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Donald Burke-Agüero

Donald Burke-Agüero

Professor

Phone: 573-884-1316
burkedh@missouri.edu
471H Bond Life Sciences Center

Donald Burke-Agüero is a professor of molecular microbiology and immunology and joint professor of biochemistry.

Burke explores the many roles of ribonucleic acid, or RNA. This substance has long been known to function in cells to help copy genetic information from DNA. But scientists are increasingly recognizing many other tasks that RNA carries out. Burke uses cell biology, biochemistry, and sophisticated computational approaches to compare millions of RNA molecules, looking for the ones that can do helpful jobs. He foresees that RNA might be harnessed for artificial metabolisms or to direct the development of stem cells. Burke has developed RNA molecules called aptamers that bind tightly to proteins from HIV and prevent this virus from replicating. His lab also uses molecular evolution techniques to develop artificial ribozymes, which are RNA molecules that catalyze chemical reactions. These have implications for the study of evolution because the earliest life on Earth is widely thought to have evolved through RNA.

Lab site: Burke Lab

News about Donald Burke-Agüero

Research Topics

2′-fluoro-modified pyrimidines enhance affinity of RNA oligonucleotides to HIV-1 reverse transcriptase. Gruenke, PR, Alam, KK, Singh K, Burke DH. RNA; 26(11):1667-1679.

Featured in this article: Paige Gruenke, Kamlendra Singh, Donald Burke-Agüero.

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Aptamers with Tunable Affinity Enable Single-Molecule Tracking and Localization of Membrane Receptors on Living Cancer Cells. Delcanale P, Porciani D, Pujals S, Jurkevich A, Chetrusca A, Tawiah KD, Burke DH, Albertazzi L. Angewandte Chemie - International Edition; 59(42):18546-18555.

Featured in this article: David Porciani, Alexander Jurkevich, Donald Burke-Agüero.

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Binding interface and impact on protease cleavage for an RNA aptamer to HIV-1 reverse transcriptase. Nguyen PDM, Zheng J, Gremminger TJ, Qiu L, Zhang D, Tuske S, Lange MJ, Griffin PR, Arnold E, Chen S-J, Zou X, Heng X, Burke DH. Nucleic Acids Research; 48(5):2709-2722.

Featured in this article: Margaret Lange, Donald Burke-Agüero.

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Tumor-cell–macrophage fusion cells as liquid biomarkers and tumor enhancers in cancer. Manjunath Y, Porciani D, Mitchem JB, Suvilesh KN, Avella DM, Kimchi ET, Staveley-o’carroll KF, Burke DH, Li G, Kaifi JT. International Journal of Molecular Sciences; 21(5):1872.

Featured in this article: David Porciani, Donald Burke-Agüero.

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Therapeutic peptide delivery: Via aptamer-displaying, disulfide-linked peptide amphiphile micelles. Smith JD, Cardwell LN, Porciani D, Nolla A, Cornelison BT, Schulte MC, Gallazzi F, Burke DH, Daniels MA, Ulery BD. Molecular Systems Design and Engineering; 5(1):269-283.

Featured in this article: David Porciani, Fabio Gallazzi, Donald Burke-Agüero.

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Strain-specific effect on biphasic DNA binding by HIV-1 integrase. Hill KJ, Rogers LC, Njenda DT, Burke DH, Sarafianos SG, Sonnerborg A, Neogi U, Singh K. AIDS; 33(3):588-592.

Featured in this article: Donald Burke-Agüero, Kamlendra Singh.

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Activation of Innate Immune Responses by a CpG Oligonucleotide Sequence Composed Entirely of Threose Nucleic Acid. Lange MJ, Burke DH, Chaput JC. Nucleic Acid Therapeutics; 29(1):51-59.

Featured in this article: Margaret Lange, Donald Burke-Agüero.

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GS-CA compounds: First-in-class HIV-1 capsid inhibitors covering multiple grounds. Singh K, Gallazzi F, Hill KJ, Burke DH, Lange MJ, Quinn TP, Neogi U, Sönnerborg A. Frontiers in Microbiology; 10(JUN):1227.

