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Donald H. Burke - Publications

Affiliations: 
1998-2005 Chemistry & Biology Indiana University, Bloomington, Bloomington, IN, United States 
 2005- Molecular Microbiology & Immunology University of Missouri-Columbia, Columbia, MO 
Area:
RNA Biochemistry, Virology
Website:
https://biochem.missouri.edu/faculty/faculty-members/burked/index.php
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77 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Sapkota K, Lucas JK, Faulkner JW, Lichte MF, Guo YL, Burke DH, Huang F. Post-transcriptional capping generates coenzyme A-linked RNA. Rna Biology. 21: 1-12. PMID 38032240 DOI: 10.1080/15476286.2023.2288740  0.413
2023 Lucas JK, Gruenke PR, Burke DH. Minimizing amplification bias during reverse transcription for in vitro selections. Rna (New York, N.Y.). PMID 37192815 DOI: 10.1261/rna.079650.123  0.389
2022 Kramer ST, Gruenke PR, Alam KK, Xu D, Burke DH. FASTAptameR 2.0: A web tool for combinatorial sequence selections. Molecular Therapy. Nucleic Acids. 29: 862-870. PMID 36159593 DOI: 10.1016/j.omtn.2022.08.030  0.732
2022 Samuelian JS, Gremminger TJ, Song Z, Poudyal RR, Li J, Zhou Y, Staller SA, Carballo JA, Roychowdhury-Saha M, Chen SJ, Burke DH, Heng X, Baum DA. An RNA aptamer that shifts the reduction potential of metabolic cofactors. Nature Chemical Biology. PMID 36097297 DOI: 10.1038/s41589-022-01121-4  0.784
2020 Gruenke PR, Alam KK, Singh K, Burke DH. 2'-Fluoro-Modified Pyrimidines Enhance Affinity of RNA Oligonucleotides to HIV-1 Reverse Transcriptase. Rna (New York, N.Y.). PMID 32732393 DOI: 10.1261/Rna.077008.120  0.827
2020 Nguyen PDM, Zheng J, Gremminger TJ, Qiu L, Zhang D, Tuske S, Lange MJ, Griffin PR, Arnold E, Chen SJ, Zou X, Heng X, Burke DH. Binding interface and impact on protease cleavage for an RNA aptamer to HIV-1 reverse transcriptase. Nucleic Acids Research. PMID 31943114 DOI: 10.1093/Nar/Gkz1224  0.522
2018 Lange MJ, Burke DH, Chaput JC. Activation of Innate Immune Responses by a Cytosine-Phosphate-Guanine Oligonucleotide Sequence Composed Entirely of Threose Nucleic Acid. Nucleic Acid Therapeutics. PMID 30526333 DOI: 10.1089/Nat.2018.0751  0.379
2018 Hill KJ, Rogers LC, Njenda DT, Burke DH, Sarafianos SG, Sönnerborg A, Neogi U, Singh K. Strain-specific effect on biphasic DNA binding by HIV-1 integrase. Aids (London, England). PMID 30475264 DOI: 10.1097/Qad.0000000000002078  0.367
2018 Alam KK, Chang JL, Lange MJ, Nguyen PDM, Sawyer AW, Burke DH. Poly-Target Selection Identifies Broad-Spectrum RNA Aptamers. Molecular Therapy. Nucleic Acids. 13: 605-619. PMID 30472639 DOI: 10.1016/J.Omtn.2018.10.010  0.789
2018 Smith JD, Cardwell LN, Porciani D, Nguyen JA, Gallazzi F, Tata RR, Burke DH, Daniels MA, Ulery B. Aptamer-displaying peptide amphiphile micelles as a cell-targeted delivery vehicle of peptide cargoes. Physical Biology. PMID 30124431 DOI: 10.1088/1478-3975/Aadb68  0.307
2018 Porciani D, Cardwell LN, Tawiah KD, Alam KK, Lange MJ, Daniels MA, Burke DH. Modular cell-internalizing aptamer nanostructure enables targeted delivery of large functional RNAs in cancer cell lines. Nature Communications. 9: 2283. PMID 29891903 DOI: 10.1038/S41467-018-04691-X  0.795
