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‐Frangos, 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 Chaperone RNA Regulation. Microbiol Spectr, 6(4), 10.1128/microbiolspec.RWR-0026-2018. doi: 10.1128/microbiolspec.RWR-0026-2018
Woodson, S.A. (2017) Probing RNA Folding Pathways via RNA Fingerprinting. Curr. Protoc. Nucleic Acid Chem, 70, 11.4.1-11.4.19. doi: 10.1002/cpnc.36
Woodson, S.A. (2015) RNA folding retrospective: lessons from ribozymes big and small. RNA, 21(4), 502-503. doi: 10.1261/rna.051110.115
Woodson, S.A. (2011) RNA folding pathways and the self-assembly of ribosomes. Acc. Chem. Res, 44(12), 1312–1319. doi: 10.1021/ar2000474
Woodson, S.A. (2010) Compact Intermediates in RNA Folding. Biophysics, 39, 61–77. doi: 10.1146/annurev.biophys.093008.131334
Woodson, S.A. (2010) Taming free energy landscapes with RNA chaperones. RNA Biol, 7(6), 677–686. doi: 10.4161/rna.7.6.13615
RNA Folding
Yu, L.D., White, E.N., Woodson, S.A. (2024) Optimized periphery-core interface increases fitness of the Bacillus subtilis glmS ribozyme. Nucleic Acids Res, gkae830. doi:10.1093/nar/gkae830
Lou, Y. & Woodson, S.A. (2024) Co-transcriptional folding of the glmS ribozyme enables a rapid response to metabolite. Nucleic Acids Res, 52(2), 872–884. doi:10.1093/nar/gkad1120
Korman, A., et. al. (2020) Light-controlled twister ribozyme with single-molecule detection resolves RNA function in time and space. Proc. Natl. Acad. Sci, 117(22), 12080–12086. doi: 10.1073/pnas.2003425117
Jones, C. P., Panja, S., Woodson, S. A. & Ferré-D’Amaré, A. R. (2019). Monitoring co-transcriptional folding of riboswitches through helicase unwinding. Methods Enzymol, 623, 209–227. doi: 10.1016/bs.mie.2019.05.031
Roh, J. et al. (2018). Effects of Preferential Counterion Interactions on the Specificity of RNA Folding. J. Phys. Chem. Lett, 9(19), 5726–5732. doi: 10.1021/acs.jpclett.8b02086
Hua, B., Panja, S., Wang, Y., Woodson, S. & Ha, T. (2018). Mimicking Co-Transcriptional RNA Folding Using a Superhelicase. J. Am. Chem. Soc, 140(32), 10067-10070. doi: 10.1021/jacs.8b03784
Hao, Y. et al. (2018). Time‐Resolved Hydroxyl Radical Footprinting of RNA with X‐Rays. Curr. Protoc. Nucleic Acid Chem, 73(1), e52. doi: 10.1002/cpnc.52
Ribosome Assembly
Rodgers, M.L, Sun, Y., Woodson, S.A. (2023) Ribosomal Protein S12 Hastens Nucleation of Co-Transcriptional Ribosome Assembly. Biomolecules, 13(6), 951. doi: 10.3390/biom13060951
Rodgers, M. L. & Woodson, S. A. (2019). Transcription increases the cooperativity of ribonucleoprotein assembly. Cell 179(6), 1370-1381.e12. doi: 10.1016/j.cell.2019.11.007
Sharma, I. M. & Woodson, S. A. (2019). RbfA and IF3 couple ribosome biogenesis and translation initiation to increase stress tolerance. Nucleic Acids Res, 48(1), 359-372. doi: 10.1093/nar/gkz1065.
Razi, A. et al. (2019). Role of Era in assembly and homeostasis of the ribosomal small subunit. Nucleic Acids Res, 47(15), 8301-8317. doi: 10.1093/nar/gkz571
Sharma, I. et al. (2018). A metastable rRNA junction essential for bacterial 30S biogenesis. Nucleic Acids Res. 46(10), 5182-5194. doi: 10.1093/nar/gky120
Small Non-Coding RNAs in Bacteria
Malecka, E.M. & Woodson, S.A. (2024) RNA compaction and iterative scanning for small RNA targets by the Hfq chaperone. Nat. Comm, 15(1), 2069. doi: 10.1038/s41467-024-46316-6
Rodgers, M.L., O’Brien, B., Woodson, S.A. (2023) Small RNAs and Hfq capture unfolded RNA target sites during transcription. Mol. Cell, 83(9), 1489–1501.e5. doi: 10.1016/j.molcel.2023.04.003
Sarni, S., Roca, J., et. al. (2022) Intrinsically disordered interaction network in an RNA chaperone revealed by native mass spectrometry. Proc. Natl. Acad. Sci, 119 (47), e2208780119. doi: 10.1073/pnas.2208780119
Cai, H., Roca J., et. al. (2022) Dynamic refolding of OxyS sRNA by the Hfq RNA chaperone.
J. Mol. Biol, 434(18), 167776. doi: 10.1016/j.jmb.2022.167776
Roca J., Santiago-Frangos, A., Woodson, S.A. (2022) Diversity of bacterial small RNAs drives competitive strategies for a mutual chaperone. Nat. Comm, 13(1), 2449. doi: 10.1038/s41467-022-30211-z
Malecka, E.M., et al. (2021) Stabilization of Hfq-mediated translational repression by the co-repressor Crc in Pseudomonas aeruginosa. Nucleic Acids Res, 49(12), 7075-7087. doi: 10.1093/nar/gkab510
Małecka, E.M. & Woodson, S.A. (2021) Stepwise sRNA targeting of structured bacterial mRNAs leads to abortive annealing. Mol. Cell, 81(9), 1988-1999.e4. doi: 10.1016/j.molcel.2021.02.019
Santiago-Frangos, A. et al. Caulobacter crescentus Hfq structure reveals a conserved mechanism of RNA annealing regulation. (2019). Proc. Natl. Acad. Sci, 116(22), 201814428. doi: 10.1073/pnas.1814428116
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, 200(10), e00704-17. doi: 10.1128/JB.00704-17
Triplet Repeat RNAs and Liquid-Liquid Phase Separation
O’Brien, B., Moulick, R., et. al. (2024). Stick-slip unfolding favors self-association of expanded HTT mRNA. Nat. Comm, 15(1), 8738. doi: 10.1038/s41467-024-52764-x
Li, P., Moulick, R., et al. (2021). RNA toxicity and perturbation of rRNA processing in spinocerebellar ataxia type 2. Movement Disorders. 36(11), 2519-2529. doi: 10.1002/mds.28729