1
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Du C, Wang Y, Gong S. Regulation of the ThiM riboswitch is facilitated by the trapped structure formed during transcription of the wild-type sequence. FEBS Lett 2021; 595:2816-2828. [PMID: 34644399 DOI: 10.1002/1873-3468.14202] [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: 06/18/2021] [Revised: 09/17/2021] [Accepted: 09/20/2021] [Indexed: 11/09/2022]
Abstract
The ThiM riboswitch from Escherichia coli is a typical mRNA device that modulates downstream gene expression by sensing TPP. The helix-based RNA folding theory is used to investigate its detailed regulatory behaviors in cells. This RNA molecule is transcriptionally trapped in a state with the unstructured SD sequence in the absence of TPP, which induces downstream gene expression. As a key step to turn on gene expression, formation of this trapped state (the genetic ON state) highly depends on the co-transcriptional folding of its wild-type sequence. Instead of stabilities of the genetic ON and OFF states, the transcription rate, pause, and ligand levels are combined to affect the ThiM riboswitch-mediated gene regulation, which is consistent with a kinetic control model.
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Affiliation(s)
- Chengyi Du
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, China
| | - Yujie Wang
- Department of Physics and Telecommunication Engineering, Zhoukou Normal University, China
| | - Sha Gong
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, China
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2
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Ender A, Etzel M, Hammer S, Findeiß S, Stadler P, Mörl M. Ligand-dependent tRNA processing by a rationally designed RNase P riboswitch. Nucleic Acids Res 2021; 49:1784-1800. [PMID: 33469651 PMCID: PMC7897497 DOI: 10.1093/nar/gkaa1282] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 12/21/2020] [Accepted: 12/29/2020] [Indexed: 11/29/2022] Open
Abstract
We describe a synthetic riboswitch element that implements a regulatory principle which directly addresses an essential tRNA maturation step. Constructed using a rational in silico design approach, this riboswitch regulates RNase P-catalyzed tRNA 5′-processing by either sequestering or exposing the single-stranded 5′-leader region of the tRNA precursor in response to a ligand. A single base pair in the 5′-leader defines the regulatory potential of the riboswitch both in vitro and in vivo. Our data provide proof for prior postulates on the importance of the structure of the leader region for tRNA maturation. We demonstrate that computational predictions of ligand-dependent structural rearrangements can address individual maturation steps of stable non-coding RNAs, thus making them amenable as promising target for regulatory devices that can be used as functional building blocks in synthetic biology.
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Affiliation(s)
- Anna Ender
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - Maja Etzel
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - Stefan Hammer
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstr. 16-18, 04107 Leipzig, Germany
| | - Sven Findeiß
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstr. 16-18, 04107 Leipzig, Germany
| | - Peter Stadler
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstr. 16-18, 04107 Leipzig, Germany.,Max Planck Institute for Mathematics in the Science, Inselstr. 22, 04103 Leipzig, Germany.,Institute for Theoretical Chemistry, University of Vienna, Währingerstr. 17, A-1090 Vienna, Austria.,Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
| | - Mario Mörl
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
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3
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Gong S, Du C, Wang Y. Regulation of the thiamine pyrophosphate (TPP)-sensing riboswitch in NMT1 mRNA from Neurospora crassa. FEBS Lett 2019; 594:625-635. [PMID: 31664711 DOI: 10.1002/1873-3468.13654] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 10/16/2019] [Accepted: 10/22/2019] [Indexed: 01/06/2023]
Abstract
The expression of Neurospora crassa NMT1 involved in thiamine pyrophosphate (TPP) metabolism is regulated at the level of mRNA splicing by a TPP-sensing riboswitch within the precursor NMT1 mRNA. Here, using the systematic helix-based computational method, we investigated the regulation of this riboswitch. We find that the function of the riboswitch does not depend on the transcription process. Whether TPP is present or not, the riboswitch predominately folds into the ON state, while the OFF state aptamer structure does not appear during transcription. Since the transition from the ON state to the aptamer structure is extremely slow, TPP may interact with the RNA before full formation of the aptamer structure, promoting the switch flipping. The potential to fully form helix P0 of the ON state is necessary to restore ligand-dependent gene control by the riboswitch.
