{"id":7,"date":"2013-09-10T12:21:41","date_gmt":"2013-09-10T12:21:41","guid":{"rendered":"https:\/\/sites.krieger.jhu.edu\/template-research\/?page_id=7"},"modified":"2024-12-04T18:46:27","modified_gmt":"2024-12-04T23:46:27","slug":"publications","status":"publish","type":"page","link":"https:\/\/sites.krieger.jhu.edu\/woodson\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"

Reviews<\/h2>\n

Rodgers, M.L. & Woodson, S.A. (2021) A roadmap for rRNA folding and assembly during transcription. Trends Biochem. Sci<\/em><\/strong>, 46(11), 889-901. doi: 10.1016\/j.tibs.2021.05.009<\/p>\n

Santiago\u2010Frangos, A. & Woodson, S.A. (2018) Hfq chaperone brings speed dating to bacterial sRNA. Wiley Interdiscip. Rev. RNA<\/em><\/strong>, 9(4), e1475. doi: 10.1002\/wrna.1475<\/p>\n

Woodson, S.A., Panja, S. & Santiago-Frangos, A. (2018) Proteins That Chaperone RNA Regulation. Microbiol Spectr<\/em><\/strong>, 6(4), 10.1128\/microbiolspec.RWR-0026-2018. doi: 10.1128\/microbiolspec.RWR-0026-2018<\/p>\n

Woodson, S.A. (2017) Probing RNA Folding Pathways via RNA Fingerprinting. Curr. Protoc. Nucleic Acid Chem<\/em><\/strong>, 70, 11.4.1-11.4.19. doi: 10.1002\/cpnc.36<\/p>\n

Woodson, S.A. (2015) RNA folding retrospective: lessons from ribozymes big and small. RNA<\/em><\/strong>, 21(4), 502-503. doi: 10.1261\/rna.051110.115<\/p>\n

Woodson, S.A. (2011) RNA folding pathways and the self-assembly of ribosomes. Acc. Chem. Res<\/em><\/strong>, 44(12), 1312\u20131319. doi: 10.1021\/ar2000474<\/p>\n

Woodson, S.A. (2010) Compact Intermediates in RNA Folding. Biophysics<\/em><\/strong>, 39, 61\u201377. doi: 10.1146\/annurev.biophys.093008.131334<\/p>\n

Woodson, S.A. (2010) Taming free energy landscapes with RNA chaperones. RNA Biol<\/em><\/strong>, 7(6), 677\u2013686. doi: 10.4161\/rna.7.6.13615<\/p>\n

RNA Folding<\/span><\/h2>\n

Yu, L.D., White, E.N., Woodson, S.A. (2024) Optimized periphery-core interface increases fitness of the Bacillus subtilis glmS\u00a0<\/em>ribozyme.\u00a0Nucleic Acids<\/strong> Res<\/strong><\/em>, gkae830. doi:10.1093\/nar\/gkae830<\/p>\n

Lou, Y. & Woodson, S.A. (2024) Co-transcriptional folding of the glmS ribozyme enables a rapid response to metabolite.\u00a0Nucleic Acids Res<\/strong><\/em>,\u00a0<\/em>52(2), 872\u2013884. doi:10.1093\/nar\/gkad1120<\/p>\n

Korman, A., et. al. (2020) Light-controlled twister ribozyme with single-molecule detection resolves RNA function in time and space. Proc. Natl. Acad. Sci<\/em><\/strong>, 117(22), 12080\u201312086. doi: 10.1073\/pnas.2003425117<\/p>\n

Jones, C. P., Panja, S., Woodson, S. A. & Ferr\u00e9-D\u2019Amar\u00e9, A. R. (2019). Monitoring co-transcriptional folding of riboswitches through helicase unwinding. Methods Enzymol<\/strong><\/em>, 623, 209\u2013227. doi: 10.1016\/bs.mie.2019.05.031<\/p>\n

