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For: Denesyuk NA, Thirumalai D. Entropic stabilization of the folded states of RNA due to macromolecular crowding. Biophys Rev 2013;5:225-232. [PMID: 28510164 DOI: 10.1007/s12551-013-0119-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2013] [Accepted: 03/25/2013] [Indexed: 11/25/2022]  Open
Number Cited by Other Article(s)
1
Lai WJC, Zhu M, Belinite M, Ballard G, Mathews DH, Ermolenko DN. Intrinsically Unstructured Sequences in the mRNA 3' UTR Reduce the Ability of Poly(A) Tail to Enhance Translation. J Mol Biol 2022;434:167877. [PMID: 36368412 PMCID: PMC9750134 DOI: 10.1016/j.jmb.2022.167877] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 09/27/2022] [Accepted: 11/01/2022] [Indexed: 11/09/2022]
2
Denton AR, Davis WJ. Influence of solvent quality on depletion potentials in colloid-polymer mixtures. J Chem Phys 2021;155:084904. [PMID: 34470346 DOI: 10.1063/5.0061370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
3
Shape changes and cooperativity in the folding of the central domain of the 16S ribosomal RNA. Proc Natl Acad Sci U S A 2021;118:2020837118. [PMID: 33658370 DOI: 10.1073/pnas.2020837118] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
4
Sung HL, Sengupta A, Nesbitt D. Smaller molecules crowd better: Crowder size dependence revealed by single-molecule FRET studies and depletion force modeling analysis. J Chem Phys 2021;154:155101. [PMID: 33887926 DOI: 10.1063/5.0045492] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]  Open
5
Zeugolis DI. Bioinspired in vitro microenvironments to control cell fate: focus on macromolecular crowding. Am J Physiol Cell Physiol 2021;320:C842-C849. [PMID: 33656930 DOI: 10.1152/ajpcell.00380.2020] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
6
Hong F, Schreck JS, Šulc P. Understanding DNA interactions in crowded environments with a coarse-grained model. Nucleic Acids Res 2020;48:10726-10738. [PMID: 33045749 PMCID: PMC7641764 DOI: 10.1093/nar/gkaa854] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 08/29/2020] [Accepted: 10/01/2020] [Indexed: 01/01/2023]  Open
7
Leopold HJ, Leighton R, Schwarz J, Boersma AJ, Sheets ED, Heikal AA. Crowding Effects on Energy-Transfer Efficiencies of Hetero-FRET Probes As Measured Using Time-Resolved Fluorescence Anisotropy. J Phys Chem B 2019;123:379-393. [PMID: 30571116 DOI: 10.1021/acs.jpcb.8b09829] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
8
mRNAs and lncRNAs intrinsically form secondary structures with short end-to-end distances. Nat Commun 2018;9:4328. [PMID: 30337527 PMCID: PMC6193969 DOI: 10.1038/s41467-018-06792-z] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 09/20/2018] [Indexed: 12/17/2022]  Open
9
Davis WJ, Denton AR. Influence of solvent quality on conformations of crowded polymers. J Chem Phys 2018;149:124901. [PMID: 30278673 DOI: 10.1063/1.5043434] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]  Open
10
Hancock R. Crowding, Entropic Forces, and Confinement: Crucial Factors for Structures and Functions in the Cell Nucleus. BIOCHEMISTRY (MOSCOW) 2018;83:326-337. [PMID: 29626920 DOI: 10.1134/s0006297918040041] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
11
Shew CY, Oda S, Yoshikawa K. Localization switching of a large object in a crowded cavity: A rigid/soft object prefers surface/inner positioning. J Chem Phys 2018;147:204901. [PMID: 29195278 DOI: 10.1063/1.5000762] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]  Open
12
Trovato F, Fumagalli G. Molecular simulations of cellular processes. Biophys Rev 2017;9:941-958. [PMID: 29185136 DOI: 10.1007/s12551-017-0363-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 11/19/2017] [Indexed: 12/12/2022]  Open
13
Palit S, He L, Hamilton WA, Yethiraj A, Yethiraj A. Combining Diffusion NMR and Small-Angle Neutron Scattering Enables Precise Measurements of Polymer Chain Compression in a Crowded Environment. PHYSICAL REVIEW LETTERS 2017;118:097801. [PMID: 28306301 DOI: 10.1103/physrevlett.118.097801] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Indexed: 06/06/2023]
14
Lim WK, Denton AR. Influence of polymer shape on depletion potentials and crowding in colloid-polymer mixtures. SOFT MATTER 2016;12:2247-2252. [PMID: 26689367 DOI: 10.1039/c5sm02863a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
15
Lim WK, Denton AR. Depletion-induced forces and crowding in polymer-nanoparticle mixtures: Role of polymer shape fluctuations and penetrability. J Chem Phys 2016;144:024904. [DOI: 10.1063/1.4939766] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]  Open
16
The structural stability and catalytic activity of DNA and RNA oligonucleotides in the presence of organic solvents. Biophys Rev 2016;8:11-23. [PMID: 28510143 DOI: 10.1007/s12551-015-0188-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/03/2015] [Indexed: 01/02/2023]  Open
17
Shew CY, Yoshikawa K. A toy model for nucleus-sized crowding confinement. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015;27:064118. [PMID: 25563689 DOI: 10.1088/0953-8984/27/6/064118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
18
Lim WK, Denton AR. Polymer crowding and shape distributions in polymer-nanoparticle mixtures. J Chem Phys 2014;141:114909. [DOI: 10.1063/1.4895612] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
19
Hyeon C, Denesyuk NA, Thirumalai D. Development and Applications of Coarse-Grained Models for RNA. Isr J Chem 2014. [DOI: 10.1002/ijch.201400029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
20
Crowding in Polymer–Nanoparticle Mixtures. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2014;307:27-71. [DOI: 10.1016/b978-0-12-800046-5.00003-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
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