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Affiliation(s)
- Sha Gong
- College of Mathematics and Physics, Huanggang Normal University, China
| | - Chengyi Du
- College of Mathematics and Physics, Huanggang Normal University, China
| | - Yanli Wang
- Department of Physics, Wuhan University, China
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4
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Yin H, Gavriliuc M, Lin R, Xu S, Wang Y. Modulation and Visualization of EF-G Power Stroke During Ribosomal Translocation. Chembiochem 2019; 20:2927-2935. [PMID: 31194278 PMCID: PMC6888950 DOI: 10.1002/cbic.201900276] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Indexed: 11/30/2022]
Abstract
During ribosome translocation, the elongation factor EF‐G undergoes large conformational change while maintaining its contact with the moving tRNA. We previously measured a power stroke accompanying EF‐G catalysis, which was consistent with structural studies. However, the role of power stroke in translocation fidelity remains unclear. Here, we report quantitative measurements of the power strokes of structurally modified EF‐Gs by using two different techniques and reveal the correlation between power stroke and translocation efficiency and fidelity. We discovered that the reduced power stroke only lowered the percentage of translocation but did not introduce translocation error. The established force ‐structure–function correlation for EF‐G indicates that power stroke drives ribosomal translocation, but the mRNA reading frame is probably maintained by ribosome itself. Furthermore, the microscope detection method reported here can be simply implemented for other biochemical applications.
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Affiliation(s)
- Heng Yin
- Department of Chemistry, University of Houston, Houston, TX, 77204, USA
| | - Miriam Gavriliuc
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204, USA
| | - Ran Lin
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204, USA
| | - Shoujun Xu
- Department of Chemistry, University of Houston, Houston, TX, 77204, USA
| | - Yuhong Wang
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204, USA
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5
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Sun TT, Zhao C, Chen SJ. Predicting Cotranscriptional Folding Kinetics For Riboswitch. J Phys Chem B 2018; 122:7484-7496. [PMID: 29985608 DOI: 10.1021/acs.jpcb.8b04249] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
On the basis of a helix-based transition rate model, we developed a new method for sampling cotranscriptional RNA conformational ensemble and the prediction of cotranscriptional folding kinetics. Applications to E. coli. SRP RNA and pbuE riboswitch indicate that the model may provide reliable predictions for the cotranscriptional folding pathways and population kinetics. For E. coli. SRP RNA, the predicted population kinetics and the folding pathway are consistent with the SHAPE profiles in the recent cotranscriptional SHAPE-seq experiments. For the pbuE riboswitch, the model predicts the transcriptional termination efficiency as a function of the force. The theoretical results show (a) a force-induced transition from the aptamer (antiterminator) to the terminator structure and (b) the different folding pathways for the riboswitch with and without the ligand (adenine). More specifically, without adenine, the aptamer structure emerges as a short-lived kinetic transient state instead of a thermodynamically stable intermediate state. Furthermore, from the predicted extension-time curves, the model identifies a series of conformational switches in the pulling process, where the predicted relative residence times for the different structures are in accordance with the experimental data. The model may provide a new tool for quantitative predictions of cotranscriptional folding kinetics, and results can offer useful insights into cotranscriptional folding-related RNA functions such as regulation of gene expression with riboswitches.
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Affiliation(s)
- Ting-Ting Sun
- Department of Physics , Zhejiang University of Science and Technology , Hangzhou 310023 , P. R. China.,Department of Physics, Department of Biochemistry, and University of Missouri Informatics Institute , University of Missouri , Columbia , Missouri 65211 , United States
| | - Chenhan Zhao
- Department of Physics, Department of Biochemistry, and University of Missouri Informatics Institute , University of Missouri , Columbia , Missouri 65211 , United States
| | - Shi-Jie Chen
- Department of Physics, Department of Biochemistry, and University of Missouri Informatics Institute , University of Missouri , Columbia , Missouri 65211 , United States
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6
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Haldar S, Kührová P, Banáš P, Spiwok V, Šponer J, Hobza P, Otyepka M. Insights into Stability and Folding of GNRA and UNCG Tetraloops Revealed by Microsecond Molecular Dynamics and Well-Tempered Metadynamics. J Chem Theory Comput 2016; 11:3866-77. [PMID: 26574468 DOI: 10.1021/acs.jctc.5b00010] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
RNA hairpins capped by 5'-GNRA-3' or 5'-UNCG-3' tetraloops (TLs) are prominent RNA structural motifs. Despite their small size, a wealth of experimental data, and recent progress in theoretical simulations of their structural dynamics and folding, our understanding of the folding and unfolding processes of these small RNA elements is still limited. Theoretical description of the folding and unfolding processes requires robust sampling, which can be achieved by either an exhaustive time scale in standard molecular dynamics simulations or sophisticated enhanced sampling methods, using temperature acceleration or biasing potentials. Here, we study structural dynamics of 5'-GNRA-3' and 5'-UNCG-3' TLs by 15-μs-long standard simulations and a series of well-tempered metadynamics, attempting to accelerate sampling by bias in a few chosen collective variables (CVs). Both methods provide useful insights. The unfolding and refolding mechanisms of the GNRA TL observed by well-tempered metadynamics agree with the (reverse) folding mechanism suggested by recent replica exchange molecular dynamics simulations. The orientation of the glycosidic bond of the GL4 nucleobase is critical for the UUCG TL folding pathway, and our data strongly support the hypothesis that GL4-anti forms a kinetic trap along the folding pathway. Along with giving useful insight, our study also demonstrates that using only a few CVs apparently does not capture the full folding landscape of the RNA TLs. Despite using several sophisticated selections of the CVs, formation of the loop appears to remain a hidden variable, preventing a full convergence of the metadynamics. Finally, our data suggest that the unfolded state might be overstabilized by the force fields used.
