Embedded Files
*The following publications were made possible through the support of CRNA’s NIH NIAID grant #U54AI150470:
2022
Xue G, Braczyk K, Gonçalves-Carneiro D, Dawidziak DM, Sanchez K, Ong H, Wan Y, Zadrozny KK, Ganser-Pornillos BK, Bieniasz PD, Pornillos O. (2022) Poly(ADP-ribose) potentiates ZAP antiviral activity. PLoS Pathog. 18(2):e1009202. doi: 10.1371. PubMed Link
Miller RM, Knoener RA, Benner BE, Frey BL, Scalf M, Shortreed MR, Sherer NM, Smith LM. (2022) Discovery of Dehydroamino Acid Residues in the Capsid and Matrix Structural Proteins of HIV-1. J Proteome Res. 21(4):993-1001. doi: 10.1021. PubMed Link
2021
Blakemore RJ, Burnett C, Swanson C, Kharytonchyk S, Telesnitsky A, Munro JB. (2021) Stability and conformation of the dimeric HIV-1 genomic RNA 5'UTR. Biophys J. 120(21):4874-4890. doi: 10.1016/j.bpj.2021.09.017. PubMed Link
Bou-Nader C, Muecksch F, Brown JB, Gordon JM, York A, Peng C, Ghirlando R, Summers MF, Bieniasz PD, Zhang J. (2021) HIV-1 matrix-tRNA complex structure reveals basis for host control of Gag localization. Cell Host Microbe. 29(9):1421-1436.e7. doi: 10.1016/j.chom.2021.07.006. PMID: 34384537 PubMed Link
Cullen BR, Tsai K. (2021) Mapping RNA Modifications Using Photo-Crosslinking-Assisted Modification Sequencing. Methods Mol Biol. 2298:123-134. doi: 10.1007/978-1-0716-1374-0_8. PubMed Link
Ding P, Kharytonchyk S, Kuo N, Cannistraci E, Flores H, Chaudhary R, Sarkar M, Dong X, Telesnitsky A, Summers MF. (2021) 5'-Cap sequestration is an essential determinant of HIV-1 genome packaging. Proc Natl Acad Sci U S A. 118(37):e2112475118. doi: 10.1073/pnas.2112475118. PubMed Link
Emery A, Swanstrom R. HIV-1: To Splice or Not to Splice, That Is the Question. Viruses. (2021) PubMed PMID: 33530363; PubMed Link
Gonçalves-Carneiro D, Bieniasz PD. (2021) Mechanisms of Attenuation by Genetic Recoding of Viruses.
mBio. 12(1):e02238-20. doi: 10.1128 PubMed Link
Gonçalves-Carneiro D, Takata MA, Ong H, Shilton A, Bieniasz PD. (2021) Origin and evolution of the zinc finger antiviral protein. PLoS Pathog. 17(4):e1009545. doi: 10.1371 PubMed Link
Irwan ID, Cullen BR. (2021) Tax Induces the Recruitment of NF-κB to Unintegrated HIV-1 DNA To Rescue Viral Gene Expression and Replication. J Virol. 95(13):e0028521. doi: 10.1128/JVI.00285-21.
PMID: 33883218 PubMed Link
Kelly ML, Chu CC, Shi H, Ganser LR, Bogerd HP, Huynh K, Hou Y, Cullen BR, Al-Hashimi HM. (2021) Understanding the characteristics of nonspecific binding of drug-like compounds to canonical stem-loop RNAs and their implications for functional cellular assays. RNA 27(1):12-26.PubMed Link
Knoener R, Evans E 3rd, Becker JT, Scalf M, Benner B, Sherer NM, Smith LM. (2021) Identification of host proteins differentially associated with HIV-1 RNA splice variants. Elife. PubMed Link
Levengood JD, Peterson J, Tolbert BS, Roche J. (2021) Thermodynamic stability of hnRNP A1 low complexity domain revealed by high-pressure NMR. Proteins. 89(7):781-791. doi: 10.1002/prot.26058.
PMID: 33550645 PubMed Link
Liu B, Shi H, Al-Hashimi HM. (2021) Developments in solution-state NMR yield broader and deeper views of the dynamic ensembles of nucleic acids. Curr Opin Struct Biol. 70:16-25. doi: 10.1016/j.sbi.2021.02.007. PubMed Link
Liu B, Shi H, Rangadurai A, Nussbaumer F, Chu CC, Erharter KA, Case DA, Kreutz C, Al-Hashimi HM. (2021)
A quantitative model predicts how m6A reshapes the kinetic landscape of nucleic acid hybridization and conformational transitions. Nat Commun. 12(1):5201. doi: 10.1038/s41467-021-25253-8.
PMID: 34465779 PubMed Link
Luo L, Chiu LY, Sugarman A, Gupta P, Rouskin S, Tolbert BS. (2021) HnRNP A1/A2 Proteins Assemble onto 7SK snRNA via Context Dependent Interactions. J Mol Biol. PubMed Link
Martinez Campos C, Tsai K, Courtney DG, Bogerd HP, Holley CL, Cullen BR. (2021) Mapping of pseudouridine residues on cellular and viral transcripts using a novel antibody-based technique. RNA. 27(11):1400-1411. doi: 10.1261/rna.078940.121. PMID: 34376564 PubMed Link
McIlwain BC, Erwin AL, Davis AR, Ben Koff B, Chang L, Bylund T, Chuang GY, Kwong PD, Ohi MD, Lai YT, Stockbridge RB. (2021) N-terminal Transmembrane-Helix Epitope Tag for X-ray Crystallography and Electron Microscopy of Small Membrane Proteins. J Mol Biol. 433(16):166909. doi: 10.1016/j.jmb.2021.166909.
