Research Articles, Reviews & Book Chapters

    2016

  1. Raghav R. Poudyal, Malak Benslimane, Melissa P. Lokugamage, Mackenzie K. Callaway, Seth Staller & Donald H. Burke "Selective Inactivation of functional RNAs by ribozyme-catalyzed covalent modification." (in review).
  2. Raghav R. Poudyal, Phuong D. M. Nguyen, Melissa P. Lokugamage, Mackenzie K. Callaway, Jesse V. Gavette, Ramanarayanan Krishnamurthy & Donald H. Burke "Nucleobase Modification by an RNA Enzyme." (in review).
  3. Bassem Shebl, Drew E. Menke, Min Pennella, Raghav R. Poudyal, Donald H. Burke & Peter V. Cornish "Preparation of ribosomes for smFRET studies: A simplified approach." Arch Biochem Biophys. 2016; 603:118-30.
  4. Daniel J. Salamango, Khalid K. Alam, Donald H. Burke & Marc C. Johnson "In Vivo Analysis of Infectivity, Fusogenicity, and Incorporation of a Mutagenic Viral Glycoprotein Library Reveals Determinants for Virus Incorporation." J Virol. 2016; 90(14):6502-14.

    5. 2015

  5. Khalid K. Alam, Jonathan L Chang & Donald H. Burke "FASTAptamer: A Bioinformatic Toolkit for High-Throughput Sequence Analysis of Combinatorial Selections." Mol Ther Nucleic Acids. 2015; 4:e230.

    6. 2014

  6. Margaret J. Lange & Donald H. Burke "Screening inhibitory potential of anti-HIV RT RNA aptamers." Methods Mol Biol. 2014; 1103:11-29.
  7. Elisa Biondi & Donald H. Burke "RNA structural analysis by enzymatic digestion." Methods Mol Biol. 2014; 1086:41-52.

    8. 2013

  8. Elisa Biondi*, Raghav R. Poudyal*, Josh Forgy, Andrew W. Sawyer, Adam W.R. Maxwell, & Donald H. Burke "Lewis Acid catalysis of phosphoryl transfer from a copper(II)-NTP complex in a kinase ribozyme." Nucleic Acids Res. 2013; 41(5):3327-3338. *Co-First Authors
  9. Angela S. Whatley, Mark A. Ditzler, Margaret J. Lange, Elisa Biondi, Andrew W. Sawyer, Jonathan L Chang, Joshua Franken & Donald H. Burke "Potent inhibition of HIV-1 Reverse Transcriptase and replication by nonpseudoknot, 'UCAA-motif' RNA aptamers." Mol Ther Nucleic Acids. 2013; 2:e71.
  10. Mark A. Ditzler, Margaret J. Lange, Debojit Bose, Chris Bottoms, Katherine Virkler, Andrew W. Sawyer, Angela S. Whatley, William Spollen, Givan Scott & Donald H. Burke "High-throughput sequence analysis reveals structural diversity and improved potency among RNA inhibitors of HIV reverse transcriptase." Nucleic Acids Res. 2013; 41(3):1873-1884.

    11. 2012

  11. Margaret J. Lange, Tarun K. Sharma, Angela S. Whatley, Linda Landon, Michael Tempesta, Marc C. Johnson & Donald H. Burke "Robust suppression of HIV replication by intracellularly expressed reverse transcriptase aptamers is independent of ribozyme processing." Mol Ther. 2012; 20(12):2304-2314.
  12. Elisa Biondi, Adam W.R. Maxwell & Donald H. Burke "A small ribozyme with dual-site kinase activity." Nucleic Acids Res. 2012; 40(15):7528-7540.
  13. Elisa Biondi & Donald H. Burke "Separating and analyzing sulfur-containing RNAs with organomercury gels." Methods in Mol Biol. 2012; 883:111-120.
  14. Donald H. Burke "Cell-Penetrating RNAs: New Keys to the Castle." Mol Ther. 2012; 20(2):251-253.
  15. Tanyaradzwa Ndongwe, Adeyemi Adedeji, Eleftherios Michailidis, Yee-Tsuei Ong, Atsuko Hachiya, Bruno Marchand, Emily Ryan, Devendra K. Rai, Karen A. Kirby, Angela S. Whatley, Donald H. Burke, Marc C. Johnson, Shilei Ding, Yi-Min Zheng, Shan-Lu Liu, Ei-Ichi Kodama, Krista A. Delviks-Frankenberry, Vinay K. Pathak, Hiroaki Mitsuya, Michael A. Parniak, Kamal Singh & Stefan G. Sarafianos "Biochemical, Inhibition, and Inhibitor Resistance Studies of Xenotropic Murine Leukemia Virus-Related Virus Reverse Transcriptase." Nucleic Acids Res. 2012; 40(1):345-359.