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Affiliation(s)
- Susanta Haldar
- Institute of Organic Chemistry and Biochemistry and Gilead Science Research Center, Academy of Sciences of the Czech Republic , Flemingovo nám. 2, 166 10 Prague 6, Czech Republic.,Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague , Albertov 6, 128 43 Prague 2, Czech Republic
| | - Petra Kührová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc , tř. 17. Listopadu 12, 771 46 Olomouc, Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc , tř. 17. Listopadu 12, 771 46 Olomouc, Czech Republic
| | - Vojtěch Spiwok
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague , Technická 3, 166 28 Prague 6, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic , Královopolská 135, 612 65 Brno, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry and Gilead Science Research Center, Academy of Sciences of the Czech Republic , Flemingovo nám. 2, 166 10 Prague 6, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc , tř. 17. Listopadu 12, 771 46 Olomouc, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc , tř. 17. Listopadu 12, 771 46 Olomouc, Czech Republic
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7
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Xu X, Yu T, Chen SJ. Understanding the kinetic mechanism of RNA single base pair formation. Proc Natl Acad Sci U S A 2016; 113:116-21. [PMID: 26699466 PMCID: PMC4711849 DOI: 10.1073/pnas.1517511113] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
RNA functions are intrinsically tied to folding kinetics. The most elementary step in RNA folding is the closing and opening of a base pair. Understanding this elementary rate process is the basis for RNA folding kinetics studies. Previous studies mostly focused on the unfolding of base pairs. Here, based on a hybrid approach, we investigate the folding process at level of single base pairing/stacking. The study, which integrates molecular dynamics simulation, kinetic Monte Carlo simulation, and master equation methods, uncovers two alternative dominant pathways: Starting from the unfolded state, the nucleotide backbone first folds to the native conformation, followed by subsequent adjustment of the base conformation. During the base conformational rearrangement, the backbone either retains the native conformation or switches to nonnative conformations in order to lower the kinetic barrier for base rearrangement. The method enables quantification of kinetic partitioning among the different pathways. Moreover, the simulation reveals several intriguing ion binding/dissociation signatures for the conformational changes. Our approach may be useful for developing a base pair opening/closing rate model.
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Affiliation(s)
- Xiaojun Xu
- Department of Physics, University of Missouri, Columbia, MO 65211; Department of Biochemistry, University of Missouri, Columbia, MO 65211; Informatics Institute, University of Missouri, Columbia, MO 65211
| | - Tao Yu
- Department of Physics, University of Missouri, Columbia, MO 65211; Department of Biochemistry, University of Missouri, Columbia, MO 65211; Informatics Institute, University of Missouri, Columbia, MO 65211; Department of Physics, Jianghan University, Wuhan, Hubei 430056, China
| | - Shi-Jie Chen
- Department of Physics, University of Missouri, Columbia, MO 65211; Department of Biochemistry, University of Missouri, Columbia, MO 65211; Informatics Institute, University of Missouri, Columbia, MO 65211;
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8
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Wachsmuth M, Domin G, Lorenz R, Serfling R, Findeiß S, Stadler PF, Mörl M. Design criteria for synthetic riboswitches acting on transcription. RNA Biol 2015; 12:221-31. [PMID: 25826571 DOI: 10.1080/15476286.2015.1017235] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Riboswitches are RNA-based regulators of gene expression composed of a ligand-sensing aptamer domain followed by an overlapping expression platform. The regulation occurs at either the level of transcription (by formation of terminator or antiterminator structures) or translation (by presentation or sequestering of the ribosomal binding site). Due to a modular composition, these elements can be manipulated by combining different aptamers and expression platforms and therefore represent useful tools to regulate gene expression in synthetic biology. Using computationally designed theophylline-dependent riboswitches we show that 2 parameters, terminator hairpin stability and folding traps, have a major impact on the functionality of the designed constructs. These have to be considered very carefully during design phase. Furthermore, a combination of several copies of individual riboswitches leads to a much improved activation ratio between induced and uninduced gene activity and to a linear dose-dependent increase in reporter gene expression. Such serial arrangements of synthetic riboswitches closely resemble their natural counterparts and may form the basis for simple quantitative read out systems for the detection of specific target molecules in the cell.