2017 Tawiah KD, Porciani D, Burke DH. Toward the Selection of Cell Targeting Aptamers with Extended Biological Functionalities to Facilitate Endosomal Escape of Cargoes. Biomedicines. 5. PMID 28837119 DOI: 10.3390/Biomedicines5030051  0.373
2017 Alam KK, Tawiah KD, Lichte MF, Porciani D, Burke DH. A Fluorescent Split Aptamer for Visualizing RNA-RNA Assembly In Vivo. Acs Synthetic Biology. PMID 28548488 DOI: 10.1021/Acssynbio.7B00059  0.806
2017 Lange MJ, Nguyen PD, Callaway MK, Johnson MC, Burke DH. RNA-protein interactions govern antiviral specificity and encapsidation of broad spectrum anti-HIV reverse transcriptase aptamers. Nucleic Acids Research. PMID 28334941 DOI: 10.1093/Nar/Gkx155  0.52
2017 Poudyal RR, Nguyen PD, Lokugamage MP, Callaway MK, Gavette JV, Krishnamurthy R, Burke DH. Nucleobase modification by an RNA enzyme. Nucleic Acids Research. 45: 1345-1354. PMID 28180302 DOI: 10.1093/Nar/Gkw1199  0.78
2016 Poudyal RR, Benslimane M, Lokugamage MP, Callaway MK, Staller S, Burke DH. Selective Inactivation of Functional RNAs by Ribozyme-Catalyzed Covalent Modification. Acs Synthetic Biology. PMID 28139121 DOI: 10.1021/Acssynbio.6B00222  0.81
2016 Poudyal RR, Nguyen PD, Lokugamage MP, Callaway MK, Gavette JV, Krishnamurthy R, Burke DH. Nucleobase modification by an RNA enzyme. Nucleic Acids Research. PMID 27923932 DOI: 10.1093/nar/gkw1199  0.769
2016 Shebl B, Menke DE, Pennella M, Poudyal RR, Burke DH, Cornish PV. Preparation of ribosomes for smFRET studies: A simplified approach. Archives of Biochemistry and Biophysics. PMID 27208427 DOI: 10.1016/J.Abb.2016.05.010  0.739
2016 Salamango DJ, Alam KK, Burke DH, Johnson MC. In vivo analysis of infectivity, fusogenicity, and incorporation of a mutagenic viral glycoprotein library reveals determinants for viral incorporation. Journal of Virology. PMID 27147747 DOI: 10.1128/Jvi.00804-16  0.752
2015 Alam KK, Chang JL, Burke DH. FASTAptamer: A Bioinformatic Toolkit for High-throughput Sequence Analysis of Combinatorial Selections. Molecular Therapy. Nucleic Acids. 4: e230. PMID 25734917 DOI: 10.1038/Mtna.2015.4  0.751
2015 Camargo C, Lange MJ, Hill KJ, Burke DH. 538. Promoter Compatibility Enables Viral Vectors to Deliver Antiviral RNA Genes Molecular Therapy. 23: S216. DOI: 10.1016/S1525-0016(16)34147-8  0.413
2015 Alam KK, Porciani D, Hill KJ, Burke DH. 493. Aptamer-Mediated Targeted Delivery of Large RNA Molecular Therapy. 23: S196. DOI: 10.1016/S1525-0016(16)34102-8  0.81
2015 Hill KJ, Lange MJ, Burke DH. 141. Combinatorial Aptamer Transcripts (CATs) for HIV RT Suppression Molecular Therapy. 23: S57. DOI: 10.1016/S1525-0016(16)33746-7  0.49
2015 Hill KJ, Swain AD, Lange MJ, Burke DH. 137. Viral Hitchhiking to Increase Therapeutic Potential: Autonomously Packaged Elements (APEs) Molecular Therapy. 23: S56. DOI: 10.1016/S1525-0016(16)33742-X  0.562
2015 Lange MJ, Nguyen PD, Callaway MK, Burke DH. 64. Broad-Spectrum Anti-HIV RT RNA Aptamers Molecular Therapy. 23: S28. DOI: 10.1016/S1525-0016(16)33669-3  0.464
