Biomolecular Modeling & Design

Jones, Roger A.

RJones rDistinguished Professor

Research Synopsis: Modified/labeled DNA fragments: synthesis and characterization

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(848) 445-4900







Research Summary

My research interests are in nucleic acid synthetic chemistry, including both nucleosides and nucleic acid fragments. This work is focused on molecules of biological importance, including specific 13C and/or 15N labeled DNA and RNA fragments, and those with thioalkyl tethers for crosslinking with proteins. In addition, we developed the first synthesis of cyclic dinucleotides and are currently working on the bacterial signaling molecule c-di-GMP and the metazoan signaling molecule c[G(2',5')pA(3',5')p].


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, 1-15.

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, 1094-1107.

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.

Shanahan, C.A.; Gaffney, B.L.; Jones R.A.; Strobel, S.A. “Differential Analog Binding by Two Classes of c-di-GMP Riboswitches” J. Am. Chem. Soc., 2011, 133, 15578–15592.

Tu, X.; 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.

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 Lett., 2010, 12, 3269–3271.

Zhang, Z; Dai, J.; Veliath, E.; Jones, R.; Yang, D. “Structure of a two-G-tetrad intramolecular G-quadruplex formed by a variant human telomeric sequence in K+ solution: insights into the interconversion of human telomeric G-quadruplex structures” Nucleic Acids Res., 2010, 38, 1009-1021.

Das, K.; Bandwar, R.P.; White, K.L.; Feng, J.Y.; Sarafianos, S.G.; Tuske, S.; Tu, X.; Clark, Jr., A.D.; Boyer, P.L.; Hou, X.; Gaffney, B.L.; Jones, R.A.; Miller, M.D.; Hughes, S.H.; Arnold, E. “Structural basis for the role of the K65R mutation in HIV-1 reverse transcriptase polymerization, excision antagonism, and tenofovir resistance” J. Biol. Chemistry, 2009, 284, 35092-35100.

Han, Q.; Sarafianos, S.G.; Arnold, E.; Parniak, M.A.; Gaffney, B.L.; Jones, R.A. “Synthesis of boranoate, selenoate, and thioate analogs of AXTp¬4A and Ap4A” Tetrahedron, 2009, 65, 7915-7920.

Han, Q.; Sarafianos, S.G.; Arnold, E.; Parniak, M.A.; Gaffney, B.L.; Jones, R.A. “Synthesis of AZTpSpCX2ppSA and AZTSpCX2ppSAZT: Hydrolysis-resistant potential inhibitors of the AZT excision reaction” Organic Lett., 2007, 9, 5243-5246.

Dai, J.; Punchihewa, C.; Ambrus, A.; Chen, D.; Jones, R.A.; Yang, D. “Structure of the intramolecular human telomeric G-quadruplex in potassium solution: A novel adenine triple formation” Nucleic Acids Res., 2007, 35, 2440 - 2450.

Dai, J.; Carver, M.; Punchihewa, C.; Jones, R.A.; Yang, D. “Structure of the Hybrid-2 type intramolecular human telomeric G-quadruplex in K+ solution: insights into structure polymorphism of the human telomeric sequence” Nucleic Acids Res., 2007, 35, 4927-4940.

Ambrus, A.; Chen, D.; Dai, J.; Bialis, T.; Jones, R. A.; Yang, D. “Human telomeric sequence forms a hybrid-type intramolecular G-quadruplex structure with mixed parallel/antiparallel strands in potassium solution” Nucleic Acids Res., 2006, 34, 2723-2735.

Zhang, Z.; Gaffney, B.L.; Jones, R.A. “Polymorphism of the Signaling Molecule c-di-GMP” J. Am. Chem. Soc., 2006, 128, 7015-7024.

Han, Q.; Gaffney, B.L.; Jones, R.A. “One-Flask Synthesis of Dinucleoside Tetra- and Pentaphosphates” Organic Lett., 2006, 8, 2075-2077.

Dai, J.; Chen, D.; Jones, R. A.; Hurley, L. H.; Yang, D. “NMR solution structure of the major G-quadruplex structure formed in the human BCL2 promoter region” Nucleic Acids Res., 2006, 34, 5133-5144.

Dai, J.; Dexheimer, T.S.; Chen, D.; Carver, M.; Ambrus, A.; Jones, R.A.; Yang, D. “An Intramolecular G-Quadruplex Structure with Mixed Parallel/Antiparallel G-Strands Formed in the Human BCL-2 Promoter Region in Solution” J. Am. Chem. Soc., 2006, 128, 1096-1098.

Fan, Y.; Gaffney, B.L.; Jones, R.A. “RNA GG•UU Motif Binds K+ but not Mg2+” J. Am. Chem. Soc., 2005, 127, 17588-17589.

Hisert, K.B; MacCoss, M.; Shiloh,M.U.; Darwin, K.H.; Singh, S.; Jones, R.A.; Ehrt, S.; Zhang, Z.; Gaffney, B.L.; Gandotra, S.; Holden, D.W.; Murray, D.; Nathan, C. “A glutamate-alanine-leucine (EAL) domain protein of Salmonella controls bacterial survival in mice, antioxidant defense and killing of macrophages: Role of cyclic diGMP” Mol. Microbiol., 2005, 56, 1234-1245.

Hoffman, L.R.; D'Argenio, D.A.; MacCoss, M.J.; Shang, Z.; Jones, R.A.; Miller, S.I. “Aminoglycoside antibiotics induce bacterial biofilm formation” Nature, 2005, 436, 1171-1175.

Ambrus, A.; Chen, D.; Dai, J.; Jones, R. A.; Yang, D. “Solution Structure of the Biologically Relevant G-Quadruplex Element in the Human c-MYC Promoter. Implications for G-Quadruplex Stabilization” Biochemistry, 2005, 44, 2048-2058.

Zhang, Z.; Gaffney, B.L.; Jones, R.A. “c-di-GMP Displays A Monovalent Metal Ion Dependent Polymorphism” J. Am. Chem. Soc., 2004, 126, 16700-16701.

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