PMID: 33676924 PubMed Link
Tsai K, Bogerd HP, Kennedy EM, Emery A, Swanstrom R, Cullen BR. (2021) Epitranscriptomic addition of m6A regulates HIV-1 RNA stability and alternative splicing. Genes Dev. 35(13-14):992-1004. doi: 10.1101/gad.348508.121. PMID: 34140354 PubMed Link
Wang Q, Gao H, Clark KM, Mugisha CS, Davis K, Tang JP, Harlan GH, DeSelm CJ, Presti RM, Kutluay SB, Shan L. (2021) CARD8 is an inflammasome sensor for HIV-1 protease activity. Science. 371(6535):eabe1707. doi: 10.1126/science.abe1707. PubMed Link
2020
Becette OB, Zong G, Chen B, Taiwo KM, Case DA, Dayie TK. Solution NMR readily reveals distinct structural folds and interactions in doubly 13C- and 19F-labeled RNAs. Sci Adv.(2020) PubMed Link
Boyd PS, Brown JB, Brown JD, Catazaro J, Chaudry I, Ding P, Dong X, Marchant J, O'Hern CT, Singh K, Swanson C, Summers MF, Yasin S. (2020) NMR Studies of Retroviral Genome Packaging. Viruses 12(10):1115. doi: 10.3390 PubMed Link
Brown JB, Summers HR, Brown LA, Marchant J, Canova PN, O'Hern CT, Abbott ST, Nyaunu C, Maxwell S, Johnson T, Moser MB, Ablan SD, Carter H, Freed EO, Summers MF.(2020) Structural and Mechanistic Studies of the Rare Myristoylation Signal of the Feline Immunodeficiency Virus. J Mol Biol. doi: 10.1016/j.jmb.2020.05.008. PubMed Link
Brown JD, Kharytonchyk S, Chaudry I, Iyer AS, Carter H, Becker G, Desai Y, Glang L, Choi SH, Singh K, Lopresti MW, Orellana M, Rodriguez T, Oboh U, Hijji J, Ghinger FG, Stewart K, Francis D, Edwards B, Chen P, Case DA, Telesnitsky A, Summers MF. (2020) Structural basis for transcriptional start site control of HIV-1 RNA fate. Science. 368(6489):413-417. doi: 10.1126/science.aaz7959. PubMed Link
Case DA. (2020) Using quantum chemistry to estimate chemical shifts in biomolecules. Biophys Chem 267:106476. doi: 10.1016 PubMed Link
Davila-Calderon J, Patwardhan NN, Chiu LY, Sugarman A, Cai Z, Penutmutchu SR, Li ML, Brewer G, Hargrove AE, Tolbert BS. (2020) IRES-targeting small molecule inhibits enterovirus 71 replication via allosteric stabilization of a ternary complex Nat Commun. 11(1):4775. doi: 10.1038 PubMed Link
Ding P, Kharytonchyk S, Waller A, Mbaekwe U, Basappa S, Kuo N, Frank HM, Quasney C, Kidane A, Swanson C, Van V, Sarkar M, Cannistraci E, Chaudhary R, Flores H, Telesnitsky A, Summers MF. (2020) Identification of the initial nucleocapsid recognition element in the HIV-1 RNA packaging signal. Proc Natl Acad Sci U S A 117(30):17737-17746. doi: 10.1073 PubMed Link
Elliott JL, Eschbach JE, Koneru PC, Li W, Puray-Chavez M, Townsend D, Lawson DQ, Engelman AN, Kvaratskhelia M, Kutluay SB. (2020) Integrase-RNA interactions underscore the critical role of integrase in HIV-1 virion morphogenesis. Elife 9:e54311. doi: 10.7554 PubMed Link
Elliott JL, Kutluay SB. (2020) Going beyond Integration: The Emerging Role of HIV-1 Integrase in Virion Morphogenesis. Viruses 12(9):1005. doi: 10.3390 PubMed Link
Esquiaqui JM, Kharytonchyk S, Drucker D, Telesnitsky A. (2020) HIV-1 spliced RNAs display transcription start site bias. RNA. 26(6):708-714. doi: 10.1261/rna.073650.119. PubMed Link
Ganser LR, Chu CC, Bogerd HP, Kelly ML, Cullen BR, Al-Hashimi HM. (2020) Probing RNA Conformational Equilibria within the Functional Cellular Context. Cell Rep. 30(8):2472-2480.e4. doi: 10.1016/j.celrep.2020.02.004. PubMed Link
Ganser LR, Kelly ML, Patwardhan NN, Hargrove AE, Al-Hashimi HM. (2020) Demonstration that Small Molecules can Bind and Stabilize Low-abundance Short-lived RNA Excited Conformational States. J Mol Biol. 432(4):1297-1304. doi: 10.1016/j.jmb.2019.12.009. PubMed Link
Hargrove AE (2020) Small molecule-RNA targeting: starting with the fundamentals. Chem Commun 56(94):14744-14756. doi: 10.1039 PubMed Link
Kladwang W, Topkar VV, Liu B, Rangan R, Hodges TL, Keane SC, Al-Hashimi H, Das R. (2020) Anomalous Reverse Transcription through Chemical Modifications in Polyadenosine Stretches. Biochemistry. 59(23):2154-2170. doi: 10.1021/acs.biochem.0c00020. PubMed Link
Kucharska I, Ding P, Zadrozny KK, Dick RA, Summers MF, Ganser-Pornillos BK, Pornillos O. Biochemical Reconstitution of HIV-1 Assembly and Maturation. (2020)J Virol. doi: 10.1128/JVI.01844-19. PubMed Link
Mugisha CS, Vuong HR, Puray-Chavez M, Kutluay SB. (2020) A facile Q-RT-PCR assay for monitoring SARS-CoV-2 growth in cell culture. bioRxiv. 2020.06.26.174698. doi: 10.1101. PubMed Link (preprint)
Nam H, Becette O, LeBlanc RM, Oh D, Case DA, Dayie TK. (2020) Deleterious effects of carbon-carbon dipolar coupling on RNA NMR dynamics. J Biomol NMR. doi: 10.1007/s10858-020-00315-z. PubMed Link
Orlovsky NI, Al-Hashimi HM, Oas TG. (2020) Exposing Hidden High-Affinity RNA Conformational States. J Am Chem Soc. 142(2):907-921. doi: 10.1021/jacs.9b10535. PubMed Link