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Affiliation(s)
- Manja Wachsmuth
- a University of Leipzig ; Institute for Biochemistry ; Leipzig , Germany
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9
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Melnykov AV, Nayak RK, Hall KB, Van Orden A. Effect of loop composition on the stability and folding kinetics of RNA hairpins with large loops. Biochemistry 2015; 54:1886-96. [PMID: 25697574 DOI: 10.1021/bi5014276] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
RNA hairpins are ubiquitous structural elements in biological RNAs, where they have the potential to regulate RNA folding and interactions with other molecules. There are established methods for predicting the thermodynamic stability of an RNA hairpin, but there are still relatively few detailed examinations of the kinetics of folding. Nonetheless, several recent studies indicate that hairpin folding does not proceed via a simple two-state model. Here, we monitor fluorescence from hairpins constructed as molecular beacons in ensemble, fluorescence correlation spectroscopy, and stopped-flow experiments to describe the folding of RNA hairpins with long (15 nucleotide) loops. Our results show that folding of these hairpins occurs through more than two states and that the mechanism of folding includes a fast intermediate phase observed on the tens of microseconds time scale and a slow phase, attributed to formation of the native folded hairpin loop and stem, observed on the milliseconds time scale. The composition of the RNA loop determines the time scale of intermediate and native folded states. Hairpins with a polyuracil loop sequence exhibit slower relaxation of the intermediate state and faster relaxation of the native folded state when compared to that of hairpins with cytosine or adenine in the loop. We hypothesize this composition dependence could be attributed to nucleobase stacking in cytosine and adenine containing regions of the loop, which would be absent in hairpins containing polyuracil loops. Such base stacking could destabilize the intermediate folds, thereby speeding the relaxation of the intermediate relative to similar sized hairpins with no base stacking in the loop. Likewise, the lower intermediate stability could prolong the relaxation of the native folded state.
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Affiliation(s)
- Artem V Melnykov
- †Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Rajesh K Nayak
- ‡Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Kathleen B Hall
- †Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Alan Van Orden
- ‡Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
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10
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RNA folding: structure prediction, folding kinetics and ion electrostatics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 827:143-83. [PMID: 25387965 DOI: 10.1007/978-94-017-9245-5_11] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Beyond the "traditional" functions such as gene storage, transport and protein synthesis, recent discoveries reveal that RNAs have important "new" biological functions including the RNA silence and gene regulation of riboswitch. Such functions of noncoding RNAs are strongly coupled to the RNA structures and proper structure change, which naturally leads to the RNA folding problem including structure prediction and folding kinetics. Due to the polyanionic nature of RNAs, RNA folding structure, stability and kinetics are strongly coupled to the ion condition of solution. The main focus of this chapter is to review the recent progress in the three major aspects in RNA folding problem: structure prediction, folding kinetics and ion electrostatics. This chapter will introduce both the recent experimental and theoretical progress, while emphasize the theoretical modelling on the three aspects in RNA folding.
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11
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Chakraborty D, Collepardo-Guevara R, Wales DJ. Energy Landscapes, Folding Mechanisms, and Kinetics of RNA Tetraloop Hairpins. J Am Chem Soc 2014; 136:18052-61. [DOI: 10.1021/ja5100756] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Debayan Chakraborty
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | | | - David J. Wales
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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12
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Chen J, Gong S, Wang Y, Zhang W. Kinetic partitioning mechanism of HDV ribozyme folding. J Chem Phys 2014; 140:025102. [DOI: 10.1063/1.4861037] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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13
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Nayak RK, Van Orden A. Counterion and polythymidine loop-length-dependent folding and thermodynamic stability of DNA hairpins reveal the unusual counterion-dependent stability of tetraloop hairpins. J Phys Chem B 2013; 117:13956-66. [PMID: 24144397 DOI: 10.1021/jp404832d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Stem-loop DNA hairpins containing a 5-base-pair (bp) stem and single-stranded polythymidine loop were investigated using thermodynamic melting analysis and stopped-flow kinetics. These studies revealed the thermodynamic stability and folding kinetics as a function of loop length and counterion concentration. Our results show the unusually high thermodynamic stability for tetraloop or 4 poly(dT) loop hairpin as compared with longer loop length hairpins. Furthermore, this exceptional stability is highly counterion-dependent. For example, in the higher counterion concentration regime of 50 mM NaCl and above, the tetraloop hairpin displays enhanced stability as compared with longer loop length hairpins. However, at lower counterion concentration of 25 mM NaCl and below, the thermal stability of tetraloop hairpin is consistent with the longer loop hairpins. The enhanced stability of tetraloop hairpins at higher counterion concentration can be explained on the basis of the combined entropic effect of loop closure as well as base stacking in the loop regions. The stability of longer loop length hairpins at all counterion concentrations as well as tetraloop hairpin at lower counterion concentration can be explained on the basis of entropic effect of loop closure alone. The thermodynamic parameters at lower and higher counterion concentrations were determined to quantify the enhanced stability of base-stacking effects occurring at higher counterion concentrations. For example, for 100 mM NaCl, excess Gibbs energy and enthalpy due to base stacking within the tetraloops were measured to be -1.2 ± 0.14 and -3.28 ± 0.32 kcal/mol, respectively, whereas, no excess of Gibbs energy and enthalpy was observed for 0, 5, 10, and 25 mM NaCl. These findings suggest significant base-stacking interactions occurring in the loop region of the tetraloop hairpins at higher counterion concentration and less significant base-stacking interactions in the lower counterion concentration regime. We suggest that at higher counterion concentrations, hydrophobic collapse of the nucleotides in the loop may be enhanced due to the increased polarity of the solvent, thereby enhancing base-stacking interactions that contribute to unusually high stability.