2014 Lange MJ, Burke DH. Screening inhibitory potential of anti-HIV RT RNA aptamers. Methods in Molecular Biology (Clifton, N.J.). 1103: 11-29. PMID 24318883 DOI: 10.1007/978-1-62703-730-3_2  0.494
2014 Biondi E, Burke DH. RNA structural analysis by enzymatic digestion. Methods in Molecular Biology (Clifton, N.J.). 1086: 41-52. PMID 24136597 DOI: 10.1007/978-1-62703-667-2_3  0.489
2013 Whatley AS, Ditzler MA, Lange MJ, Biondi E, Sawyer AW, Chang JL, Franken JD, Burke DH. Potent Inhibition of HIV-1 Reverse Transcriptase and Replication by Nonpseudoknot, "UCAA-motif" RNA Aptamers. Molecular Therapy. Nucleic Acids. 2: e71. PMID 23385524 DOI: 10.1038/Mtna.2012.62  0.785
2013 Biondi E, Poudyal RR, Forgy JC, Sawyer AW, Maxwell AW, Burke DH. Lewis acid catalysis of phosphoryl transfer from a copper(II)-NTP complex in a kinase ribozyme. Nucleic Acids Research. 41: 3327-38. PMID 23358821 DOI: 10.1093/Nar/Gkt039  0.726
2013 Ditzler MA, Lange MJ, Bose D, Bottoms CA, Virkler KF, Sawyer AW, Whatley AS, Spollen W, Givan SA, Burke DH. High-throughput sequence analysis reveals structural diversity and improved potency among RNA inhibitors of HIV reverse transcriptase. Nucleic Acids Research. 41: 1873-84. PMID 23241386 DOI: 10.1093/Nar/Gks1190  0.795
2012 Lange MJ, Sharma TK, Whatley AS, Landon LA, Tempesta MA, Johnson MC, Burke DH. Robust suppression of HIV replication by intracellularly expressed reverse transcriptase aptamers is independent of ribozyme processing. Molecular Therapy : the Journal of the American Society of Gene Therapy. 20: 2304-14. PMID 22948672 DOI: 10.1038/Mt.2012.158  0.498
2012 Biondi E, Maxwell AW, Burke DH. A small ribozyme with dual-site kinase activity. Nucleic Acids Research. 40: 7528-40. PMID 22618879 DOI: 10.1093/Nar/Gks356  0.392
2012 Biondi E, Burke DH. Separating and analyzing sulfur-containing RNAs with organomercury gels. Methods in Molecular Biology (Clifton, N.J.). 883: 111-20. PMID 22589128 DOI: 10.1007/978-1-61779-839-9_8  0.435
2012 Burke DH. Cell-penetrating RNAs: new keys to the castle. Molecular Therapy : the Journal of the American Society of Gene Therapy. 20: 251-3. PMID 22297821 DOI: 10.1038/Mt.2011.306  0.355
2012 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 YM, Liu SL, et al. Biochemical, inhibition and inhibitor resistance studies of xenotropic murine leukemia virus-related virus reverse transcriptase. Nucleic Acids Research. 40: 345-59. PMID 21908397 DOI: 10.1093/Nar/Gkr694  0.438
2011 Ditzler MA, Bose D, Shkriabai N, Marchand B, Sarafianos SG, Kvaratskhelia M, Burke DH. Broad-spectrum aptamer inhibitors of HIV reverse transcriptase closely mimic natural substrates. Nucleic Acids Research. 39: 8237-47. PMID 21727088 DOI: 10.1093/Nar/Gkr381  0.792
2011 Roychowdhury-Saha M, Roychowdhury S, Burke DH. Conformational heterogeneity and the determinants of tertiary stabilization in the hammerhead ribozyme from Dolichopoda cave crickets. Rna Biology. 8: 893-903. PMID 21712651 DOI: 10.4161/Rna.8.5.16036  0.392
