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For: Allred BE, Gebala M, Herschlag D. Determination of Ion Atmosphere Effects on the Nucleic Acid Electrostatic Potential and Ligand Association Using AH+·C Wobble Formation in Double-Stranded DNA. J Am Chem Soc 2017;139:7540-7548. [PMID: 28489947 PMCID: PMC5466006 DOI: 10.1021/jacs.7b01830] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Number Cited by Other Article(s)
1
Chhetri KB. A review on salt-induced DNA compaction and charge inversion. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2024;195:15-22. [PMID: 39577799 DOI: 10.1016/j.pbiomolbio.2024.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 10/19/2024] [Accepted: 11/12/2024] [Indexed: 11/24/2024]
2
Templeton C, Hamilton I, Russell R, Elber R. Impact of Ion-Mixing Entropy on Orientational Preferences of DNA Helices: FRET Measurements and Computer Simulations. J Phys Chem B 2023;127:8796-8808. [PMID: 37815452 PMCID: PMC11341850 DOI: 10.1021/acs.jpcb.3c04354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
3
Gupta P, Khadake RM, Panja S, Shinde K, Rode AB. Alternative RNA Conformations: Companion or Combatant. Genes (Basel) 2022;13:1930. [PMID: 36360167 PMCID: PMC9689429 DOI: 10.3390/genes13111930] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/19/2022] [Accepted: 10/19/2022] [Indexed: 09/06/2024]  Open
4
Wen T, Yang K, Greenberg MM. Local Alteration of Ionic Strength in a Nucleosome Core Particle and Its Effect on N7-Methyl-2'-deoxyguanosine Depurination. Biochemistry 2022;61:2221-2228. [PMID: 36136907 PMCID: PMC9670023 DOI: 10.1021/acs.biochem.2c00342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
5
Zhou K, Mei Z, Lei Y, Guan Z, Mao C, Li Y. Boosted Productivity in Single-Tile-Based DNA Polyhedra Assembly by Simple Cation Replacement. Chembiochem 2022;23:e202200138. [PMID: 35676202 DOI: 10.1002/cbic.202200138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 06/08/2022] [Indexed: 11/11/2022]
6
Hamilton I, Gebala M, Herschlag D, Russell R. Direct Measurement of Interhelical DNA Repulsion and Attraction by Quantitative Cross-Linking. J Am Chem Soc 2022;144:1718-1728. [PMID: 35073489 PMCID: PMC8815069 DOI: 10.1021/jacs.1c11122] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Indexed: 12/30/2022]
7
Jambrec D, Gebala M. DNA Electrostatics: From Theory to Application. ChemElectroChem 2022. [DOI: 10.1002/celc.202101415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
8
Gong YP, Yang J, Fang JW, Li Q, Yu ZY, Guan A, Gong HY. A DNA small molecular probe with increasing K+ concentration promoted selectivity. RSC Adv 2021;11:15030-15035. [PMID: 35424063 PMCID: PMC8697834 DOI: 10.1039/d0ra06274j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 03/28/2021] [Indexed: 11/21/2022]  Open
9
Subramanian S, Golla H, Divakar K, Kannan A, de Sancho D, Naganathan AN. Slow Folding of a Helical Protein: Large Barriers, Strong Internal Friction, or a Shallow, Bumpy Landscape? J Phys Chem B 2020;124:8973-8983. [PMID: 32955882 PMCID: PMC7659034 DOI: 10.1021/acs.jpcb.0c05976] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
10
Gopi S, Naganathan AN. Non-specific DNA-driven quinary interactions promote structural transitions in proteins. Phys Chem Chem Phys 2020;22:12671-12677. [PMID: 32458879 DOI: 10.1039/d0cp01758b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
11
Ganser LR, Kelly ML, Herschlag D, Al-Hashimi HM. The roles of structural dynamics in the cellular functions of RNAs. Nat Rev Mol Cell Biol 2020;20:474-489. [PMID: 31182864 DOI: 10.1038/s41580-019-0136-0] [Citation(s) in RCA: 295] [Impact Index Per Article: 73.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