    16. 2011

  16. Mark A. Ditzler, Debojit Bose, Nikolozi Shkriabai, Bruno Marchand, Stefan G. Sarafianos, Mamuka Kvaratskhelia & Donald H. Burke "Broad-spectrum aptamer inhibitors of HIV-reverse transcriptase closely mimic natural substrates." Nucleic Acids Res. 2011; 39(18):8237-8247.
  17. Manami Roychowdhury-Saha, Sugata Roychowdhury & Donald H. Burke "Conformational heterogeneity and the determinants of tertiary stabilization in the hammerhead ribozyme from Dolichopoda cave crickets." RNA Biol. 2011; 8(5):893-903.

    18. 2010

  18. Donald H. Burke & Steven S. Rhee "Active site assembly within a kinase ribozyme." RNA 2010; 16(12):2349-2359.
  19. David G. Nickens, Nirmala Bardiya, James T. Patterson & Donald H. Burke "Template-directed ligation of tethered mononucleotides by t4 DNA ligase for kinase ribozyme selection." PLoS One. 2010; 5(8):e12368.
  20. Elisa Biondi, David G. Nickens, Samantha Warren & Donald H. Burke "Convergent donor and acceptor substrate utilization among kinase ribozymes." Nucleic Acids Res. 2010; 38(19):6785-6795.

    21. 2008

  21. Daniel Michalowski, Rebecca Chitima-Matsiga, Daniel M. Held & Donald H. Burke "Novel bimodular DNA aptamers with guanosine quadruplexes inhibit phylogenetically diverse HIV -1 reverse transcriptases." Nucleic Acids Res. 2008; 36:7124-7135.

    22. 2007

  22. Jay D. Kissel, Daniel M. Held, Richard W. Hardy & Donald H. Burke "Active site binding and sequence requirements for inhibition of HIV-1 reverse transcriptase by the RT1 Family of Single-Stranded DNA Aptamers." Nucleic Acids Res. 2007; 35(15):5039-5050.
  23. Manami Roychowdhury-Saha & Donald H. Burke "Distinct reaction pathway promoted by non-divalent-metal cations in a tertiary stabilized hammerhead ribozyme." RNA 2007; 13(6):841-848.
  24. James T. Patterson, David G. Nickens & Donald H. Burke "HIV-1 reverse transcriptase pausing at bulky 2' adducts is relieved by deletion of the RNase H domain." RNA Biol. 2006; 3:163-169.
  25. Jay D. Kissel, Daniel M. Held & Donald H. Burke "Single-stranded DNA aptamer RT1t49 inhibits RT polymerase and RNase H functions of HIV type1, HIV type 2, and SIVCPR RTs." AIDS Res Hum Retroviruses. 2007; 23(5):699-708.
  26. Daniel M. Held, Jay D. Kissel, Sarah Thacker, Daniel Michalowski, Dayal Saran, Jianfei Ji, Richard W. Hardy, John R. Rossi, & Donald H. Burke "Cross-clade inhibition of recombinant human immunodeficiency virus type 1 (HIV-1), HIV-2, and simian immunodeficiency virus SIVcpz reverse transcriptases by RNA pseudoknot aptamers." J Virol. 2007; 81(10):5375-5384.
  27. Dayal Saran & Donald H. Burke "A versatile photocleaveable bifunctional linker for facile synthesis of substrate-DNA conjugates for the selection of nucleic acid catalysts." Bioconj Chem. 2007; 18(1):275-279.
  28. Bong-Rae Cho & Donald H. Burke "Conformational Dynamics of self-thiophosphorylating RNA." Bull. Korean Chem. Soc. 28:463-466.