Featured in this article: Kamlendra Singh, Fabio Gallazzi, Donald Burke-Agüero, Margaret Lange, Thomas Quinn.

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Poly-Target Selection Identifies Broad-Spectrum RNA Aptamers. Alam KK, Chang JL, Lange MJ, Nguyen PDM, Sawyer AW, Burke DH. Molecular Therapy - Nucleic Acids; 13:605-619.

Featured in this article: Margaret Lange, Donald Burke-Agüero.

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Modular cell-internalizing aptamer nanostructure enables targeted delivery of large functional RNAs in cancer cell lines. Porciani D, Cardwell LN, Tawiah KD, Alam KK, Lange MJ, Daniels MA, Burke DH. Nature Communications; 9(1):2283.

Featured in this article: David Porciani, Margaret Lange, Donald Burke-Agüero.

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Aptamer-displaying peptide amphiphile micelles as a cell-targeted delivery vehicle of peptide cargoes. Smith JD, Cardwell LN, Porciani D, Nguyen JA, Zhang R, Gallazzi F, Tata RR, Burke DH, Daniels MA, Ulery BD. Physical Biology; 15(6):065006.

Featured in this article: David Porciani, Fabio Gallazzi, Donald Burke-Agüero.

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A Fluorescent Split Aptamer for Visualizing RNA-RNA Assembly in Vivo. Alam KK, Tawiah KD, Lichte MF, Porciani D, Burke DH. ACS Synthetic Biology; 6(9):1710-1721.

Featured in this article: David Porciani, Donald Burke-Agüero.

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Toward the selection of cell targeting aptamers with extended biological functionalities to facilitate endosomal escape of cargoes. Tawiah KD, Porciani D, Burke DH. Biomedicines; 5(3):51.

Featured in this article: David Porciani, Donald Burke-Agüero.

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RNA-protein interactions govern antiviral specificity and encapsidation of broad spectrum anti-HIV reverse transcriptase aptamers. Lange MJ, Nguyen PDM, Callaway MK, Johnson MC, Burke DH. Nucleic Acids Research; 45(10):6087-6097.

Featured in this article: Margaret Lange, Marc Johnson, Donald Burke-Agüero.

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Selective Inactivation of Functional RNAs by Ribozyme-Catalyzed Covalent Modification. Poudyal RR, Benslimane M, Lokugamage MP, Callaway MK, Staller S, Burke DH. ACS Synthetic Biology; 6(3):528-534.

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Nucleobase modification by an RNA enzyme. Poudyal RR, Nguyen PDM, Lokugamage MP, Callaway MK, Gavette JV, Krishnamurthy R, Burke DH. Nucleic Acids Research; 45(3):1345-1354.

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Preparation of ribosomes for smFRET studies: A simplified approach. Shebl B, Menke DE, Pennella M, Poudyal RR, Burke DH, Cornish PV. Archives of Biochemistry and Biophysics; 603:118-130.

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In vivo analysis of infectivity, fusogenicity, and incorporation of a mutagenic viral glycoprotein library reveals determinants for virus incorporation. Salamango DJ, Alam KK, Burke DH, Johnson MC. Journal of Virology; 90(14):6502-6514.

Featured in this article: Donald Burke-Agüero, Marc Johnson.

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FASTAptamer: A bioinformatic toolkit for high-throughput sequence analysis of combinatorial selections. Alam KK, Chang JL, Burke DH. Molecular Therapy - Nucleic Acids; 4(3):e230.

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Preface. Burke-Aguero DH. Methods in Enzymology; 550:xv-xix.

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Preface. Chen S-J, Burke-Agüero DH. Methods in Enzymology; 553:xv-xvii.

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Preface. Burke-Aguero DH. Methods in Enzymology; 549(C):xix-xxiii.

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RNA structural analysis by enzymatic digestion. Biondi E, Burke DH. Methods in Molecular Biology; 1086:41-52.

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Screening inhibitory potential of anti-HIV RT RNA aptamers. Lange MJ, Burke DH. Methods in Molecular Biology; 1103:11-29.

Featured in this article: Margaret Lange, Donald Burke-Agüero.

