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For: Pollack L. SAXS studies of ion-nucleic acid interactions. Annu Rev Biophys 2011;40:225-42. [PMID: 21332357 DOI: 10.1146/annurev-biophys-042910-155349] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Number Cited by Other Article(s)
1
Rolband LA, Chopra K, Danai L, Beasock D, van Dam HJJ, Krueger JK, Byrnes J, Afonin KA. Small-Angle X-ray Scattering (SAXS) Combined with SAXS-Driven Molecular Dynamics for Structural Analysis of Multistranded RNA Assemblies. ACS APPLIED MATERIALS & INTERFACES 2024;16:67178-67191. [PMID: 39593218 PMCID: PMC11637918 DOI: 10.1021/acsami.4c12397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2024]
2
Kolesnikov ES, Xiong Y, Onufriev AV. Implicit Solvent with Explicit Ions Generalized Born Model in Molecular Dynamics: Application to DNA. J Chem Theory Comput 2024;20:8724-8739. [PMID: 39283928 PMCID: PMC11465471 DOI: 10.1021/acs.jctc.4c00833] [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] [Received: 06/27/2024] [Revised: 08/27/2024] [Accepted: 08/28/2024] [Indexed: 09/21/2024]
3
Bertini L, Libera V, Catalini S, Schirò G, Orecchini A, Campanella R, Arciuolo V, Pagano B, Petrillo C, De Michele C, Comez L, Paciaroni A. Hindered intermolecular stacking of anti-parallel telomeric G-quadruplexes. J Chem Phys 2024;161:105101. [PMID: 39248241 DOI: 10.1063/5.0225371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Accepted: 08/21/2024] [Indexed: 09/10/2024]  Open
4
Chakraborty G, Balinin K, Villar-Guerra RD, Emondts M, Portale G, Loznik M, Niels Klement WJ, Zheng L, Weil T, Chaires JB, Herrmann A. Supramolecular DNA-based catalysis in organic solvents. iScience 2024;27:109689. [PMID: 38706840 PMCID: PMC11067378 DOI: 10.1016/j.isci.2024.109689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 10/04/2023] [Accepted: 04/05/2024] [Indexed: 05/07/2024]  Open
5
Kodikara S, Gyawali P, Gleeson JT, Jákli A, Sprunt S, Balci H. Impact of Divalent Cations on In-Layer Positional Order of DNA-Based Liquid Crystals: Implications for DNA Condensation. Biomacromolecules 2024;25:1009-1017. [PMID: 38166360 PMCID: PMC10866144 DOI: 10.1021/acs.biomac.3c01086] [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] [Received: 10/10/2023] [Revised: 12/12/2023] [Accepted: 12/12/2023] [Indexed: 01/04/2024]
6
Paul H, Bera MK, Macke N, Rowan SJ, Tirrell MV. Quantitative Determination of Metal Ion Adsorption on Cellulose Nanocrystals Surfaces. ACS NANO 2024;18:1921-1930. [PMID: 38195086 PMCID: PMC10811751 DOI: 10.1021/acsnano.3c06140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/11/2024]
7
Alston JJ, Soranno A. Condensation Goes Viral: A Polymer Physics Perspective. J Mol Biol 2023;435:167988. [PMID: 36709795 PMCID: PMC10368797 DOI: 10.1016/j.jmb.2023.167988] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 01/18/2023] [Accepted: 01/21/2023] [Indexed: 01/27/2023]
8
Kührová P, Mlýnský V, Otyepka M, Šponer J, Banáš P. Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes. J Chem Inf Model 2023;63:2133-2146. [PMID: 36989143 PMCID: PMC10091408 DOI: 10.1021/acs.jcim.2c01438] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Indexed: 03/30/2023]
9
Nepal P, Al Bashit A, Yang L, Makowski L. Small-angle X-ray microdiffraction from fibrils embedded in tissue thin sections. J Appl Crystallogr 2022;55:1562-1571. [PMID: 36570653 PMCID: PMC9721334 DOI: 10.1107/s1600576722009955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 10/11/2022] [Indexed: 11/22/2022]  Open
10
San Emeterio J, Pabit SA, Pollack L. Contrast variation SAXS: Sample preparation protocols, experimental procedures, and data analysis. Methods Enzymol 2022;677:41-83. [PMID: 36410957 PMCID: PMC10015503 DOI: 10.1016/bs.mie.2022.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
11
Predicting solution scattering patterns with explicit-solvent molecular simulations. Methods Enzymol 2022;677:433-456. [DOI: 10.1016/bs.mie.2022.08.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