Roh, J. et al. (2018). Effects of Preferential Counterion Interactions on the Specificity of RNA Folding. J. Phys. Chem. Lett<\/strong><\/em>, 9(19), 5726\u20135732. doi: 10.1021\/acs.jpclett.8b02086<\/p>\n

Hua, B., Panja, S., Wang, Y., Woodson, S. & Ha, T. (2018). Mimicking Co-Transcriptional RNA Folding Using a Superhelicase. J. Am. Chem. Soc<\/strong><\/em>, 140(32), 10067-10070. doi: 10.1021\/jacs.8b03784<\/p>\n

Hao, Y. et al. (2018). Time\u2010Resolved Hydroxyl Radical Footprinting of RNA with X\u2010Rays. Curr. Protoc. Nucleic Acid Chem<\/strong><\/em>, 73(1), e52. doi: 10.1002\/cpnc.52<\/p>\n

Ribosome Assembly<\/h2>\n

Rodgers, M.L, Sun, Y., Woodson, S.A. (2023) Ribosomal Protein S12 Hastens Nucleation of Co-Transcriptional Ribosome Assembly.\u00a0Biomolecules<\/strong><\/em>, 13(6), 951. doi: 10.3390\/biom13060951<\/p>\n

Rodgers, M. L. & Woodson, S. A. (2019). Transcription increases the cooperativity of ribonucleoprotein assembly. Cell<\/strong><\/em> 179(6), 1370-1381.e12. doi: 10.1016\/j.cell.2019.11.007<\/p>\n

Sharma, I. M. & Woodson, S. A. (2019). RbfA and IF3 couple ribosome biogenesis and translation initiation to increase stress tolerance. Nucleic Acids Res<\/em><\/strong>, 48(1), 359-372. doi: 10.1093\/nar\/gkz1065.<\/p>\n

Razi, A. et al. (2019). Role of Era in assembly and homeostasis of the ribosomal small subunit. Nucleic Acids<\/strong> Res<\/strong><\/em>, 47(15), 8301-8317. doi: 10.1093\/nar\/gkz571<\/p>\n

Sharma, I. et al. (2018). A metastable rRNA junction essential for bacterial 30S biogenesis. Nucleic Acids Res. <\/strong><\/em>46(10), 5182-5194. doi: 10.1093\/nar\/gky120<\/p>\n

Small Non-Coding RNAs in Bacteria<\/h2>\n

Malecka, E.M. & Woodson, S.A. (2024) RNA compaction and iterative scanning for small RNA targets by the Hfq chaperone.\u00a0Nat. Comm, <\/em><\/strong>15(1), 2069.\u00a0<\/em>doi: 10.1038\/s41467-024-46316-6<\/p>\n

Rodgers, M.L., O’Brien, B., Woodson, S.A. (2023) Small RNAs and Hfq capture unfolded RNA target sites during transcription.\u00a0Mol. Cell<\/strong><\/em>, 83(9), 1489\u20131501.e5. doi: 10.1016\/j.molcel.2023.04.003<\/p>\n

Sarni, S., Roca, J., et. al. (2022) Intrinsically disordered interaction network in an RNA chaperone revealed by native mass spectrometry. Proc. Natl. Acad. Sci<\/strong><\/em>, 119 (47), e2208780119. doi: 10.1073\/pnas.2208780119<\/p>\n

Cai, H., Roca J., et. al. (2022) Dynamic refolding of OxyS sRNA by the Hfq RNA chaperone.\u00a0
\nJ. Mol.<\/strong> Biol<\/strong><\/em>, 434(18), 167776. doi: 10.1016\/j.jmb.2022.167776<\/p>\n

Roca J., Santiago-Frangos, A., Woodson, S.A. (2022) Diversity of bacterial small RNAs drives competitive strategies for a mutual chaperone.\u00a0Nat. Comm<\/strong><\/em>, <\/em>13(1), 2449. doi: 10.1038\/s41467-022-30211-z<\/p>\n