Padroni G, Patwardhan NN, Schapira M, Hargrove AE. (2020) Systematic analysis of the interactions driving small molecule-RNA recognition RSC Med Chem 11(7):802-813. doi: 10.1039 PubMed Link
Shema Mugisha C, Tenneti K, Kutluay SB. (2020) Clip for studying protein-RNA interactions that regulate virus replication. Methods 183:84-92. doi: 10.1016 Pub Med Link
Shema Mugisha C, Vuong HR, Puray-Chavez M, Bailey AL, Fox JM, Chen RE, Wessel AW, Scott JM, Harastani HH, Boon ACM, Shin H, Kutluay SB. (2020) A Simplified Quantitative Real-Time PCR Assay for Monitoring SARS-CoV-2 Growth in Cell Culture mSphere 5(5):e00658-20. doi: 10.1128 PubMed Link
Tomezsko PJ, Corbin VDA, Gupta P, Swaminathan H, Glasgow M, Persad S, Edwards MD, Mcintosh L, Papenfuss AT, Emery A, Swanstrom R, Zang T, Lan TCT, Bieniasz P, Kuritzkes DR, Tsibris A, Rouskin S. (2020) Determination of RNA structural diversity and its role in HIV-1 RNA splicing. Nature 582(7812):438-442. doi: 10.1038. PubMed Link
Tomezsko P, Swaminathan H, Rouskin S. (2020) Viral RNA structure analysis using DMS-MaPseq. Methods. 3;doi: 10.1016/j.ymeth.2020.04.001. PubMed Link
Tsai K, Cullen BR. (2020) Epigenetic and epitranscriptomic regulation of viral replication. Nat Rev Microbiol 18(10):559-570. doi: 10.1038. PubMed Link
Tsai K, Jaguva Vasudevan AA, Martinez Campos C, Emery A, Swanstrom R, Cullen BR. (2020) Acetylation of Cytidine Residues Boosts HIV-1 Gene Expression by Increasing Viral RNA Stability. Cell Host Microbe 28(2):306-312.e6. doi: 10.1016. PubMed Link
Umuhire Juru A, Cai Z, Jan A, Hargrove AE. (2020) Template-guided selection of RNA ligands using imine-based dynamic combinatorial chemistry. Chem Commun (Camb). 56(24):3555-3558. doi: 10.1039/d0cc00266f. PubMed Link
2019
Abulwerdi FA, Xu W, Ageeli AA, Yonkunas MJ, Arun G, Nam H, Schneekloth JS Jr, Dayie TK, Spector D, Baird N, Le Grice SFJ. (2019) Selective Small-Molecule Targeting of a Triple Helix Encoded by the Long Noncoding RNA, MALAT1. ACS Chem Biol. 14(2):223-235. PubMed Link
Bohn JA, DaSilva J, Kharytonchyk S, Mercedes M, Vosters J, Telesnitsky A, Hatziioannou T, Smith JL. (2019) Flexibility in nucleic acid binding is central to APOBEC3H antiviral activity. J Virol. pii: JVI.01275-19. PubMed Link
Bou-Nader C, Gordon JM, Henderson FE, Zhang J. (2019) The search for a PKR code-differential regulation of protein kinase R activity by diverse RNA and protein regulators. RNA. 25(5):539-556. PubMed Link
Brigham BS, Kitzrow JP, Reyes JC, Musier-Forsyth K, Munro JB. (2019) Intrinsic conformational dynamics of the HIV-1 genomic RNA 5'UTR. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1902271116. PubMed Link
Courtney DG, Tsai K, Bogerd HP, Kennedy EM, Law BA, Emery A, Swanstrom R, Holley CL, Cullen BR. (2019) Epitranscriptomic Addition of m5C to HIV-1 Transcripts Regulates Viral Gene Expression. Cell Host Microbe 26(2):217-227. PubMed Link
Eubanks CS, Hargrove AE. (2019) RNA Structural Differentiation: Opportunities with Pattern Recognition. Biochemistry. 58(4):199-213. PubMed Link
Eubanks CS, Zhao B, Patwardhan NN, Thompson RD, Zhang Q, Hargrove AE. (2019) Visualizing RNA Conformational Changes via Pattern Recognition of RNA by Small Molecules. J Am Chem Soc. 141(14):5692-5698. PubMed Link
Ge Z, Su Z, Simmons CR, Li J, Jiang S, Li W, Yang Y, Liu Y, Chiu W, Fan C, Yan H. (2019) Redox Engineering of Cytochrome c using DNA Nanostructure-Based Charged Encapsulation and Spatial Control. ACS Appl Mater Interfaces. 11(15):13874-13880. PubMed Link
Guo M, Zhang K, Zhu Y, Pintilie GD, Guan X, Li S, Schmid MF, Ma Z, Chiu W, Huang Z. (2019) Coupling of ssRNA cleavage with DNase activity in type III-A CRISPR-Csm revealed by cryo-EM and biochemistry. Cell Res. 29(4):305-312. Pub MedLink
Jun H, Shepherd TR, Zhang K, Bricker WP, Li S, Chiu W, Bathe M. (2019) Automated Sequence Design of 3D Polyhedral Wireframe DNA Origami with Honeycomb Edges. ACS Nano. 13(2):2083-2093. PubMed Link
Kutluay SB, Emery A, Penumutchu SR, Townsend D, Tenneti K, Madison MK, Stukenbroeker AM, Powell C, Jannain D, Tolbert BS, Swanstrom RI, Bieniasz PD. (2019) Genome-Wide Analysis of Heterogeneous Nuclear Ribonucleoprotein (hnRNP) Binding to HIV-1 RNA Reveals a Key Role for hnRNP H1 in Alternative Viral mRNA Splicing. J Virol. 93(21). pii: e01048-19. PubMed Link
Li S, Su Z, Lehmann J, Stamatopoulou V, Giarimoglou N, Henderson FE, Fan L, Pintilie GD, Zhang K, Chen M, Ludtke SJ, Wang YX, Stathopoulos C, Chiu W, Zhang J. (2019) Structural basis of amino acid surveillance by higher-order tRNA-mRNA interactions. Nat Struct Mol Biol. 26(12):1094-1105. PubMed Link
Marchant, J., Summers, MF, Johnson BA (2019)Assigning NMR spectra of RNA, peptides and small organic molecules using molecular networkvisualization software. J Biomol NMR. doi: 10.1007/s10858-019-00271-3. PubMed Link