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Lewis acid catalysis of phosphoryl transfer from a copper(II)-NTP complex in a kinase ribozyme. Biondi E, Poudyal RR, Forgy JC, Sawyer AW, Maxwell AWR, Burke DH. Nucleic Acids Research; 41(5):3327-3328.

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High-throughput sequence analysis reveals structural diversity and improved potency among RNA inhibitors of HIV reverse transcriptase. Ditzler MA, Lange MJ, Bose D, Bottoms CA, Virkler KF, Sawyer AW, Whatley AS, Spollen W, Givan SA, Burke DH. Nucleic Acids Research; 41(3):1873-1884.

Featured in this article: Margaret Lange, Christopher Bottoms, Bill Spollen , Scott Givan, Donald Burke-Agüero.

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Potent inhibition of HIV-1 reverse transcriptase and replication by nonpseudoknot, “UCAA-motif” RNA aptamers. Whatley AS, Ditzler MA, Lange MJ, Biondi E, Sawyer AW, Chang JL, Franken JD, Burke DH. Molecular Therapy - Nucleic Acids; 2:e71.

Featured in this article: Margaret Lange, Donald Burke-Agüero.

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A small ribozyme with dual-site kinase activity. Biondi E, Maxwell AWR, Burke DH. Nucleic Acids Research; 40(15):7528-7540.

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Cell-penetrating RNAs: New keys to the castle. Burke DH. Molecular Therapy; 20(2):251-253.

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Separating and analyzing sulfur-containing rnas with organomercury gels. Biondi E, Burke DH. Methods in Molecular Biology; 883:111-120.

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Robust suppression of HIV replication by intracellularly expressed reverse transcriptase aptamers is independent of ribozyme processing. Lange MJ, Sharma TK, Whatley AS, Landon LA, Tempesta MA, Johnson MC, Burke DH. Molecular Therapy; 20(12):2304-2314.

Featured in this article: Margaret Lange, Marc Johnson, Donald Burke-Agüero.

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Biochemical, inhibition and inhibitor resistance studies of xenotropic murine leukemia virus-related virus reverse transcriptase. Ndongwe TP, Adedeji AO, Michailidis E, Ong YT, Hachiya A, Marchand B, Ryan EM, Rai DK, Kirby KA, Whatley AS, Burke DH, Johnson M, Ding S, Zheng Y-M, Liu S-L, Kodama E-I, Delviks-Frankenberry KA, Pathak VK, Mitsuya H, Parniak MA, Singh K, Sarafianos SG. Nucleic Acids Research; 40(1):345-359.

Featured in this article: Donald Burke-Agüero, Marc Johnson, Kamlendra Singh.

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Broad-spectrum aptamer inhibitors of HIV reverse transcriptase closely mimic natural substrates. Ditzler MA, Bose D, Shkriabai N, Marchand B, Sarafianos SG, Kvaratskhelia M, Burke DH. Nucleic Acids Research; 39(18):8237-8247.

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Conformational heterogeneity and the determinants of tertiary stabilization in the hammerhead ribozyme from Dolichopoda cave crickets. Roychowdhury-Saha M, Roychowdhury S, Burke DH. RNA Biology; 8(5).

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Assembly and activation of a kinase ribozyme. Burke DH, Rhee SS. RNA; 16(12):2349-2359.

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Template-directed ligation of tethered mononucleotides by T4 DNA ligase for kinase ribozyme selection. Nickens DG, Bardiya N, Patterson JT, Burke DH. PLoS ONE; 5(8):e12368.

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Convergent donor and acceptor substrate utilization among kinase ribozymes. Biondi E, Nickens DG, Warren S, Saran D, Burke DH. Nucleic Acids Research; 38(19):6785-6795.

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Novel bimodular DNA aptamers with guanosine quadruplexes inhibit phylogenetically diverse HIV-1 reverse transcriptases. Michalowski D, Chitima-Matsiga R, Held DM, Burke DH. Nucleic Acids Research; 36(22):7124-7135.

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Active site binding and sequence requirements for inhibition of HIV-1 reverse transcriptase by the RT1 family of single-stranded DNA aptamers. Kissel JD, Held DM, Hardy RW, Burke DH. Nucleic Acids Research; 35(15):5039-5050.

