K, Damha MJ.Nucleic Acids Res. 2001 Nov 1;29(21):4284-93. Multiple oligonucleotide synthesis in tandem on solid-phase supports for small and large scale synthesis.Pon RT, Yu S, Sanghvi YS.Nucleosides Nucleotides Nucleic Acids. 2001 Apr-Jul;20(4-7):985-9. Properties of arabinonucleic acids (ANA & 20'F-ANA): implications for the design of antisense therapeutics that invoke RNase H cleavage of RNA.Damha MJ, Noronha AM, Wilds CJ, Trempe JF, Denisov A, Pon RT, Gehring K.Nucleosides Nucleotides Nucleic Acids. 2001 Apr-Jul;20(4-7):429-40. NMR solution structure of an oligonucleotide hairpin with a 2'F-ANA/RNA stem: implications for RNase H specificity toward DNA/RNA hybrid duplexes.Trempe JF, Wilds CJ, Denisov AY, Pon RT, Damha MJ, Gehring K.J Am Chem Soc. 2001 May 30;123(21):4896-903. Solid-phase oligonucleotide synthesis and flow cytometric analysis with microspheres encoded with covalently attached fluorophores.Nanthakumar A, Pon RT, Mazumder A, Yu S, Watson A.Bioconjug Chem. 2000 Mar-Apr;11(2):282-8. Rapid esterification of nucleosides to solid-phase supports for oligonucleotide synthesis using uronium and phosphonium coupling reagents.Pon RT, Yu S, Sanghvi YS.Bioconjug Chem. 1999 Nov-Dec;10(6):1051-7.

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