Morgan BS, Sanaba BG, Donlic A, Karloff DB, Forte JE, Zhang Y, Hargrove AE. (2019) R-BIND: An Interactive Database for Exploring and Developing RNA-Targeted Chemical Probes. ACS Chem Biol. 14(12):2691-2700. PubMed Link
Patwardhan NN, Cai Z, Umuhire Juru A, Hargrove AE. (2019) Driving factors in amiloride recognition of HIV RNA targets. Org Biomol Chem. 17(42):9313-9320. PubMed Link
Patwardhan NN, Cai Z, Newson CN, Hargrove AE. (2019) Fluorescent peptide displacement as a general assay for screening small molecule libraries against RNA. Org Biomol Chem. 17(7):1778-1786. PubMed Link
Pornillos O, Ganser-Pornillos BK. (2019) Maturation of retroviruses. Curr Opin Virol. 36:47-55. PubMed Link
Read DF, Atindaana E, Pyaram K, Yang F, Emery S, Cheong A, Nakama KR, Burnett C, Larragoite ET, Battivelli E, Verdin E, Planelles V, Chang CH, Telesnitsky A, Kidd JM. (2019) Stable integrant-specific differences in bimodal HIV-1 expression patterns revealed by high-throughput analysis. PLoS Pathog. 15(10):e1007903. PubMed Link
Schmidt F, Keele BF, Del Prete GQ, Voronin D, Fennessey CM, Soll S, Kane M, Raymond A, Gifford RJ, KewalRamani V, Lifson JD, Bieniasz PD, Hatziioannou T. (2019) Derivation of simian tropic HIV-1 infectious clone reveals virus adaptation to a new host. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1818059116. PubMed Link
Singer JB, Thomson EC, Hughes J, Aranday-Cortes E, McLauchlan J, da Silva Filipe A, Tong L, Manso CF, Gifford RJ, Robertson DL, Barnes E, Ansari MA, Mbisa JL, Bibby DF, Bradshaw D, Smith D. (2019) Interpreting Viral Deep Sequencing Data with GLUE. Viruses. 11(4). doi: 10.3390/v11040323. PubMed Link
Strickland M, Catazaro J, Rajasekaran R, Strub MP, O'Hern C, Bermejo GA, Summers MF, Marchant J, Tjandra N. (2019) Long-Range RNA Structural Information via a Paramagnetically Tagged Reporter Protein. J Am Chem Soc. 141(4):1430-1434. PubMed Link
Umuhire Juru A, Patwardhan NN, Hargrove AE. (2019) Understanding the Contributions of Conformational Changes, Thermodynamics, and Kinetics of RNA-Small Molecule Interactions. ACS Chem Biol. doi: 10.1021/acschembio.8b00945. PubMed Link
2018
Bieniasz PD, Kutluay SB. (2018) CLIP-related methodologies and their application to retrovirology. Retrovirology. 15(1):35. PubMed Link
Blanco-Melo D, Gifford RJ, Bieniasz PD. (2018) Reconstruction of a replication-competent ancestral murine endogenous retrovirus-L. Retrovirology. 15(1):34. PubMed Link
Bohn JA, Thummar K, York A, Raymond A, Brown WC, Bieniasz PD, Hatziioannou T, Smith JL. (2018) APOBEC3H structure reveals an unusual mechanism of interaction with duplex RNA. Nat Commun. 8(1):1021. PubMed Link
Chen B, Longhini AP, Nußbaumer F, Kreutz C, Dinman JD, Dayie TK. (2018) CCR5 RNA Pseudoknots: Residue and Site-Specific Labeling correlate Internal Motions with microRNA Binding. Chemistry 24(21):5462-5468. PubMed Link
Evans EL 3rd, Becker JT, Fricke SL, Patel K, Sherer NM. (2018) HIV-1 Vif's Capacity To Manipulate the Cell Cycle Is Species Specific. J Virol 92(7). pii: e02102-17. PubMed Link
Fritz M, Quinn CM, Wang M, Hou G, Lu X, Koharudin LMI, Struppe J, Case DA, Polenova T, Gronenborn AM. (2018) Determination of accurate backbone chemical shift tensors in microcrystalline proteins by integrating MAS NMR and QM/MM. Phys Chem Chem Phys. 20(14):9543-9553. PubMed Link
Gaines CR, Tkacik E, Rivera-Oven A, Somani P, Achimovich A, Alabi T, Zhu A, Getachew N, Yang AL, McDonough M, Hawkins T, Spadaro Z, Summers MF. (2018) HIV-1 Matrix Protein Interactions with tRNA: Implications for Membrane Targeting. J Mol Biol. pii: S0022-2836(18)30364-4. PubMed Link
Hron T, Farkašová H, Gifford RJ, Benda P, Hulva P, Görföl T, Pačes J, Elleder D. (2018) Remnants of an Ancient Deltaretrovirus in the Genomes of Horseshoe Bats (Rhinolophidae). Viruses 10(4). pii: E185. PubMed Link
Itano MS, Arnion H, Wolin SL, Simon SM. (2018) Recruitment of 7SL RNA to assembling HIV-1 virus-like particles. Traffic (1):36-43. PubMed Link
Johnson BA. (2018) From Raw Data to Protein Backbone Chemical Shifts Using NMRFx Processing and NMRViewJ Analysis. Methods Mol Biol. 1688:257-310. PubMed Link
Kimsey IJ, Szymanski ES, Zahurancik WJ, Shakya A, Xue Y, Chu CC, Sathyamoorthy B, Suo Z, Al- Hashimi HM. (2018) Dynamic basis for dG•dT misincorporation via tautomerization and ionization. Nature 554(7691):195-201. PubMed Link
Kraus J, Gupta R, Yehl J, Lu M, Case DA, Gronenborn AM, Akke M, Polenova T. (2018) Chemical Shifts of the Carbohydrate Binding Domain of Galectin-3 from Magic Angle Spinning NMR and Hybrid Quantum Mechanics/Molecular Mechanics Calculations. J Phys Chem B. 122(11):2931-2939. PubMed Link