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Affiliation(s)
- Rajesh K Nayak
- Department of Chemistry, Colorado State University , Fort Collins, Colorado 80523, United States
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14
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Stancik AL, Brauns EB. Investigating the thermodynamics of UNCG tetraloops using infrared spectroscopy. J Phys Chem B 2013; 117:13556-60. [PMID: 24079463 DOI: 10.1021/jp408496z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Using infrared (IR) absorption spectroscopy, we have explored the folding thermodynamics of the UNCG class of RNA hairpin tetraloops (N = U, A, C, or G). Without the need to introduce non-native probes, IR spectroscopy makes it possible to distinguish specific structural elements such as base pairing versus base stacking or loop versus stem motions. Our results show that different structural components exhibit different thermodynamics. Specifically, we have found that tetraloop melting proceeds in a thermally sequential fashion, where base pairing in the stem is disrupted before (i.e., at a lower temperature) base stacking along the entire chain. In addition, for N = A, our data argue that the structure immediately surrounding adenine is particularly stable and melts at a higher temperature than either base-pairing or base-stacking interactions. Taken together, these results suggest that hairpin loop formation is not a simple two-state process, even in the equilibrium limit.
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Affiliation(s)
- Aaron L Stancik
- Department of Chemistry, University of Idaho , Moscow, Idaho, 83844-2343
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15
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Kührová P, Banáš P, Best RB, Šponer J, Otyepka M. Computer Folding of RNA Tetraloops? Are We There Yet? J Chem Theory Comput 2013; 9:2115-25. [DOI: 10.1021/ct301086z] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Petra Kührová
- Regional Centre of Advanced Technologies
and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies
and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska
135, 612 65 Brno, Czech Republic
| | - Robert B. Best
- Laboratory of Chemical Physics,
National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520,
United States
| | - Jiří Šponer
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska
135, 612 65 Brno, Czech Republic
- CEITEC − Central European
Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced Technologies
and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska
135, 612 65 Brno, Czech Republic
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16
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Nayak RK, Peersen OB, Hall KB, Van Orden A. Millisecond Time-Scale Folding and Unfolding of DNA Hairpins Using Rapid-Mixing Stopped-Flow Kinetics. J Am Chem Soc 2012; 134:2453-6. [DOI: 10.1021/ja208490w] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | - Kathleen B. Hall
- Department
of Biochemistry and
Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
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17
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Yin Y, Wang P, Yang XX, Li X, He C, Zhao XS. Panorama of DNA hairpin folding observed via diffusion-decelerated fluorescence correlation spectroscopy. Chem Commun (Camb) 2012; 48:7413-7415. [DOI: 10.1039/c2cc31986a] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A wide kinetic range from ∼0.1 μs to 1 s is offered by diffusion-decelerated FCS, allowing simultaneously monitoring multi-kinetic components.
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Affiliation(s)
- Yandong Yin
- Beijing National Laboratory for Molecular Sciences and Department of Chemical Biology
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing 100871
- China
| | - Peng Wang
- Beijing National Laboratory for Molecular Sciences and Department of Chemical Biology
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing 100871
- China
| | - Xin Xing Yang
- Beijing National Laboratory for Molecular Sciences and Department of Chemical Biology
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing 100871
- China
| | - Xun Li
- Beijing National Laboratory for Molecular Sciences and Department of Chemical Biology
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing 100871
- China
| | - Chuan He
- Beijing National Laboratory for Molecular Sciences and Department of Chemical Biology
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing 100871
- China
| | - Xin Sheng Zhao
- Beijing National Laboratory for Molecular Sciences and Department of Chemical Biology
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing 100871
- China
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18
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Tan ZJ, Chen SJ. Importance of diffuse metal ion binding to RNA. Met Ions Life Sci 2011; 9:101-24. [PMID: 22010269 PMCID: PMC4883094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
RNAs are highly charged polyanionic molecules. RNA structure and function are strongly correlated with the ionic condition of the solution. The primary focus of this article is on the role of diffusive ions in RNA folding. Due to the long-range nature of electrostatic interactions, the diffuse ions can contribute significantly to RNA structural stability and folding kinetics. We present an overview of the experimental findings as well as the theoretical developments on the diffuse ion effects in RNA folding. This review places heavy emphasis on the effect of magnesium ions. Magnesium ions play a highly efficient role in stabilizing RNA tertiary structures and promoting tertiary structural folding. The highly efficient role goes beyond the mean-field effect such as the ionic strength. In addition to the effects of specific ion binding and ion dehydration, ion-ion correlation for the diffuse ions can contribute to the efficient role of the multivalent ions such as the magnesium ions in RNA folding.