12
Sanbonmatsu K. Getting to the bottom of lncRNA mechanism: structure-function relationships. Mamm Genome 2021;33:343-353. [PMID: 34642784 PMCID: PMC8509902 DOI: 10.1007/s00335-021-09924-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/28/2021] [Indexed: 12/14/2022]
13
Yu B, Iwahara J. Experimental approaches for investigating ion atmospheres around nucleic acids and proteins. Comput Struct Biotechnol J 2021;19:2279-2285. [PMID: 33995919 PMCID: PMC8102144 DOI: 10.1016/j.csbj.2021.04.033] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/14/2021] [Accepted: 04/14/2021] [Indexed: 01/26/2023]  Open
14
Lin C, Qiang X, Dong HL, Huo J, Tan ZJ. Multivalent Ion-Mediated Attraction between Like-Charged Colloidal Particles: Nonmonotonic Dependence on the Particle Charge. ACS OMEGA 2021;6:9876-9886. [PMID: 33869968 PMCID: PMC8047654 DOI: 10.1021/acsomega.1c00613] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/26/2021] [Indexed: 06/12/2023]
15
Templeton C, Elber R. Simple and Analytical Model of RNA Collapse. J Phys Chem B 2020;124:5149-5155. [PMID: 32459501 DOI: 10.1021/acs.jpcb.0c03584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
16
Meng W, Timsina R, Bull A, Andresen K, Qiu X. Additive Modulation of DNA-DNA Interactions by Interstitial Ions. Biophys J 2020;118:3019-3025. [PMID: 32470322 DOI: 10.1016/j.bpj.2020.05.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 04/04/2020] [Accepted: 04/28/2020] [Indexed: 11/26/2022]  Open
17
Zhang R, Niu G, Lu Q, Huang X, Chau JHC, Kwok RTK, Yu X, Li MH, Lam JWY, Tang BZ. Cancer cell discrimination and dynamic viability monitoring through wash-free bioimaging using AIEgens. Chem Sci 2020;11:7676-7684. [PMID: 34094146 PMCID: PMC8159538 DOI: 10.1039/d0sc01213k] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 04/29/2020] [Indexed: 11/21/2022]  Open
18
Thermodynamic stability condition can judge whether a nanoparticle dispersion can be considered a solution in a single phase. J Colloid Interface Sci 2020;575:472-479. [PMID: 32402826 DOI: 10.1016/j.jcis.2020.04.101] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 04/12/2020] [Accepted: 04/23/2020] [Indexed: 11/20/2022]
19
Zhao J, Cramer SM, McGown LB. Mechanism of sequence-based separation of single-stranded DNA in capillary zone electrophoresis. Electrophoresis 2020;41:705-713. [PMID: 32031267 DOI: 10.1002/elps.201900418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 12/28/2019] [Accepted: 01/30/2020] [Indexed: 11/09/2022]
20
Welty R, Rau M, Pabit S, Dunstan MS, Conn GL, Pollack L, Hall KB. Ribosomal Protein L11 Selectively Stabilizes a Tertiary Structure of the GTPase Center rRNA Domain. J Mol Biol 2019;432:991-1007. [PMID: 31874150 DOI: 10.1016/j.jmb.2019.12.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 12/03/2019] [Accepted: 12/04/2019] [Indexed: 01/14/2023]
21
Plumridge A, Andresen K, Pollack L. Visualizing Disordered Single-Stranded RNA: Connecting Sequence, Structure, and Electrostatics. J Am Chem Soc 2019;142:109-119. [PMID: 31804813 DOI: 10.1021/jacs.9b04461] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
22
Chakraborty G, Balinin K, Portale G, Loznik M, Polushkin E, Weil T, Herrmann A. Electrostatically PEGylated DNA enables salt-free hybridization in water. Chem Sci 2019;10:10097-10105. [PMID: 32055364 PMCID: PMC6991176 DOI: 10.1039/c9sc02598g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 09/11/2019] [Indexed: 12/18/2022]  Open
23
Pal A, Levy Y. Structure, stability and specificity of the binding of ssDNA and ssRNA with proteins. PLoS Comput Biol 2019;15:e1006768. [PMID: 30933978 PMCID: PMC6467422 DOI: 10.1371/journal.pcbi.1006768] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 04/16/2019] [Accepted: 01/01/2019] [Indexed: 02/06/2023]  Open
24