Krupovic M, Blomberg J, Coffin JM, Dasgupta I, Fan H, Geering AD, Gifford R, Harrach B, Hull R, Johnson W, Kreuze JF, Lindemann D, Llorens C, Lockhart B, Mayer J, Muller E, Olszewski NE, Pappu HR, Pooggin MM, Richert-Pöggeler KR, Sabanadzovic S, Sanfaçon H, Schoelz JE, Seal S, Stavolone L, Stoye JP, Teycheney PY, Tristem M, Koonin EV, Kuhn JH. (2018) Ortervirales: New Virus Order Unifying Five Families of Reverse-Transcribing Viruses. J Virol. 92(12). pii: e00515-18. PubMed Link
Levengood JD, Tolbert BS. (2018) Idiosyncrasies of hnRNP A1-RNA recognition: Can binding mode influence function. Semin Cell Dev Biol. pii: S1084-9521(17)30470-6. PubMed Link
Marchant J, Bax A, Summers MF. (2018) Accurate Measurement of Residual Dipolar Couplings in Large RNAs by Variable Flip Angle NMR. J Am Chem Soc. 140(22):6978-6983. PubMed Link
Nguyen H, Case DA, Rose AS. (2018) NGLview-interactive molecular graphics for Jupyter notebooks. Bioinformatics. 34(7):1241-1242. PubMed Link
Pham VV, Salguero C, Khan SN, Meagher JL, Brown WC, Humbert N, de Rocquigny H, Smith JL, D'Souza VM. (2018) HIV-1 Tat interactions with cellular 7SK and viral TAR RNAs identifies dual structural mimicry. Nat Commun. 9(1):4266. doi: 10.1038/s41467-018-06591-6. PubMed Link
Penumutchu SR, Chiu LY, Meagher JL, Hansen AL, Stuckey JA, Tolbert BS. (2018) Differential Conformational Dynamics Encoded by the Linker between Quasi RNA Recognition Motifs of Heterogeneous Nuclear Ribonucleoprotein H. J Am Chem Soc. 140(37):11661-11673. doi: 10.1021/jacs.8b05366. PubMed Link
Qi X, Zhang F, Su Z, Jiang S, Han D, Ding B, Liu Y, Chiu W, Yin P, Yan H. (2018) Programming molecular topologies from single-stranded nucleic acids. Nat Commun. 9(1):4579. doi: 10.1038/s41467-018-07039-7. PubMed Link
Sharma A, Lawry SM, Klein BS, Wang X, Sherer NM, Zumwalde NA, Gumperz JE. (2018) LFA-1 Ligation by High-Density ICAM-1 Is Sufficient To Activate IFN-γ Release by Innate T Lymphocytes. Epub 201(8):2452-2461 PubMed Link
Shi H, Clay MC, Rangadurai A, Sathyamoorthy B, Case DA, Al-Hashimi HM. (2018) Atomic structures of excited state A-T Hoogsteen base pairs in duplex DNA by combining NMR relaxation dispersion, mutagenesis, and chemical shift calculations. J Biomol NMR. 70(4):229-244. PubMed Link
Takata MA, Soll SJ, Emery A, Blanco-Melo D, Swanstrom R, Bieniasz PD. (2018) Global synonymous mutagenesis identifies cis-acting RNA elements that regulate HIV-1 splicing and replication. PLoS Pathog. 14(1):e1006824. PubMed Link
Zhang K, Keane SC, Su Z, Irobalieva RN, Chen M, Van V, Sciandra CA, Marchant J, Heng X, Schmid MF, Case DA, Ludtke SJ, Summers MF, Chiu W. (2018) Structure of the 30 kDa HIV-1 RNA Dimerization Signal by a Hybrid Cryo-EM, NMR, and Molecular Dynamics Approach. Structure S0969-2126(18)30001-7. PubMed Link
2017
Takata MA, Gonçalves-Carneiro D, Zang TM, Soll SJ, York A, Blanco-Melo D, Bieniasz PD. (2017) CG dinucleotide suppression enables antiviral defense targeting non-self RNA. Nature 550(7674):124- 127. PubMed Link
Bewley MC, Reinhart L, Stake MS, Nadaraia-Hoke S, Parent LJ and Flanagan JM. (2017) A non- cleavable hexahistidine affinity tag at the carboxyl-terminus of the HIV-1 Pr55(Gag) polyprotein alters nucleic acid binding properties. Protein Expr Purif 130:137-145. PubMed Link
Boeras I, Seufzer B, Brady S, Rendahl A, Heng X, Boris-Lawrie K. (2017) The basal translation rate of authentic HIV-1 RNA is regulated by 5'UTR nt-pairings at junction of R and U5. Sci Rep 7(1):6902. PubMed Link
Bogerd HP, Kennedy EM, Whisnant AW and Cullen BR. (2017) Induced packaging of cellular microRNAs into HIV-1 virions can inhibit infectivity. MBio 8(1) e02125-16. PubMed Link
Emery A, Zhou S, Pollom E, Swanstrom R. (2017) Characterizing HIV-1 Splicing by Using Next-Generation Sequencing. J Virol 91(6) e02515-16. PubMed Link
Eubanks CS, Forte JE, Kapral GJ, Hargrove AE. (2017) Small Molecule-Based Pattern Recognition To Classify RNA Structure. J Am Chem Soc 139(1):409-416. PubMed Link
Jain N, Lin HC, Morgan CE, Harris ME, Tolbert BS. (2017) Rules of RNA specificity of hnRNP A1 revealed by global and quantitative analysis of its affinity distribution. Proc Natl Acad Sci USA 114(9):2206-2211. PubMed Link
Madison MK, Lawson DQ, Elliott J, Ozantürk AN, Koneru PC, Townsend D, Errando M, Kvaratskhelia M, Kutluay SB. (2017) Allosteric HIV-1 Integrase Inhibitors Lead to Premature Degradation of the Viral RNA Genome and Integrase in Target Cells. J Virol 91(17) e00821-17. PubMed Link
Miller CM, Akiyama H, Agosto LM, Emery A, Ettinger CR, Swanstrom RI, Henderson AJ, Gummuluru S. (2017) Virion-Associated Vpr Alleviates a Postintegration Block to HIV-1 Infection of Dendritic Cells. J Virol 91(13) e00051-17. PubMed Link
Naorem SS, Han J, Wang S, Lee WR, Heng X, Miller JF, Guo H. (2017) DGR mutagenic transposition occurs via hypermutagenic reverse transcription primed by nicked template RNA. Proc Natl Acad Sci U S A 114(47):E10187. PubMed Link