12
Lu C, Quan G, Su M, Nimmagadda A, Chen W, Pan M, Teng P, Yu F, Liu X, Jiang L, Du W, Hu W, Yao F, Pan X, Wu C, Liu D, Cai J. Molecular Architecture and Charging Effects Enhance the In Vitro and In Vivo Performance of Multi‐Arm Antimicrobial Agents Based on Star‐Shaped Poly( l ‐lysine). ADVANCED THERAPEUTICS 2019;2:1900147. [DOI: 10.1002/adtp.201900147] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Indexed: 02/05/2023]
13
Quantitative Studies of an RNA Duplex Electrostatics by Ion Counting. Biophys J 2019;117:1116-1124. [PMID: 31466697 DOI: 10.1016/j.bpj.2019.08.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 08/01/2019] [Accepted: 08/05/2019] [Indexed: 01/22/2023]  Open
14
Munshi S, Gopi S, Asampille G, Subramanian S, Campos LA, Atreya HS, Naganathan AN. Tunable order-disorder continuum in protein-DNA interactions. Nucleic Acids Res 2019;46:8700-8709. [PMID: 30107436 PMCID: PMC6158747 DOI: 10.1093/nar/gky732] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 07/31/2018] [Indexed: 11/23/2022]  Open
15
Gebala M, Johnson SL, Narlikar GJ, Herschlag D. Ion counting demonstrates a high electrostatic field generated by the nucleosome. eLife 2019;8:e44993. [PMID: 31184587 PMCID: PMC6584128 DOI: 10.7554/elife.44993] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 06/08/2019] [Indexed: 01/04/2023]  Open
16
Ong AAL, Toh DFK, Patil KM, Meng Z, Yuan Z, Krishna MS, Devi G, Haruehanroengra P, Lu Y, Xia K, Okamura K, Sheng J, Chen G. General Recognition of U-G, U-A, and C-G Pairs by Double-Stranded RNA-Binding PNAs Incorporated with an Artificial Nucleobase. Biochemistry 2019;58:1319-1331. [PMID: 30775913 DOI: 10.1021/acs.biochem.8b01313] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
17
Yildirim A, Brenner N, Sutherland R, Feig M. Role of protein interactions in stabilizing canonical DNA features in simulations of DNA in crowded environments. BMC BIOPHYSICS 2018;11:8. [PMID: 30555686 PMCID: PMC6286541 DOI: 10.1186/s13628-018-0048-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 11/21/2018] [Indexed: 11/28/2022]
18
Dao EH, Poitevin F, Sierra RG, Gati C, Rao Y, Ciftci HI, Akşit F, McGurk A, Obrinski T, Mgbam P, Hayes B, De Lichtenberg C, Pardo-Avila F, Corsepius N, Zhang L, Seaberg MH, Hunter MS, Liang M, Koglin JE, Wakatsuki S, Demirci H. Structure of the 30S ribosomal decoding complex at ambient temperature. RNA (NEW YORK, N.Y.) 2018;24:1667-1676. [PMID: 30139800 PMCID: PMC6239188 DOI: 10.1261/rna.067660.118] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 08/14/2018] [Indexed: 05/29/2023]
19
Yang L, Zhong Z, Tong C, Jia H, Liu Y, Chen G. Single-Molecule Mechanical Folding and Unfolding of RNA Hairpins: Effects of Single A-U to A·C Pair Substitutions and Single Proton Binding and Implications for mRNA Structure-Induced -1 Ribosomal Frameshifting. J Am Chem Soc 2018;140:8172-8184. [PMID: 29884019 DOI: 10.1021/jacs.8b02970] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
20
Chen Z, Xia H, Shen H, Xu X, Arbab AAI, Li M, Zhang H, Mao Y, Yang Z. Pathological Features of Staphylococcus aureus Induced Mastitis in Dairy Cows and Isobaric-Tags-for-Relative-and-Absolute-Quantitation Proteomic Analyses. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018;66:3880-3890. [PMID: 29595974 DOI: 10.1021/acs.jafc.7b05461] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
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