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Distinct reaction pathway promoted by non-divalent-metal cations in a tertiary stabilized hammerhead ribozyme. Roychowdhury-Saha M, Burke DH. RNA; 13(6):841-848.

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Single-stranded DNA aptamer RT1t49 inhibits RT polymerase and RNase H functions of HIV type 1, HIV type 2, and SIVCPZ RTs. Kissel JD, Held DM, Hardy RW, Burke DH. AIDS Research and Human Retroviruses; 23(5):699-708.

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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. Held DM, Kissel JD, Thacker SJ, Michalowski D, Saran D, Ji A, Hardy RW, Rossi JJ, Burke DH. Journal of Virology; 81(10):5375-5384.

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Conformational dynamics of self-thiophosphorylating RNA. Cho B-R, Burke DH. Bulletin of the Korean Chemical Society; 28(3):463-466.

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A versatile photocleavable bifunctional linker for facile synthesis of substrate-DNA conjugates for the selection of nucleic acid catalysts. Saran D, Burke DH. Bioconjugate Chemistry; 18(1):275-279.

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Topological rearrangement yields structural stabilization and interhelical distance constraints in the Kin.46 self-phosphorylating ribozyme. Cho B, Burke DH. RNA; 12(12):2118-2125.

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Multiple-turnover thio-ATP hydrolase and phospho-enzyme intermediate formation activities catalyzed by an RNA enzyme. Saran D, Held DM, Burke DH. Nucleic Acids Research; 34(11):3201-3208.

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Extraordinary rates of transition metal ion-mediated ribozyme catalysis. Roychowdhury-Saha M, Burke DH. RNA; 12(10):1846-1852.

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Differential susceptibility of HIV-1 reverse transcriptase to inhibition by RNA aptamers in enzymatic reactions monitoring specific steps during genome replication. Held DM, Kissel JD, Saran D, Michalowski D, Burke DH. Journal of Biological Chemistry; 281(35):25712-25722.

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HIV-1 reverse transcriptase pausing at bulky 2′ adducts is relieved by deletion of the RNase H domain. Patterson JT, Nickens DG, Burke DH. RNA Biology; 3(4):163-169.

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HIV-1 inactivation by nucleic acid aptamers. Held DM, Kissel JD, Patterson JT, Nickens DG, Burke DH. Frontiers in Bioscience; 11(1 P.1-446):89-112.

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A trans acting ribozyme that phosphorylates exogenous RNA. Saran D, Nickens DG, Burke DH. Biochemistry; 44(45):15007-15016.

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Low-magnesium, trans-cleavage activity by type III, tertiary stabilized hammerhead ribozymes with stem 1 discontinuities. Burke DH, Travis Greathouse S. BMC Biochemistry; 6:14.

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Artificial tertiary motifs stabilize trans-cleaving hammerhead ribozymes under conditions of submillimolar divalent ions and high temperatures. Saksmerprome V, Roychowdhury-Saha M, Jayasena S, Khvorova A, Burke DH. RNA; 10(12):1916-1924.

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Deprotonation stimulates productive folding in allosteric TRAP hammerhead ribozymes. Saksmerprome V, Burke DH. Journal of Molecular Biology; 341(3):685-694.

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Tris(2-carboxyethyl)phosphine stabilization of RNA: Comparison with dithiothreitol for use with nucleic acid and thiophosphoryl chemistry. Rhee SS, Burke DH. Analytical Biochemistry; 325(1):137-143.

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The tyranny of adenosine recognition among RNA aptamers to coenzyme A. Saran D, Frank J, Burke DH. BMC Evolutionary Biology; 3:26.

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Structural Flexibility and the Thermodynamics of Helix Exchange Constrain Attenuation and Allosteric Activation of Hammerhead Ribozyme TRAPs. Saksmerprome V, Burke DH. Biochemistry; 42(47):13879-13886.

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Inhibition of HIV-1 reverse transcriptase by RNA aptamers in Escherichia coli. Nickens DG, Patterson JT, Burke DH. RNA; 9(9):1029-1033.

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Evolutionary landscapes for the acquisition of new ligand recognition by RNA aptamers. Held DM, Greathouse ST, Agrawal A, Burke DH. Journal of Molecular Evolution; 57(3):299-308.