Patwardhan NN, Ganser LR, Kapral GJ, Eubanks CS, Lee J, Sathyamoorthy B, Al-Hashimi HM, Hargrove AE. (2017) Amiloride as a new RNA-binding scaffold with activity against HIV-1 TAR. Medchemcomm 8(5):1022-1036. PubMed Link
Roy S, Lammert H, Hayes RL, Chen B, LeBlanc R, Dayie TK, Onuchic JN, Sanbonmatsu KY. (2017) A magnesium-induced triplex pre-organizes the SAM-II riboswitch. PLoS Comput Biol 13(3):e1005406. PubMed Link
Singh G, Fritz SM, Ranji A, Singh D, Boris-Lawrie K. (2017) Isolation of Cognate RNA-protein Complexes from Cells Using Oligonucleotide-directed Elution. J Vis (119). PubMed Link
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2016
Boeras I, Song Z, Moran A, Franklin J, Brown WC, Johnson M, Boris-Lawrie K, Heng X. (2016) DHX9/RHA Binding to the PBS-Segment of the Genomic RNA during HIV-1 Assembly Bolsters Virion Infectivity. J Mol Biol. 428(11):2418-29. PubMed Link
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Eckwahl MJ, Arnion H, Kharytonchyk S, Zang T, Bieniasz PD, Telesnitsky A, Wolin SL. (2016) Analysis of the human immunodeficiency virus-1 RNA packageome. RNA. 22(8):1228-38. PubMed Link
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Johnson J, Case DA, Yamazaki T, Gusarov S, Kovalenko A, Luchko T. (2016) Small Molecule Solvation Energy and Entropy from 3D-RISM. J. Phys. Cond. Mat. 28(34):344002 PubMed Link
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Kharytonchyk S, King SR, Ndongmo CB, Stilger KL, An W, Telesnitsky A. (2016) Resolution of specific nucleotide mismatches by wild type and AZT-resistant reverse transcriptases during HIV-1 replication. J Mol Biol doi:10.1016/j.jmb.2016.04.005. PubMed Link
Kharytonchyk S, Monti S, Smaldino P, Van V, Bolden NC, Russo E, Shuey A, Swanson C, Brown J, Telesnitsky A, Summers MF. (2016) Transcriptional start site heterogeneity modulates the structure and function of the HIV-1 genome. Proc Natl Acad Sci USA 113:13378-13383. Pubmed Link
Khisamutdinov EF, Jasinski DL, Li H, Zhang K, Chiu W, Guo P. (2016) Fabrication of RNA 3D Nanoprisms for Loading and Protection of Small RNAs and Model Drugs. Adv Mater. doi:10.1002/adma.201603180. Pubmed Link
Kutluay SB, Bieniasz PD. (2016) Analysis of HIV-1 Gag-RNA interactions in cells andvirions by CLIP-seq. Methods Mol Biol1354:119-31. PubMed Link
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Li H, Zhang K, Pi F, Guo S, Shlyakhtenko L, Chiu W, Shu D, Guo P. (2016) Controllable Self-Assembly of RNA Tetrahedrons with Precise Shape and Size for Cancer Targeting. Adv Mater. 28(34):7501-7. Pubmed Link
Longhini AP, LeBlanc RM, Becette O, Salguero C, Wunderlich CH, Johnson BA, D'Souza VM, Kreutz C, Dayie TK. (2016) Chemo-enzymatic synthesis of site-specific isotopically labeled nucleotides for use in NMR resonance assignment, dynamics and structural characterizations. Nucleic Acids Res. 44(6):e52. Pubmed Link
Mercredi PY, Bucca N, Loeliger B, Gaines CR, Mehta M, Bhargava P, Tedbury PR, Charlier L, Floquet N, Muriaux D, Favard C, Sanders CR, Freed EO, Marchant J, Summers MF. (2016) Structural and Molecular Determinants of Membrane Binding by the HIV-1 Matrix Protein. J Mol Biol. 428(8):1637-55. PubMed Link
Norris M, Fetler B, Marchant J, Johnson BA. (2016) NMRFx Processor: a cross-platform NMR data processing program. J Biomol NMR. 65(3-4):205-16. PubMed Link
Nguyen HT, Pabit SA, Pollack L, Case DA. (2016) Extracting water and ion distributions from small angle X-ray scattering experiments. J Chem Phys. 144(21):214105. PubMed Link
Rye-McCurdy T, Olson ED, Liu S, Binkley C, Reyes JP, Thompson BR, Flanagan JM, Parent LJ and Musier-Forsyth K. (2016) Functional equivalence of retroviral MA domains in facilitating Psi RNA binding specificity by Gag. Viruses 8:E256. PubMed Link
Telesnitsky A, Wolin SL. (2016) The Host RNAs in Retroviral Particles. Viruses. 8(8). pii: E235. PubMed Link
Veneziano R, Ratanalert S, Zhang K, Zhang F, Yan H, Chiu W, Bathe M. (2016) Designer nanoscale DNA assemblies programmed from the top down. Science. 352(6293):1534. PubMed Link
Wagner JM, Zadrozny K, Chrustowicz J, Purdy MD, Yeager M, Ganser-Pornillos BK and Pornillos O. (2016) Crystal structure of an HIV assembly and maturation switch. ELife 5: e17063. PubMed Link
York A, Kutluay SB, Errando M, Bieniasz PD. (2016) The RNA Binding Specificity of Human APOBEC3 Proteins Resembles That of HIV-1 Nucleocapsid. PLoS Pathog. 12(8):e1005833. PubMed Link
Zhang H, Hou G, Lu M, Ahn J, Byeon IJ, Langmead CJ, Perilla JR, Hung I, Gor’kov PL, Gan Z, Brey W, Case DA, Schulten K, Gronenborn AM, Polenova T. (2016) Functional Dynamics in HIV-1 Capsid Determined by Integrated Magic-Angle-Spinning NMR, QM/MM, and MD Approach. (Submitted for publication.)