2010 Burke DH, Rhee SS. Assembly and activation of a kinase ribozyme. Rna (New York, N.Y.). 16: 2349-59. PMID 20935068 DOI: 10.1261/Rna.2302810  0.395
2010 Nickens DG, Bardiya N, Patterson JT, Burke DH. Template-directed ligation of tethered mononucleotides by t4 DNA ligase for kinase ribozyme selection. Plos One. 5: e12368. PMID 20811490 DOI: 10.1371/Journal.Pone.0012368  0.679
2010 Biondi E, Nickens DG, Warren S, Saran D, Burke DH. Convergent donor and acceptor substrate utilization among kinase ribozymes. Nucleic Acids Research. 38: 6785-95. PMID 20511589 DOI: 10.1093/Nar/Gkq433  0.337
2008 Michalowski D, Chitima-Matsiga R, Held DM, Burke DH. Novel bimodular DNA aptamers with guanosine quadruplexes inhibit phylogenetically diverse HIV-1 reverse transcriptases. Nucleic Acids Research. 36: 7124-35. PMID 18996899 DOI: 10.1093/Nar/Gkn891  0.438
2007 Kissel JD, Held DM, Hardy RW, Burke DH. Active site binding and sequence requirements for inhibition of HIV-1 reverse transcriptase by the RT1 family of single-stranded DNA aptamers. Nucleic Acids Research. 35: 5039-50. PMID 17644816 DOI: 10.1093/Nar/Gkm420  0.799
2007 Kissel JD, Held DM, Hardy RW, Burke DH. Single-stranded DNA aptamer RT1t49 inhibits RT polymerase and RNase H functions of HIV type 1, HIV type 2, and SIVCPZ RTs. Aids Research and Human Retroviruses. 23: 699-708. PMID 17530996 DOI: 10.1089/Aid.2006.0262  0.803
2007 Held DM, Kissel JD, Thacker SJ, Michalowski D, Saran D, Ji J, Hardy RW, Rossi JJ, Burke DH. 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. Journal of Virology. 81: 5375-84. PMID 17329328 DOI: 10.1128/Jvi.01923-06  0.815
2007 Saran D, Burke DH. A versatile photocleavable bifunctional linker for facile synthesis of substrate-DNA conjugates for the selection of nucleic acid catalysts. Bioconjugate Chemistry. 18: 275-9. PMID 17226983 DOI: 10.1021/Bc060221F  0.395
2007 Cho BR, Burke DH. Conformational dynamics of self-thiophosphorylating RNA Bulletin of the Korean Chemical Society. 28: 463-466. DOI: 10.5012/Bkcs.2007.28.3.463  0.477
2006 Patterson JT, Nickens DG, Burke DH. HIV-1 reverse transcriptase pausing at bulky 2' adducts is relieved by deletion of the RNase H domain. Rna Biology. 3: 163-9. PMID 17396357 DOI: 10.4161/Rna.3.4.4020  0.695
2006 Cho B, Burke DH. Topological rearrangement yields structural stabilization and interhelical distance constraints in the Kin.46 self-phosphorylating ribozyme. Rna (New York, N.Y.). 12: 2118-25. PMID 17068208 DOI: 10.1261/Rna.173506  0.357
2006 Held DM, Kissel JD, Saran D, Michalowski D, Burke DH. Differential susceptibility of HIV-1 reverse transcriptase to inhibition by RNA aptamers in enzymatic reactions monitoring specific steps during genome replication. The Journal of Biological Chemistry. 281: 25712-22. PMID 16798747 DOI: 10.1074/Jbc.M604460200  0.825
2006 Saran D, Held DM, Burke DH. Multiple-turnover thio-ATP hydrolase and phospho-enzyme intermediate formation activities catalyzed by an RNA enzyme. Nucleic Acids Research. 34: 3201-8. PMID 16790565 DOI: 10.1093/Nar/Gkl413  0.415
2006 Held DM, Kissel JD, Patterson JT, Nickens DG, Burke DH. HIV-1 inactivation by nucleic acid aptamers. Frontiers in Bioscience : a Journal and Virtual Library. 11: 89-112. PMID 16146716 DOI: 10.2741/1782  0.79