    29. 2006

  29. Bong-Rae Cho & Donald H. Burke "Topical rearrangement yields structural stabilization and interhelical distance constraints in the Kin. 46 self-phosphorylating ribozyme." RNA 2006; 12(12):2118-2125.
  30. Manami Roychowdhury-Saha & Donald H. Burke "Extraordinary rates of transition metal ion-mediated ribozyme catalysis." RNA 2006; 12(10):1846-1852.
  31. Daniel M. Held, Jay D. Kissel, Dayal Saran, Daniel Michalowski & Donald H. Burke "Differential susceptibility of HIV-1 reverse transcriptase to inhibition by RNA aptamers in enzymatic reactions monitoring specific steps during genome replication." J Biol Chem. 2006; 281(35):25712-25722.
  32. Dayal Saran, Daniel M. Held & Donald H. Burke "Multiple-turnover thio-ATP hydrolase and phospho-enzyme intermediate formation activities catalyzed by an RNA enzyme." Nucleic Acids Res. 2006; 34(11):3201–3208.
  33. Daniel M. Held, Jay D. Kissel, James T. Patterson, David G. Nickens & Donald H. Burke "HIV-1 inactivation by nucleic acid aptamers." Front Biosci. 2006; 11:89-112.

    34. 2005

  34. Dayal Saran, David G. Nickens & Donald H. Burke "A trans acting ribozyme that phosphorylates exogenous RNA." Biochemistry 2005; 44(45):15007-15016.
  35. Donald H. Burke & S. S. Travis Greathouse "Low-magnesium, trans-cleavage activity by type III, tertiary stabilized hammerhead ribozymes with stem 1 discontinuities." BMC Biochem. 2005; 6:14.

    36. 2004

  36. Vanvimon Saksmerprome, Manami Roychowdhury-Saha, Sumedha Jayasena, Anastasia Khvorova & Donald H. Burke "Artificial tertiary motifs stabilize trans-cleaving hammerhead ribozymes under conditions of submillimolar divalent ions and high temperatures." RNA 2004; 10(12):1916-1924.
  37. Vanvimon Saksmerprome & Donald H. Burke "Deprotonation stimulates productive folding in allosteric TRAP hammerhead ribozymes." J Mol Biol. 2004; 341(3):685-694.
  38. Donald H. Burke "Ribozyme-catalyzed genetics." Chapter 4 of Genetic Code and the Origin of Life, ed Lluis Ribas de Pauplana
  39. Steven S. Rhee & Donald H. Burke "Tris(2-carboxyethyl)phosphine stabilization of RNA: comparison with dithiothreitol for use with nucleic acid and thiophosphoryl chemistry." Anal Biochem. 2004; 325(1):137-143.

    40. 2003

  40. Sanchita Hati, Amy R. Boles, Amanda Posto, John Zaborske, Brett Bergman & Donald H. Burke "Nickel2+-mediated assembly of RNA-amino acid complex." Chem & Biol. 2003; 10(11):1129-1137.
  41. Vanvimon Saksmerprome & Donald H. Burke "Structural flexibility and the thermodynamics of helix exchange constrain attenuation and allosteric activation of hammerhead ribozyme TRAPs." Biochemistry 2003; 42(47):13879-13886.
  42. David G. Nickens, James T. Patterson & Donald H. Burke "Inhibition of HIV-1 reverse transcriptase by RNA aptamers in Escherichia coli." RNA 2003; 9(9):1029-1033.
  43. Daniel M. Held, S. S. Travis Greathouse, Amit Agrawal & Donald H. Burke "Evolutionary landscapes for the acquisition of new ligand recognition by RNA aptamers." J Mol Evol. 2003; 57(3):299-308.
  44. Dayal Saran, Joseph Frank & Donald H. Burke "The tyranny of adenosine recognition among RNA aptamers to coenzyme A." BMC Evol Biol. 2003; 3:26.

    45. 2002

  45. Donald H. Burke & David G. Nickens "Expressing RNA aptamers inside cells to reveal proteome and ribonome function." Brief Funct Genomic and Proteomic 2002; 1(2):169-188.
  46. Donald H. Burke, Nicole D.S. Ozerova & Marit Nilsen-Hamilton "Allosteric hammerhead ribozyme TRAPs." Biochemistry 2002; 41(21):6588-6594.
  47. Susan M. Lato, Nicole D.S. Ozerova, Kaizhang He, Zinaida Sergueeva, Barbara Ramsey Shaw & Donald H. Burke "Boron-containing aptamers to ATP." Nucleic Acids Res. 2002; 30(6):1401-1407.
  48. Manami Roychowdhury-Saha, Susan M. Lato, Eric D. Shank & Donald H. Burke "Flavin recognition by an RNA aptamer targeted toward FAD." Biochemistry 2002; 41(8):2492-2499.