Zhou H, Kimsey IJ, Nikolova EN, Sathyamoorthy B, Grazioli G, McSally J, Bai T, Wunderlich CH, Kreutz C, Andricioaei I, Al-Hashimi HM. m(1)A and m(1)G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs. Nat Struct Mol Biol. 23(9):803-10. PubMed Link
Ganser LR, Al-Hashimi HM. (2016) HIV-1 leader RNA dimeric interface revealed by NMR. Proc Natl Acad Sci U S A 113(47):13263-13265. PubMed Link
2015
Brown JD, Summers MF, Johnson BA. (2015) Prediction of hydrogen and carbon chemical shifts from RNA using database mining and support vector regression. J Biomol NMR 63:39-52. PubMed Link
Eckwahl MJ, Sim S, Smith D, Telesnitsky A, Wolin SL. (2015) A retrovirus packages nascent host noncoding RNAs from a novel surveillance pathway. Genes Dev 29:646-657. PubMed Link
Giambaşu GM, Gebala MK, Panteva MT, Luchko T, Case DA, York DM. (2015) Competitive interaction of monovalent cations with DNA predicted by 3D-RISM. Nucleic Acids Res 43:8405-15. PubMed Link
Giambaşu GM, York DM, Case DA. (2015) Structural fidelity and NMR relaxation analysis in a prototype RNA hairpin. RNA 21:963-74. PubMed Link
Holmes M, Zhang F, Bieniasz PD. (2015) Single-cell and single-cycle analysis of HIV-1 replication. PLoS Pathog 11(6):e1004961. PubMed Link
Irobalieva RN, Fogg JM, Catanese DJ Jr, Sutthibutpong T, Chen M, Barker AK, Ludtke SJ, Harris SA, Schmid MF, Chiu W, Zechiedrich L. (2015) Structural diversity of supercoiled DNA. Nat Commun 6:8440 doi: 10.1038/ncomms9440 PubMed Link
Keane SC, Heng X, Lu K, Kharytonchyk S, Ramakrishnan V, Carter G, Barton S, Hosic A, Florwick A, Santos J, Bolden NC, McCowin S, Case DA, Johnson BA, Salemi M, Telesnitsky A, Summers MF. (2015) Structure of the HIV-1 RNA packaging signal. Science 348:917-21. PubMed Link
Leung DW, Borek D, Luthra P, Binning JM, Anantpadma M, Liu G, Harvey IB, Su Z, Endlich-Frazier A, Pan J, Shabman RS, Chiu W, Davey RA, Otwinowski Z, Basler CF, and Amarasinghe GK. (2015) An intrinsically disordered peptide from Ebola virus VP35 controls viral RNA synthesis by modulating nucleoprotein-RNA interactions. Cell Rep 11:376-389. PubMed Link
Liu C, Janowski PA, Case DA. (2015) All-atom crystal simulations of DNA and RNA duplexes. Biochim Biophys Acta 1850:1059-71. PubMed Link
Morgan CE, Meagher JL, Levengood JD, Delproposto J, Rollins C, Stuckey JA, Tolbert BS. (2015) The first crystal structure of the UP1 domain of hnRNP A1 bound to RNA reveals a new look for an old RNA binding protein. J Mol Biol 427:3241-57. PubMed Link
Rice AP. (2015) Roles of microRNAs and long-noncoding RNAs in human immunodeficiency virus replication. Wiley Interdisicip Rev RNA 6:661-70. PubMed Link
Rihn SJ, Hughes J, Wilson SJ, Bieniasz PD. (2015) Uneven genetic robustness of HIV-1 integrase. J Virol 89:552-67. PubMed Link
Salmon L, Giambaşu GM, Nikolova EN, Petzold K, Bhattacharya A, Case DA, Al-Hashimi HM. (2015) Modulating RNA alignment using directional dynamic kinks: application in determining an atomic-resolution ensemble for a hairpin using NMR residual dipolar couplings. J Am Chem Soc 137:12954-65. PubMed Link
Stake MS, Singh D, Hernandez JM, Singh S, Kaddis RJ, Parent LJ, Boris-Lawrie K. (2015) HIV-1 and two genetically simpler avian retrovirus 5' untranslated regions bind orthologous human and chicken RNA binding proteins. Virology 486:307-20. PubFact Link
Swanson MD, Boudreaux DM, Salmon L, Chugh J, Winter HC, Meagher JL, André S, Murphy PV, Oscarson S, Roy R, King S, Kaplan MH, Goldstein IJ, Tarbet EB, Hurst BL, Smee DF, de la Fuente C, Hoffmann HH, Xue Y, Rice CM, Schols D, Garcia JV, Stuckey JA, Gabius HJ, Al-Hashimi HM, Markovitz DM. (2015) Molecular engineering of a therapeutic lectin: uncoupling mitogenicity from antiviral activity. Cell 163(3):746-58. PubMed Link
Wunderlich CH, Juen MA, LeBlanc RM, Longhini AP, Dayie TK, Kreutz C. (2015) Stable isotope-labeled RNA phosphoramidites to facilitate dynamics by NMR. Methods Enzymol 565:461-94. PubMed Link
Xue Y, Kellogg D, Kimsey IJ, Sathyamoorthy B, Stein ZW, McBrairty M, Al-Hashimi HM. (2015) Characterizing RNA excited states using NMR relaxation dispersion. Methods Enzymol 558:39-73. PubMed Link
Yang S, Al-Hashimi HM. (2015) Unveiling Inherent Degeneracies in Determining Population-Weighted Ensembles of Interdomain Orientational Distributions Using NMR Residual Dipolar Couplings: Application to RNA Helix Junction Helix Motifs. J Phys Chem B.119(30):9614-26. PubMed Link