Giambasu GM, Case DA, York DM. Predicting Site-Binding Modes of Ions and Water to Nucleic Acids Using Molecular Solvation Theory. J Am Chem Soc 2019;141:2435-2445. [PMID: 30632365 PMCID: PMC6574206 DOI: 10.1021/jacs.8b11474] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
25
Erlenbach N, Grünewald C, Krstic B, Heckel A, Prisner TF. "End-to-end" stacking of small dsRNA. RNA (NEW YORK, N.Y.) 2019;25:239-246. [PMID: 30404925 PMCID: PMC6348986 DOI: 10.1261/rna.068130.118] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 11/06/2018] [Indexed: 05/08/2023]
26
Roh JH, Kilburn D, Behrouzi R, Sung W, Briber RM, Woodson SA. Effects of Preferential Counterion Interactions on the Specificity of RNA Folding. J Phys Chem Lett 2018;9:5726-5732. [PMID: 30211556 PMCID: PMC6351067 DOI: 10.1021/acs.jpclett.8b02086] [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: 06/08/2023]
27
Plumridge A, Katz AM, Calvey GD, Elber R, Kirmizialtin S, Pollack L. Revealing the distinct folding phases of an RNA three-helix junction. Nucleic Acids Res 2018;46:7354-7365. [PMID: 29762712 PMCID: PMC6101490 DOI: 10.1093/nar/gky363] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/17/2018] [Accepted: 04/24/2018] [Indexed: 01/08/2023]  Open
28
Cordeiro M, Otrelo-Cardoso AR, Svergun DI, Konarev PV, Lima JC, Santos-Silva T, Baptista PV. Optical and Structural Characterization of a Chronic Myeloid Leukemia DNA Biosensor. ACS Chem Biol 2018;13:1235-1242. [PMID: 29562136 DOI: 10.1021/acschembio.8b00029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
29
Ivanović MT, Bruetzel LK, Shevchuk R, Lipfert J, Hub JS. Quantifying the influence of the ion cloud on SAXS profiles of charged proteins. Phys Chem Chem Phys 2018;20:26351-26361. [DOI: 10.1039/c8cp03080d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
30
Lee EY, Takahashi T, Curk T, Dobnikar J, Gallo RL, Wong GCL. Crystallinity of Double-Stranded RNA-Antimicrobial Peptide Complexes Modulates Toll-Like Receptor 3-Mediated Inflammation. ACS NANO 2017;11:12145-12155. [PMID: 29016111 PMCID: PMC5936640 DOI: 10.1021/acsnano.7b05234] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
31
Jacobson DR, Saleh OA. Counting the ions surrounding nucleic acids. Nucleic Acids Res 2017;45:1596-1605. [PMID: 28034959 PMCID: PMC5389524 DOI: 10.1093/nar/gkw1305] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 12/21/2016] [Indexed: 01/29/2023]  Open
32
Meisburger SP, Thomas WC, Watkins MB, Ando N. X-ray Scattering Studies of Protein Structural Dynamics. Chem Rev 2017;117:7615-7672. [PMID: 28558231 PMCID: PMC5562295 DOI: 10.1021/acs.chemrev.6b00790] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
33
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] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
34
Plumridge A, Meisburger SP, Pollack L. Visualizing single-stranded nucleic acids in solution. Nucleic Acids Res 2017;45:e66. [PMID: 28034955 PMCID: PMC5435967 DOI: 10.1093/nar/gkw1297] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 12/09/2016] [Accepted: 12/13/2016] [Indexed: 02/06/2023]  Open
35
Nguyen HT, Pabit SA, Pollack L, Case DA. Extracting water and ion distributions from solution x-ray scattering experiments. J Chem Phys 2017;144:214105. [PMID: 27276943 DOI: 10.1063/1.4953037] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]  Open
36
Bruetzel LK, Gerling T, Sedlak SM, Walker PU, Zheng W, Dietz H, Lipfert J. Conformational Changes and Flexibility of DNA Devices Observed by Small-Angle X-ray Scattering. NANO LETTERS 2016;16:4871-4879. [PMID: 27356232 DOI: 10.1021/acs.nanolett.6b01338] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
37
Nucleic acid polymeric properties and electrostatics: Directly comparing theory and simulation with experiment. Adv Colloid Interface Sci 2016;232:49-56. [PMID: 26482088 DOI: 10.1016/j.cis.2015.09.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 09/18/2015] [Accepted: 09/29/2015] [Indexed: 11/24/2022]
38
