Researcher Publications

Roger A. Jones, PhD

Selected Publications

  1. Gaffney, B.L.; Veliath, E.; Zhao, J.; Jones, R.A. “One-Flask Syntheses of c-di-GMP and the [Rp,Rp] and [Rp,Sp] Thiophosphate Analogues” Organic Letters, 2010, 12, 3269–3271. doi 10.1021/ol101236b.
  2. Lescrinier, E.; Dyubankova, N.; Nauwelaerts, K.; Jones, R.; Herdewijn, P. “Structure Determination of the Top-Loop of the Conserved 3’-Terminal Secondary Structure in the Genome of Flaviviruses” Chembiochem, 2010, DOI: 10.1002/cbic.200900765
  3. Tu,; Kalyan,K.; Han,Q.; Bauman,J.D.; Clark, Jr. A.D.; Hou,X.; Yulia V Frenkel,Y.V.; Gaffney,B.L.; Jones,R.A.; Boyer,P.L.; Hughes,S.H.; Sarafianos,S.G.; Arnold, E. “Structural basis of HIV-1 resistance to AZT by excision” Nat. Struct. Mol. Biol. 2010, 17, 1202–1209. doi: 10.1028/nsmb.1908
  4. Shanahan, C.A.; Gaffney, B.L.; Jones A.; Strobel, S.A. “Differential Analog Binding by Two Classes of c-di-GMP Riboswitches” J. Am. Chem. Soc., 2011, 133, 15578–15592. DOI: 10.1021/ja204650q
  5. Guza, R.; Kotandeniya, D.; Murphy, K.; Dissanayake, T.; Lin, C.; Giambasu, G.M..; Lad, R.R.; Wojciechowski, F.; Amin, S.; Sturla, S.J; Hudson, R.H.E.; York, D.M.; Jankowiak, R.; Jones, R.A.; and Tretyakova, N.Y. “Influence of C-5 substituted cytosine and related nucleoside analogs on the formation of benzo[a]pyrene diol epoxide-dG adducts at CG base pairs of DNA” Nucleic Acids Res. 2011; 39, 3988–4006. doi:  1093/nar/gkq1341
  6. Shanahan, C. A.; Gaffney, B. L.; Jones, R. A.; Strobel, S. A. “Identification of c-di-GMP derivatives resistant to an EAL domain phosphodiesterase” Biochemistry, 2013, 52, 365-577. PMID23256840
  7. Gao P.; Ascano M.; Wu Y.; Barchet W.; Gaffney B. L.; Zillinger T.; Serganov, A. A.; Liu, Y.; Jones, R. A.; Hartmann, G.; Tuschl, T.; and Patel, D.J. “Cyclic [G(2',5')pA(3',5')p] is the metazoan second messenger produced by DNA-activated cyclic GMP-AMP synthase” Cell, 2013, 153, 1094-107.
  8. Gao, P.; Ascano, M.; Zillinger, T.; Wang, W.; Dai, P.; Serganov, A. A.; Gaffney, B. L.; Shuman, S.; Jones, R. A.; Deng, L.; Hartmann, G.; Barchet, W.; Tuschl, T.; and Patel, D. J. “Structure-Function Analysis of STING Activation by c[G(2',5')pA(3',5')p] and Targeting by Antiviral DMXAA” Cell, 2013, 154, 748-762.
  9. Gaffney, B.L.; and Jones, R.A. “Synthesis of c-di-GMP analogs with thiourea, urea, carbodiimide, and guanidinium linkages” Organic Lett. 2014, 16, 158-161.
  10. Veliath, E.; Gaffney, B.L.; and Jones, R.A. “Synthesis of capped RNA using a DMT group as a purification handle” Nucleosides Nucleotides Nucl. Acids, 2014, 33, 40-52.
  11. Ming, X.; Matter, B.; Song, M.; Veliath, E.; Shanley, R.; Jones, R.; and Tretyakova, N. “Mapping Structurally Defined Guanine Oxidation Products along DNA Duplexes: Influence of Local Sequence Context and Endogenous Cytosine Methylation” Am. Chem. Soc., 2014, 136, 4223–4235. DOI: 10.1021/ja411636j
  12. Meehan, R.E.; Torgerson, C.D.; Gaffney, B.L.; Jones, R.A.; and Strobel, S.A. "Nuclease-resistant c-di-AMP derivatives that differentially recognize RNA and protein receptors" Biochemistry, 2016, 55, 837-849.

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