2005 Saran D, Nickens DG, Burke DH. A trans acting ribozyme that phosphorylates exogenous RNA. Biochemistry. 44: 15007-16. PMID 16274247 DOI: 10.1021/Bi051086H  0.419
2005 Burke DH, Greathouse ST. Low-magnesium, trans-cleavage activity by type III, tertiary stabilized hammerhead ribozymes with stem 1 discontinuities. Bmc Biochemistry. 6: 14. PMID 16095542 DOI: 10.1186/1471-2091-6-14  0.773
2004 Saksmerprome V, Roychowdhury-Saha M, Jayasena S, Khvorova A, Burke DH. Artificial tertiary motifs stabilize trans-cleaving hammerhead ribozymes under conditions of submillimolar divalent ions and high temperatures. Rna (New York, N.Y.). 10: 1916-24. PMID 15547137 DOI: 10.1261/Rna.7159504  0.441
2004 Saksmerprome V, Burke DH. Deprotonation stimulates productive folding in allosteric TRAP hammerhead ribozymes. Journal of Molecular Biology. 341: 685-94. PMID 15288779 DOI: 10.1016/J.Jmb.2004.06.027  0.307
2004 Rhee SS, Burke DH. Tris(2-carboxyethyl)phosphine stabilization of RNA: comparison with dithiothreitol for use with nucleic acid and thiophosphoryl chemistry. Analytical Biochemistry. 325: 137-43. PMID 14715294 DOI: 10.1016/J.Ab.2003.10.019  0.477
2003 Saran D, Frank J, Burke DH. The tyranny of adenosine recognition among RNA aptamers to coenzyme A. Bmc Evolutionary Biology. 3: 26. PMID 14687414 DOI: 10.1186/1471-2148-3-26  0.492
2003 Hati S, Boles AR, Zaborske JM, Bergman B, Posto AL, Burke DH. Nickel2+-mediated assembly of an RNA-amino acid complex. Chemistry & Biology. 10: 1129-37. PMID 14652080 DOI: 10.1016/J.Chembiol.2003.11.002  0.422
2003 Saksmerprome V, Burke DH. Structural flexibility and the thermodynamics of helix exchange constrain attenuation and allosteric activation of hammerhead ribozyme TRAPs. Biochemistry. 42: 13879-86. PMID 14636055 DOI: 10.1021/Bi034960K  0.472
2003 Held DM, Greathouse ST, Agrawal A, Burke DH. Evolutionary landscapes for the acquisition of new ligand recognition by RNA aptamers. Journal of Molecular Evolution. 57: 299-308. PMID 14629040 DOI: 10.1007/S00239-003-2481-Y  0.807
2003 Nickens DG, Patterson JT, Burke DH. Inhibition of HIV-1 reverse transcriptase by RNA aptamers in Escherichia coli. Rna (New York, N.Y.). 9: 1029-33. PMID 12923252 DOI: 10.1261/Rna.5550103  0.742
2002 Burke DH, Nickens DG. Expressing RNA aptamers inside cells to reveal proteome and ribonome function. Briefings in Functional Genomics & Proteomics. 1: 169-88. PMID 15239903 DOI: 10.1093/Bfgp/1.2.169  0.509
2002 Burke DH, Ozerova ND, Nilsen-Hamilton M. Allosteric hammerhead ribozyme TRAPs. Biochemistry. 41: 6588-94. PMID 12022862 DOI: 10.1021/Bi0201522  0.517
2002 Lato SM, Ozerova ND, He K, Sergueeva Z, Shaw BR, Burke DH. Boron-containing aptamers to ATP. Nucleic Acids Research. 30: 1401-7. PMID 11884639 DOI: 10.1093/Nar/30.6.1401  0.483
2002 Roychowdhury-Saha M, Lato SM, Shank ED, Burke DH. Flavin recognition by an RNA aptamer targeted toward FAD. Biochemistry. 41: 2492-9. PMID 11851395 DOI: 10.1021/Bi015719D  0.529