    49. 1998

  49. Donald H. Burke & John H. Willis "Recombination, RNA evolution, and bifuncitonal RNA molecules isolated through chimeric SELEX." RNA 1998; 4(9):1165-1175.
  50. Donald H. Burke & David C. Hoffman "A novel acidophillic RNA motif that recognizes coenzyme A." Biochemistry 1998; 37(13):4653-4663.

    51. 1997

  51. Donald H. Burke, David C. Hoffman, Analisa Brown, Mark Hanson, Arthur Pardi & Larry Gold "RNA aptamers to the peptidyl transferase inhibitor chloramphenicol." Chem Biol. 1997; 4(11):833-843.
  52. Donald H. Burke & Larry Gold "RNA aptamers to the adenosine moiety of S-adenosyl methionine: structural inferences from variations on a theme and the reproducibility of SELEX." Nucleic Acids Res. 1997; 25(10):2020-2024.

    53. 1996

  53. Donald H. Burke, Lori Scates, Katy Andrews, Zdenek Hostomsky & Larry Gold "Bent pseudoknots and novel RNA inhibitors of type 1 human immunodeficiency virus (HIV-1) reverse transcriptase." J Mol Biol. 1996; 264(4):650-666.

    54. 1995

  54. Marie A. Alberti, Donald H. Burke & John E. Hearst "Structure and sequence of the photosynthesis gene cluster." Chapter 50 in Anoxygenic Photosynthetic Bacteria, R. E. Blankenship, M. T. Madigan, and C. E. Bauer, eds, Kluwer Academic Publishers, The Netherlands.

    55. 1994

  55. Bhupinder Hundle, Marie A. Alberti, Vitus Nievelstein, Peter Beyer, Hans Kleinig, Gregory A. Armstrong, Donald H. Burke & John E. Hearst "Functional assignment of Erwinia herbicola Eho10 carotenoid genes expressed in Escherichia coli." Mol Gen Genet. 1994; 245(4):406-416.

    56. 1993

  56. James M. Nolan, Donald H. Burke & Norman R. Pace (1993) "Circularly permuted tRNAs as specific photoaffinity probes of ribonuclease P RNA structure." Science 1993; 261(5122):762-765.
  57. Donald H. Burke, Linda Raubeson, Diana Stein, Marie A. Alberti & John E. Hearst (1993) "Phylogenetic distribution of genes for the chlorophyll iron protein subunit (chlL) of light-independent protochlorophyllide reductase." Plant Systematics and Evolution 187:89-102.
  58. Gregory A. Armstrong, David N. Cook, Dzwokai Ma, Marie A. Alberti, Donald H. Burke & John E. Hearst "Regulation of carotenoid and bacteriochlorophyll biosynthesis genes and identification of an evolutionarily conserved gene required for bacteriochlorophyll accumulation." J Gen Microbiol 1993; 139(5):897-906.
  59. Donald H. Burke, John E. Hearst & Arend Sidow "Early evolution of photosynthesis: Clues from nitrogenase and chlorophyll iron proteins." Proc Natl Acad Sci USA 1993; 90(15):7134-7138.
  60. Donald H. Burke, Marie A. Alberti & John E. Hearst "bchFNBH bacteriochlorophyll synthesis genes of Rhodobacter capsulatus and identification of the third subunit of light-independent protochlorophyllide reductase in bacteria and plants." J Bacteriol. 1993; 175(8):2414-2422.
  61. Donald H. Burke, Marie A. Alberti & John E. Hearst "The Rhodobacter capsulatus chlorin reductase-encoding locus, bchA consists of three genes bchX, bchY, and bchZ." J Bacteriol. 1993; 175(8):2407-2413.

    62. 1990

  62. Donald H. Burke-Agüero & John E. Hearst "An RNA Holliday Junction? Structural and dynamic considerations of the T4 gene 60 interruption." J Mol Biol. 1990; 213(2):199-201.

Books & Edited Volumes

  1. Methods in Enzymology special issue on Riboswitches: Discovery, Structure and Function, Donald H Burke, Editor (in preparation for 2014).
  2. Methods in Enzymology special issue on Riboswitches: Antibiotic Targets and Tools for Synthetic Biology, Donald H Burke, Editor (in preparation for 2014).
  3. Methods in Enzymology special issue on Computational Methods for Riboswitches, Shi-Jie Chen & Donald H Burke, Editors (in preparation for 2015).