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Affiliation(s)
- Zhi-Jie Tan
- Department of Physics and Key Laboratory of Artificial Micro- and Nano-Structures of the Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430 072, China
| | - Shi-Jie Chen
- Department of Physics & Astronomy and Department of Biochemistry, University of Missouri, Columbia MO 65211, USA
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19
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Zuo G, Li W, Zhang J, Wang J, Wang W. Folding of a Small RNA Hairpin Based on Simulation with Replica Exchange Molecular Dynamics. J Phys Chem B 2010; 114:5835-9. [DOI: 10.1021/jp904573r] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Guanghong Zuo
- T-Life Research Center, Department of Physics, Fudan University, Shanghai 200433, China, National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University, 210093, China, and State Key Lab of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210093, China
| | - Wenfei Li
- T-Life Research Center, Department of Physics, Fudan University, Shanghai 200433, China, National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University, 210093, China, and State Key Lab of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210093, China
| | - Jian Zhang
- T-Life Research Center, Department of Physics, Fudan University, Shanghai 200433, China, National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University, 210093, China, and State Key Lab of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210093, China
| | - Jin Wang
- T-Life Research Center, Department of Physics, Fudan University, Shanghai 200433, China, National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University, 210093, China, and State Key Lab of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210093, China
| | - Wei Wang
- T-Life Research Center, Department of Physics, Fudan University, Shanghai 200433, China, National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University, 210093, China, and State Key Lab of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210093, China
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20
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Lu HM, Liang J. Perturbation-based Markovian transmission model for probing allosteric dynamics of large macromolecular assembling: a study of GroEL-GroES. PLoS Comput Biol 2009; 5:e1000526. [PMID: 19798437 PMCID: PMC2741606 DOI: 10.1371/journal.pcbi.1000526] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2009] [Accepted: 08/31/2009] [Indexed: 11/19/2022] Open
Abstract
Large macromolecular assemblies are often important for biological processes in cells. Allosteric communications between different parts of these molecular machines play critical roles in cellular signaling. Although studies of the topology and fluctuation dynamics of coarse-grained residue networks can yield important insights, they do not provide characterization of the time-dependent dynamic behavior of these macromolecular assemblies. Here we develop a novel approach called Perturbation-based Markovian Transmission (PMT) model to study globally the dynamic responses of the macromolecular assemblies. By monitoring simultaneous responses of all residues (>8,000) across many (>6) decades of time spanning from the initial perturbation until reaching equilibrium using a Krylov subspace projection method, we show that this approach can yield rich information. With criteria based on quantitative measurements of relaxation half-time, flow amplitude change, and oscillation dynamics, this approach can identify pivot residues that are important for macromolecular movement, messenger residues that are key to signal mediating, and anchor residues important for binding interactions. Based on a detailed analysis of the GroEL-GroES chaperone system, we found that our predictions have an accuracy of 71-84% judged by independent experimental studies reported in the literature. This approach is general and can be applied to other large macromolecular machineries such as the virus capsid and ribosomal complex.
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Affiliation(s)
- Hsiao-Mei Lu
- Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Jie Liang
- Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois, United States of America
- * E-mail:
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21
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Stancik AL, Brauns EB. Rearrangement of Partially Ordered Stacked Conformations Contributes to the Rugged Energy Landscape of a Small RNA Hairpin. Biochemistry 2008; 47:10834-40. [DOI: 10.1021/bi801170c] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Aaron L. Stancik
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343
| | - Eric B. Brauns
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343
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22
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Gell C, Sabir T, Westwood J, Rashid A, Smith DAM, Harris SA, Stockley PG. Single-molecule fluorescence resonance energy transfer assays reveal heterogeneous folding ensembles in a simple RNA stem-loop. J Mol Biol 2008; 384:264-78. [PMID: 18805425 DOI: 10.1016/j.jmb.2008.08.088] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2008] [Revised: 08/25/2008] [Accepted: 08/27/2008] [Indexed: 11/30/2022]
Abstract
We have examined the folding ensembles present in solution for a series of RNA oligonucleotides that encompass the replicase translational operator stem-loop of the RNA bacteriophage MS2. Single-molecule (SM) fluorescence assays suggest that these RNAs exist in solution as ensembles of differentially base-paired/base-stacked states at equilibrium. There are two distinct ensembles for the wild-type sequence, implying the existence of a significant free energy barrier between "folded" and "unfolded" ensembles. Experiments with sequence variants are consistent with an unfolding mechanism in which interruptions to base-paired duplexes, in this example by the single-stranded loop and a single-base bulge in the base-paired stem, as well as the free ends, act as nucleation points for unfolding. The switch between folded and unfolded ensembles is consistent with a transition that occurs when all base-pairing and/or base-stacking interactions that would orientate the legs of the RNA stem are broken. Strikingly, a U-to-C replacement of a residue in the loop, which creates a high-affinity form of the operator for coat protein binding, results in dramatically different (un)folding behaviour, revealing distinct subpopulations that are either stabilised or destabilised with respect to the wild-type sequence. This result suggests additional reasons for selection against the C-variant stem-loop in vivo and provides an explanation for the increased affinity.