2014
Afonin KA, Viard M, Koyfman AY, Martins AN, Kasprzak WK, Panigaj M, Desai R, Santhanam A, Grabow WW, Jaeger L, Heldman E, Reiser J, Chiu W, Freed EO and Shapiro BA. (2014) Multifunctional RNA nanoparticles. Nano Lett 14:5662-71. PubMed Link
Alvarado LJ, Longhini AP, LeBlanc RM, Chen B, Kreutz C, Dayie TK. (2014) Chemo-enzymatic synthesis of selectively 13C/15N-labeled RNA for NMR structural and dynamics studies. Methods Enzymol 549:133-62. PubMed Link
Alvarado LJ, LeBlanc RM, Longhini AP, Keane SC, Jain N, Yildiz ZF, Tolbert BS, D'Souza VM, Summers MF, Kreutz C, Dayie TK. (2014) Regio-selective chemical-enzymatic synthesis of pyrimidine nucleotides facilitates RNA structure and dynamics studies. Chembiochem 15:1573-7. PubMed Link
Bleck M, Itano MS, Johnson DS, Thomas VK, North AJ, Bieniasz PD, Simon SM. (2014) Temporal and spatial organization of ESCRT protein recruitment during HIV-1 budding. Proc Natl Acad Sci USA 111:12211-6. PubMed Link
Giambaşu GM, Luchko T, Herschlag D, York DM, Case DA. (2014) Ion counting from explicit-solvent simulations and 3D-RISM. Biophys J 106:883-94. PubMed Link
Ganser LR, Mustoe AM, Al-Hashimi HM. (2014) An RNA tertiary switch by modifying how helices are tethered. Genome Biol 15:425. PubMed Link
Johnson DS, Toledo-Crow R, Mattheyses AL, Simon SM. (2014) Polarization-controlled TIRFM with focal drift and spatial field intensity correction. Biophys J 106:1008-19. PubMed Link
Johnson SF, Collins JT, D'Souza VM, Telesnitsky A. (2014) Determinants of Moloney murine leukemia virus Gag-Pol and genomic RNA proportions. J Virol 88:7267-75. PubMed Link
Kutluay SB, Zang T, Blanco-Melo D, Powell C, Jannain D, Errando M, Bieniasz PD. (2014) Global changes in the RNA binding specificity of HIV-1 gag regulate virion genesis. Cell 159:1096-109. PubMed Link
Lamers SL, Fogel GB, Nolan DJ, McGrath MS, Salemi M. (2014) HIV-associated neuropathogenesis: a systems biology perspective for modeling and therapy. Biosystems 119:53-61. PubMed Link
Nguyen HT, Pabitt SA, Meisburger SP, Pollack L, Case DA. (2014) Accurate small and wide angle X-ray scattering profiles from atomic models of proteins and nucleic acids. J Chem Phys 141:22D508. PubMed Link
Quek BL, Beemon K. (2014) Retroviral strategy to stabilize viral RNA. Curr Opin Microbiol 18:78-82. PubMed Link
Ravera E, Salmon L, Fragai M, Parigi G, Al-Hashimi H, Luchinat C. (2014) Insights into domain-domain motions in proteins and RNA from solution NMR. Acc Chem Res 47(10):3118-26. PubMed Link
Rollins C, Levengood JD, Rife BD, Salemi M, Tolbert BS. (2014) Thermodynamic and phylogenetic insights into hnRNP A1 recognition of the HIV-1 exon splicing silencer 3 element. Biochemistry 53:2172-84. PubMed Link
Salmon L, Yang S, Al-Hashimi HM. (2014) Advances in the determination of nucleic acid conformational ensembles. Annu Rev Phys Chem 65:293-316. PubMed Link
Sathyamoorthy B, Lee J, Kimsey I, Ganser LR, Al-Hashimi H. (2014) Development and application of aromatic [13C, 1H] SOFAST-HMQC NMR experiment for nucleic acids. J Biomol NMR 60:77-83. PubMed Link
2013
Barton S, Heng X, Johnson BA, Summers MF. (2013) Database proton NMR chemical shifts for RNA signal assignment and validation. J Biomol NMR 55:33-46. PubMed Link
Cheatham TE III, Case DA. (2013) Twenty-five years of nucleic acid simulations. Biopolymers 99:969-77. PubMed Link
Lamers SL, Nolan DJ, Strickland SL, Prosperi M, Fogel GB, Goodenow MM, Salemi M. (2013) Longitudinal analysis of intra-host simian immunodeficiency virus recombination in varied tissues of the rhesus macaque model of neuroAIDS. J Gen Virol 94:2469-79. PubMed Link
Leblanc J, Weil J, Beemon K. (2013) Posttranscriptional regulation of retroviral gene expression: primary RNA transcripts play three roles as pre-mRNA, mRNA, and genomic RNA. Wiley Interdiscip Rev RNA 4:567-80. PubMed Link
Lee J, Vogt CE, McBrairty M, Al-Hashimi HM. (2013) Influence of dimethylsulfoxide on RNA structure and ligand binding. Anal Chem 85:9692-8. PubMed Link
Stake MS, Bann DV, Kaddis RJ, Parent LJ. (2013) Nuclear trafficking of retroviral RNAs and Gag proteins during late steps of replication. Viruses 5:2767-95. PubMed Link
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