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In vivo-like nearest neighbor parameters improve prediction of fractional RNA base-pairing in cells.
Nucleic Acids Res. 2023 Nov 10;51(20):11298-11317. doi: 10.1093/nar/gkad807.
Nucleic Acids Res. 2023.
PMID: 37855684
Free PMC article.
Functional Roles of Chelated Magnesium Ions in RNA Folding and Function.
Yamagami R, Sieg JP, Bevilacqua PC.
Yamagami R, et al. Among authors: sieg jp.
Biochemistry. 2021 Aug 10;60(31):2374-2386. doi: 10.1021/acs.biochem.1c00012. Epub 2021 Jul 28.
Biochemistry. 2021.
PMID: 34319696
Free PMC article.
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RNA sequence and structure control assembly and function of RNA condensates.
Poudyal RR, Sieg JP, Portz B, Keating CD, Bevilacqua PC.
Poudyal RR, et al. Among authors: sieg jp.
RNA. 2021 Dec;27(12):1589-1601. doi: 10.1261/rna.078875.121. Epub 2021 Sep 22.
RNA. 2021.
PMID: 34551999
Free PMC article.
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Genome-wide analysis of the in vivo tRNA structurome reveals RNA structural and modification dynamics under heat stress.
Yamagami R, Sieg JP, Assmann SM, Bevilacqua PC.
Yamagami R, et al. Among authors: sieg jp.
Proc Natl Acad Sci U S A. 2022 Jun 21;119(25):e2201237119. doi: 10.1073/pnas.2201237119. Epub 2022 Jun 13.
Proc Natl Acad Sci U S A. 2022.
PMID: 35696576
Free PMC article.
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The Metabolome Weakens RNA Thermodynamic Stability and Strengthens RNA Chemical Stability.
Sieg JP, McKinley LN, Huot MJ, Yennawar NH, Bevilacqua PC.
Sieg JP, et al.
Biochemistry. 2022 Nov 15;61(22):2579-2591. doi: 10.1021/acs.biochem.2c00488. Epub 2022 Oct 28.
Biochemistry. 2022.
PMID: 36306436
Free PMC article.
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MeltR software provides facile determination of nucleic acid thermodynamics.
Sieg JP, Arteaga SJ, Znosko BM, Bevilacqua PC.
Sieg JP, et al.
Biophys Rep (N Y). 2023 Mar 2;3(2):100101. doi: 10.1016/j.bpr.2023.100101. eCollection 2023 Jun 14.
Biophys Rep (N Y). 2023.
PMID: 37006960
Free PMC article.
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Regulation of OmpA Translation and Shigella dysenteriae Virulence by an RNA Thermometer.
Murphy ER, Roßmanith J, Sieg J, Fris ME, Hussein H, Kouse AB, Gross K, Zeng C, Hines JV, Narberhaus F, Coschigano PW.
Murphy ER, et al.
Infect Immun. 2020 Feb 20;88(3):e00871-19. doi: 10.1128/IAI.00871-19. Print 2020 Feb 20.
Infect Immun. 2020.
PMID: 31792074
Free PMC article.
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