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Nickel2+-mediated assembly of an RNA-amino acid complex. Hati S, Boles AR, Zaborske JM, Bergman B, Posto AL, Burke DH. Chemistry and Biology; 10(11):1129-1137.

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Expressing RNA aptamers inside cells to reveal proteome and ribonome function. Burke DH, Nickens DG. Briefings in Functional Genomics and Proteomics; 1(2):169-188.

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Allosteric hammerhead ribozyme TRAPs. Burke DH, Ozerova NDS, Nilsen-Hamilton M. Biochemistry; 41(21):6588-6594.

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Boron-containing aptamers to ATP. Lato SM, Ozerova NDS, He K, Sergueeva Z, Shaw BR, Burke DH. Nucleic Acids Research; 30(6):1401-1407.

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Flavin recognition by an RNA aptamer targeted toward FAD. Roychowdhury-Saha M, Lato SM, Shank ED, Burke DH. Biochemistry; 41(8):2492-2499.

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Recombination, RNA evolution, and bifunctional RNA molecules isolated through chimeric SELEX. Burke DH, Willis JH. RNA; 4(9):1165-1175.

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A novel acidophilic RNA motif that recognizes coenzyme A. Burke DH, Hoffman DC. Biochemistry; 37(13):4653-4663.

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RNA aptamers to the adenosine moiety of S-adenosyl methionine: Structural inferences from variations on a theme and the reproducibility of SELEX. Burke DH, Gold L. Nucleic Acids Research; 25(0):2020-2024.

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RNA aptamers to the peptidyl transferase inhibitor chloramphenicol. Burke DH, Hoffman DC, Brown A, Hansen M, Pardi A, Gold L. Chemistry and Biology; 4(11):833-843.

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Bent pseudoknots and novel RNA inhibitors of type 1 human immunodeficiency virus (HIV-1) reverse transcriptase. Burke DH, Scates L, Andrews K, Gold L. Journal of Molecular Biology; 264(4):650-666.

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Functional assignment of Erwinia herbicola Eho10 carotenoid genes expressed in Escherichia coli. Hundle B, Alberti M, Nievelstein V, Beyer P, Kleinig H, Armstrong GA, Burke DH, Hearst JE. MGG Molecular & General Genetics; 245(4):406-416.

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The chlL (frxC) gene: Phylogenetic distribution in vascular plants and DNA sequence from Polystichum acrostichoides (Pteridophyta) and Synechococcus sp. 7002 (Cyanobacteria). Burke DH, Raubeson LA, Alberti M, Hearst JE, Jordan ET, Kirch SA, Valinski AEC, Conant DS, Stein DB. Plant Systematics and Evolution; 187(1-4):89-102.

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bchFNBH Bacteriochlorophyll synthesis genes of Rhodobacter capsulatus and identification of the third subunit of light-independent protochlorophyllide reductase in bacteria and plants. Burke DH, Alberti M, Hearst JE. Journal of Bacteriology; 175(8):2414-2422.

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The Rhodobacter capsulatus chlorin reductase-encoding locus, bchA, consists of three genes, bchX, bchY, and bchZ. Burke DH, Alberti M, Hearst JE. Journal of Bacteriology; 175(8):2407-2413.

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Early evolution of photosynthesis: Clues from nitrogenase and chlorophyll iron proteins. Burke DH, Hearst JE, Sidow A. Proceedings of the National Academy of Sciences of the United States of America; 90(15):7134-7138.

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Circularly permuted tRNAs as specific photoaffinity probes of ribonuclease P RNA structure. Nolan JM, Burke DH, Pace NR. Science; 261(5122):762-765.

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Regulation of carotenoid and bacteriochlorophyll biosynthesis genes and identification of an evolutionarily conserved gene required for bacteriochlorophyll accumulation. Armstrong GA, Cook DN, Ma D, Alberti M, Burke DH, Hearst JE. Journal of General Microbiology; 139(5):879-906.

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An RNA holliday junction? Structural and dynamic considerations of the bacteriophage T4 gene 60 interruption. Burke-Agüero DH, Hearst JE. Journal of Molecular Biology; 213(2):199-201.

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