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Affiliation(s)
- Christopher Gell
- School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK; Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS29JT, UK
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23
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Abstract
RNA folding is a remarkably complex problem that involves ion-mediated electrostatic interaction, conformational entropy, base pairing and stacking, and noncanonical interactions. During the past decade, results from a variety of experimental and theoretical studies pointed to (a) the potential ion correlation effect in Mg2+-RNA interactions, (b) the rugged energy landscapes and multistate RNA folding kinetics even for small RNA systems such as hairpins and pseudoknots, (c) the intraloop interactions and sequence-dependent loop free energy, and (d) the strong nonadditivity of chain entropy in RNA pseudoknot and other tertiary folds. Several related issues, which have not been thoroughly resolved, require combined approaches with thermodynamic and kinetic experiments, statistical mechanical modeling, and all-atom computer simulations.
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Affiliation(s)
- Shi-Jie Chen
- Department of Physics and Astronomy and Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, USA.
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24
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Lu HM, Liang J. Perturbation-based Markovian Transmission Model for macromolecular machinery in cell. ACTA ACUST UNITED AC 2008; 2007:5029-34. [PMID: 18003136 DOI: 10.1109/iembs.2007.4353470] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The study of the dynamics of a complex system is an important problem that includes large macromolecular complexes, molecular interaction networks, and cell functional modules. Large macromolecular complexes in cellular machinery can be modeled as a connected network, as in the elastic or Gaussian network models as demonstrated by Bahar and colleagues. Here we propose the Perturbation-based Markovian Transmission Model for studying the dynamics of signal transmission in macromolecular machinery. The initial perturbation is transmitted by a Markovian processes, and the dynamics of the probability flow is analytically solved using the master equation. Due to the large size of macromolecular complexes, it is very difficult to obtain analytical time-dependent Markovian dynamics of all atoms from the first perturbation until stationary state. To overcome it, we decrease the level of complexity of the transition matrix using a Krylov subspace method. This method is equivalent to integrating all eigen modes, and we show it can provide a globally accurate solution to the dynamics problem of signal transmission for very large macromolecular complexes with reasonable computational time. We give results of the dynamics of the GroEL-GroES chaperone system by applying uniform perturbation to all residues. We are able to identify experimentally found important residues and provide a set of predicted pivot, messenger, and effector residues, each with distinct dynamic behavior. Further results of selective perturbation on the surface of ATP binding pocket identifies the path of maximal probability flow of signal.
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Affiliation(s)
- Hsiao-Mei Lu
- Department of Bioengineering, SEO, MC-063 University of Illinois at Chicago 851 S. Morgan Street, Room 218 Chicago, IL 60607-7052, U.S.A
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25
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Abstract
Single-stranded junctions/loops are frequently occurring structural motifs in nucleic acid structures. Due to the polyanionic nature of the nucleic acid backbone, metal ions play a crucial role in the loop stability. Here we use the tightly bound ion theory, which can account for the possible ion correlation and ensemble (fluctuation) effects, to predict the ion-dependence of loop and stem-loop (hairpin) free energies. The predicted loop free energy is a function of the loop length, the loop end-to-end distance, and the ion (Na(+) and Mg(2+) in this study) concentrations. Based on the statistical mechanical calculations, we derive a set of empirical formulas for the loop thermodynamic parameters as functions of Na(+) and Mg(2+) concentrations. For three specific types of loops, namely, hairpin, bulge, and internal loops, the predicted free energies agree with the experimental data. Further applications of these empirical formulas to RNA and DNA hairpin stability lead to good agreements with the available experimental data. Our results indicate that the ion-dependent loop stability makes significant contribution to the overall ion-dependence of the hairpin stability.
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26
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Orden AV, Jung J. Review fluorescence correlation spectroscopy for probing the kinetics and mechanisms of DNA hairpin formation. Biopolymers 2008; 89:1-16. [PMID: 17696144 DOI: 10.1002/bip.20826] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
This article reviews the application of fluorescence correlation spectroscopy (FCS) and related techniques to the study of nucleic acid hairpin conformational fluctuations in free aqueous solutions. Complimentary results obtained using laser-induced temperature jump spectroscopy, single-molecule fluorescence spectroscopy, optical trapping, and biophysical theory are also discussed. The studies cited reveal that DNA and RNA hairpin folding occurs by way of a complicated reaction mechanism involving long- and short-lived reaction intermediates. Reactions occurring on the subnanoseconds to seconds time scale have been observed, pointing out the need for experimental techniques capable of probing a broad range of reaction times in the study of such complex, multistate reactions.