Malecka, E.M., et al. (2021) Stabilization of Hfq-mediated translational repression by the co-repressor Crc in Pseudomonas aeruginosa. Nucleic Acids Res<\/em><\/strong>, 49(12), 7075-7087. doi: 10.1093\/nar\/gkab510<\/p>\n

Ma\u0142ecka, E.M. & Woodson, S.A. (2021) Stepwise sRNA targeting of structured bacterial mRNAs leads to abortive annealing. Mol. Cell<\/em><\/strong>, 81(9), 1988-1999.e4. doi: 10.1016\/j.molcel.2021.02.019<\/p>\n

Santiago-Frangos, A. et al. Caulobacter crescentus Hfq structure reveals a conserved mechanism of RNA annealing regulation. (2019). Proc. Natl. Acad. Sci<\/em><\/strong>, 116(22), 201814428. doi: 10.1073\/pnas.1814428116<\/p>\n

Djapgne, L. et al. (2018). The Pseudomonas aeruginosa PrrF1 and PrrF2 Small Regulatory RNAs Promote 2-Alkyl-4-Quinolone Production through Redundant Regulation of the antR mRNA. J. Bacteriol<\/em><\/strong>, 200(10), e00704-17. doi: 10.1128\/JB.00704-17<\/p>\n

Triplet Repeat RNAs and Liquid-Liquid Phase Separation<\/h2>\n

O’Brien, B., Moulick, R., et. al. (2024). Stick-slip unfolding favors self-association of expanded HTT<\/em> mRNA. Nat. Comm<\/strong>, <\/em>15(1), \u00a08738. doi: 10.1038\/s41467-024-52764-x<\/p>\n

Li, P., Moulick, R., et al. (2021). <\/span>RNA toxicity and perturbation of rRNA processing in spinocerebellar ataxia type 2. Movement Disorders<\/strong><\/em>. 36(11), 2519-2529. doi: 10.1002\/mds.28729<\/p>\n

Complete List of Publications<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"

Reviews Rodgers, M.L. & Woodson, S.A. (2021) A roadmap for rRNA folding and assembly during transcription. Trends Biochem. Sci, 46(11), 889-901. doi: 10.1016\/j.tibs.2021.05.009 Santiago\u2010Frangos, A. & Woodson, S.A. (2018) Hfq chaperone brings speed dating to bacterial sRNA. Wiley Interdiscip. Rev. RNA, 9(4), e1475. doi: 10.1002\/wrna.1475 Woodson, S.A., Panja, S. & Santiago-Frangos, A. (2018) Proteins That […]<\/p>\n","protected":false},"author":40,"featured_media":0,"parent":0,"menu_order":2,"comment_status":"open","ping_status":"open","template":"","meta":{"_acf_changed":false,"footnotes":""},"class_list":["post-7","page","type-page","status-publish","hentry"],"acf":[],"_links":{"self":[{"href":"https:\/\/sites.krieger.jhu.edu\/woodson\/wp-json\/wp\/v2\/pages\/7","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sites.krieger.jhu.edu\/woodson\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sites.krieger.jhu.edu\/woodson\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sites.krieger.jhu.edu\/woodson\/wp-json\/wp\/v2\/users\/40"}],"replies":[{"embeddable":true,"href":"https:\/\/sites.krieger.jhu.edu\/woodson\/wp-json\/wp\/v2\/comments?post=7"}],"version-history":[{"count":5,"href":"https:\/\/sites.krieger.jhu.edu\/woodson\/wp-json\/wp\/v2\/pages\/7\/revisions"}],"predecessor-version":[{"id":298,"href":"https:\/\/sites.krieger.jhu.edu\/woodson\/wp-json\/wp\/v2\/pages\/7\/revisions\/298"}],"wp:attachment":[{"href":"https:\/\/sites.krieger.jhu.edu\/woodson\/wp-json\/wp\/v2\/media?parent=7"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}