Tokuda JM, Pabit SA, Pollack L. Protein-DNA and ion-DNA interactions revealed through contrast variation SAXS. Biophys Rev 2016;8:139-149. [PMID: 27551324 PMCID: PMC4991782 DOI: 10.1007/s12551-016-0196-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 03/10/2016] [Indexed: 12/29/2022]  Open
39
Kim HS, Martel A, Girard E, Moulin M, Härtlein M, Madern D, Blackledge M, Franzetti B, Gabel F. SAXS/SANS on Supercharged Proteins Reveals Residue-Specific Modifications of the Hydration Shell. Biophys J 2016;110:2185-94. [PMID: 27224484 PMCID: PMC4880798 DOI: 10.1016/j.bpj.2016.04.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/09/2016] [Accepted: 04/08/2016] [Indexed: 11/26/2022]  Open
40
Chen Y, Pollack L. SAXS studies of RNA: structures, dynamics, and interactions with partners. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016;7:512-26. [PMID: 27071649 DOI: 10.1002/wrna.1349] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 02/11/2016] [Accepted: 03/01/2016] [Indexed: 12/29/2022]
41
Meisburger SP, Pabit SA, Pollack L. Determining the Locations of Ions and Water around DNA from X-Ray Scattering Measurements. Biophys J 2016;108:2886-95. [PMID: 26083928 DOI: 10.1016/j.bpj.2015.05.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 04/30/2015] [Accepted: 05/11/2015] [Indexed: 10/23/2022]  Open
42
Wu YY, Bao L, Zhang X, Tan ZJ. Flexibility of short DNA helices with finite-length effect: From base pairs to tens of base pairs. J Chem Phys 2016;142:125103. [PMID: 25833610 DOI: 10.1063/1.4915539] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]  Open
43
Nguyen HT, Pabit SA, Meisburger SP, Pollack L, Case DA. Accurate small and wide angle x-ray scattering profiles from atomic models of proteins and nucleic acids. J Chem Phys 2015;141:22D508. [PMID: 25494779 DOI: 10.1063/1.4896220] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]  Open
44
Small-angle X-ray scattering: a bridge between RNA secondary structures and three-dimensional topological structures. Curr Opin Struct Biol 2015;30:147-160. [PMID: 25765781 DOI: 10.1016/j.sbi.2015.02.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 02/17/2015] [Accepted: 02/18/2015] [Indexed: 11/20/2022]
45
Gruner SM, Lattman EE. Biostructural Science Inspired by Next-Generation X-Ray Sources. Annu Rev Biophys 2015;44:33-51. [PMID: 25747590 DOI: 10.1146/annurev-biophys-060414-033813] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Pasi M, Maddocks JH, Lavery R. Analyzing ion distributions around DNA: sequence-dependence of potassium ion distributions from microsecond molecular dynamics. Nucleic Acids Res 2015;43:2412-23. [PMID: 25662221 PMCID: PMC4344516 DOI: 10.1093/nar/gkv080] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]  Open
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Panteva MT, Dissanayake T, Chen H, Radak BK, Kuechler ER, Giambaşu GM, Lee TS, York DM. Multiscale methods for computational RNA enzymology. Methods Enzymol 2015;553:335-74. [PMID: 25726472 PMCID: PMC4739856 DOI: 10.1016/bs.mie.2014.10.064] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Gabel F. Small-Angle Neutron Scattering for Structural Biology of Protein–RNA Complexes. Methods Enzymol 2015;558:391-415. [DOI: 10.1016/bs.mie.2015.02.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Ovanesyan Z, Medasani B, Fenley MO, Guerrero-García GI, de la Cruz MO, Marucho M. Excluded volume and ion-ion correlation effects on the ionic atmosphere around B-DNA: theory, simulations, and experiments. J Chem Phys 2014;141:225103. [PMID: 25494770 PMCID: PMC4265039 DOI: 10.1063/1.4902407] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 11/12/2014] [Indexed: 12/19/2022]  Open
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Structural studies of a double-stranded RNA from trypanosome RNA editing by small-angle X-ray scattering. Methods Mol Biol 2014;1240:165-89. [PMID: 25352145 DOI: 10.1007/978-1-4939-1896-6_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
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