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Affiliation(s)
- Alan Van Orden
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA.
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27
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Kuznetsov SV, Ren CC, Woodson SA, Ansari A. Loop dependence of the stability and dynamics of nucleic acid hairpins. Nucleic Acids Res 2007; 36:1098-112. [PMID: 18096625 PMCID: PMC2275088 DOI: 10.1093/nar/gkm1083] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Hairpin loops are critical to the formation of nucleic acid secondary structure, and to their function. Previous studies revealed a steep dependence of single-stranded DNA (ssDNA) hairpin stability with length of the loop (L) as approximately L(8.5 +/- 0.5), in 100 mM NaCl, which was attributed to intraloop stacking interactions. In this article, the loop-size dependence of RNA hairpin stabilities and their folding/unfolding kinetics were monitored with laser temperature-jump spectroscopy. Our results suggest that similar mechanisms stabilize small ssDNA and RNA loops, and show that salt contributes significantly to the dependence of hairpin stability on loop size. In 2.5 mM MgCl2, the stabilities of both ssDNA and RNA hairpins scale as approximately L(4 +/- 0.5), indicating that the intraloop interactions are weaker in the presence of Mg2+. Interestingly, the folding times for ssDNA hairpins (in 100 mM NaCl) and RNA hairpins (in 2.5 mM MgCl2) are similar despite differences in the salt conditions and the stem sequence, and increase similarly with loop size, approximately L(2.2 +/- 0.5) and approximately L(2.6 +/- 0.5), respectively. These results suggest that hairpins with small loops may be specifically stabilized by interactions of the Na+ ions with the loops. The results also reinforce the idea that folding times are dominated by an entropic search for the correct nucleating conformation.
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Affiliation(s)
- Serguei V Kuznetsov
- Department of Physics (M/C 273), University of Illinois at Chicago, 845 W. Taylor St., Chicago, IL 60607, USA
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28
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Kim HJ, Kwon M, Yu J. Elucidation of the RNA target of linezolid by using a linezolid-neomycin B heteroconjugate and genomic SELEX. Bioorg Med Chem 2007; 15:7688-95. [PMID: 17869523 DOI: 10.1016/j.bmc.2007.08.053] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2007] [Revised: 08/25/2007] [Accepted: 08/28/2007] [Indexed: 01/03/2023]
Abstract
A covalently modified heteroconjugate between linezolid and neomycin B leads to an enhanced and more specific binding affinity to hairpin RNA targets in comparison to neomycin B itself. This heteroconjugate was used as a lure to select linezolid-specific hairpin RNA from an Escherichia coli genome RNA. The selected RNA obtained after eight cycles not only has typical stem-loop structures but also includes known sequences of the linezolid binding site. The results of RNA footprinting show that the binding site of the heteroconjugate encompasses both stem and loop regions, suggesting that the possible binding site for linezolid is in the terminal loop. In addition, findings from application of a surface plasmon resonance assay clearly demonstrate that linezolid binds to selected hairpin RNA in a highly specific manner with a low millimolar affinity. The results suggest that heteroconjugates might represent a generally useful approach in studies aimed at uncovering loop-specific RNA binding ligands that would be otherwise difficult to identify owing to their weak affinities.
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Affiliation(s)
- Hyun Jin Kim
- Department of Chemistry and Education, Seoul National University, Seoul 151-742, Republic of Korea
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29
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Abstract
A recently developed tightly bound ion model can account for the correlation and fluctuation (i.e., different binding modes) of bound ions. However, the model cannot treat mixed ion solutions, which are physiologically relevant and biologically significant, and the model was based on B-DNA helices and thus cannot directly treat RNA helices. In the present study, we investigate the effects of ion correlation and fluctuation on the thermodynamic stability of finite length RNA helices immersed in a mixed solution of monovalent and divalent ions. Experimental comparisons demonstrate that the model gives improved predictions over the Poisson-Boltzmann theory, which has been found to underestimate the roles of multivalent ions such as Mg2+ in stabilizing DNA and RNA helices. The tightly bound ion model makes quantitative predictions on how the Na+-Mg2+ competition determines helix stability and its helix length-dependence. In addition, the model gives empirical formulas for the thermodynamic parameters as functions of Na+/Mg2+ concentrations and helix length. Such formulas can be quite useful for practical applications.
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Affiliation(s)
- Zhi-Jie Tan
- Department of Physics and Astronomy and Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, USA
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