1998 Burke DH, Willis JH. Recombination, RNA evolution, and bifunctional RNA molecules isolated through chimeric SELEX. Rna (New York, N.Y.). 4: 1165-75. PMID 9740133 DOI: 10.1017/S1355838298980542  0.535
1998 Burke DH, Hoffman DC. A novel acidophilic RNA motif that recognizes coenzyme A. Biochemistry. 37: 4653-63. PMID 9521786 DOI: 10.1021/Bi972877P  0.527
1997 Burke DH, Hoffman DC, Brown A, Hansen M, Pardi A, Gold L. RNA aptamers to the peptidyl transferase inhibitor chloramphenicol. Chemistry & Biology. 4: 833-43. PMID 9384530 DOI: 10.1016/S1074-5521(97)90116-2  0.683
1997 Burke DH, Gold L. RNA aptamers to the adenosine moiety of S-adenosyl methionine: structural inferences from variations on a theme and the reproducibility of SELEX. Nucleic Acids Research. 25: 2020-4. PMID 9115371 DOI: 10.1093/Nar/25.10.2020  0.643
1996 Burke DH, Scates L, Andrews K, Gold L. Bent pseudoknots and novel RNA inhibitors of type 1 human immunodeficiency virus (HIV-1) reverse transcriptase. Journal of Molecular Biology. 264: 650-66. PMID 8980676 DOI: 10.1006/Jmbi.1996.0667  0.699
1994 Hundle B, Alberti M, Nievelstein V, Beyer P, Kleinig H, Armstrong GA, Burke DH, Hearst JE. Functional assignment of Erwinia herbicola Eho10 carotenoid genes expressed in Escherichia coli. Molecular & General Genetics : Mgg. 245: 406-16. PMID 7808389 DOI: 10.1007/Bf00302252  0.496
1993 Burke DH, Alberti M, Hearst JE. The Rhodobacter capsulatus chlorin reductase-encoding locus, bchA, consists of three genes, bchX, bchY, and bchZ. Journal of Bacteriology. 175: 2407-13. PMID 8468299 DOI: 10.1128/Jb.175.8.2407-2413.1993  0.52
1993 Burke DH, Alberti M, Hearst JE. bchFNBH bacteriochlorophyll synthesis genes of Rhodobacter capsulatus and identification of the third subunit of light-independent protochlorophyllide reductase in bacteria and plants. Journal of Bacteriology. 175: 2414-22. PMID 8385667 DOI: 10.1128/Jb.175.8.2414-2422.1993  0.519
1993 Burke DH, Hearst JE, Sidow A. Early evolution of photosynthesis: clues from nitrogenase and chlorophyll iron proteins. Proceedings of the National Academy of Sciences of the United States of America. 90: 7134-8. PMID 8346226 DOI: 10.1073/Pnas.90.15.7134  0.506
1993 Armstrong GA, Cook DN, Ma D, Alberti M, Burke DH, Hearst JE. Regulation of carotenoid and bacteriochlorophyll biosynthesis genes and identification of an evolutionarily conserved gene required for bacteriochlorophyll accumulation. Journal of General Microbiology. 139: 897-906. PMID 8336108 DOI: 10.1099/00221287-139-5-897  0.517
1993 Nolan JM, Burke DH, Pace NR. Circularly permuted tRNAs as specific photoaffinity probes of ribonuclease P RNA structure. Science (New York, N.Y.). 261: 762-5. PMID 7688143 DOI: 10.1126/Science.7688143  0.477
1993 Burke DH, Raubeson LA, Alberti M, Hearst JE, Jordan ET, Kirch SA, Valinski AEC, Conant DS, Stein DB. The ch1L (frxC) gene: Phylogenetic distribution in vascular plants and DNA sequence from Polystichum acrostichoides (Pteridophyta) and Synechococcus sp. 7002 (Cyanobacteria) Plant Systematics and Evolution. 187: 89-102. DOI: 10.1007/Bf00994092  0.474
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