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Pant P. CHIMERA_NA: A Customizable Mutagenesis Tool for Structural Manipulations in Nucleic Acids and Their Complexes. ACS OMEGA 2024; 9:40061-40066. [PMID: 39346815 PMCID: PMC11425829 DOI: 10.1021/acsomega.4c05954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 08/29/2024] [Accepted: 09/10/2024] [Indexed: 10/01/2024]
Abstract
Studying the structure and dynamics of nucleic acids and their complexes is crucial for understanding fundamental biological processes and developing therapeutic interventions. However, the limited availability of experimentally characterized nucleic acid structures poses a challenge for exploring their properties comprehensively. To address this, we developed a customizable mutagenesis tool, CHIMERA_NA, to manipulate nucleic acid structures and their complexes. Utilizing the user-friendly CHIMERA_NA, researchers can perform mutations in nucleic acid structures, enabling the exploration of diverse structural configurations and dynamic behaviors. The tool offers the flexibility to generate all possible combinations of mutations or specific user-defined mutations based on research requirements. CHIMERA_NA leverages the capabilities of UCSF Chimera software, a widely used platform for molecular structure analysis, to facilitate the generation of mutations in nucleic acids. Our tool modifies the reference structure of nucleic acids or their complexes to generate initial coordinates of mutated structures/complexes within seconds for further computational exploration. This capability allows users to extend their investigations beyond structural repositories, enabling the study of DNA/RNA drug recognition, nucleic acid-protein interactions, and the intrinsic structural and dynamic properties of nucleic acids. By providing a user-friendly and customizable approach to nucleic acid mutagenesis, CHIMERA_NA contributes to advancing our understanding of nucleic acid biology and facilitating drug discovery efforts targeting nucleic acid-based mechanisms. CHIMERA_NA is freely available in the Supporting Information of this article.
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Affiliation(s)
- Pradeep Pant
- Department of Biotechnology, Bennett University, Uttar Pradesh 201310, India
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2
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Wang F, Li W, Li B, Xie L, Tong Y, Xu X. cRNAsp12 Web Server for the Prediction of Circular RNA Secondary Structures and Stabilities. Int J Mol Sci 2023; 24:ijms24043822. [PMID: 36835231 PMCID: PMC9959564 DOI: 10.3390/ijms24043822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/29/2023] [Accepted: 02/07/2023] [Indexed: 02/17/2023] Open
Abstract
Circular RNAs (circRNAs) are a novel class of non-coding RNA that, unlike linear RNAs, form a covalently closed loop without the 5' and 3' ends. Growing evidence shows that circular RNAs play important roles in life processes and have great potential implications in clinical and research fields. The accurate modeling of circRNAs structure and stability has far-reaching impact on our understanding of their functions and our ability to develop RNA-based therapeutics. The cRNAsp12 server offers a user-friendly web interface to predict circular RNA secondary structures and folding stabilities from the sequence. Through the helix-based landscape partitioning strategy, the server generates distinct ensembles of structures and predicts the minimal free energy structures for each ensemble with the recursive partition function calculation and backtracking algorithms. For structure predictions in the limited structural ensemble, the server also provides users with the option to set the structural constraints of forcing the base pairs and/or forcing the unpaired bases, such that only structures that meet the criteria are enumerated recursively.
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Affiliation(s)
- Fengfei Wang
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Wei Li
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Baiyi Li
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Liangxu Xie
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Yunguang Tong
- Department of Pharmacy, China Jiliang University, Hangzhou 310000, China
| | - Xiaojun Xu
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou 213001, China
- Correspondence:
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Bayard CJ, Yingling YG. Computer-Assisted Design and Characterization of RNA Nanostructures. Methods Mol Biol 2023; 2709:31-49. [PMID: 37572271 DOI: 10.1007/978-1-0716-3417-2_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/14/2023]
Abstract
Molecular dynamics (MD) simulations can aid in the design and characterization of RNA nanomaterials, providing details about structural and dynamical properties as a function of sequence and environment. Here, we describe how to perform explicit and implicit solvent all-atom MD simulations for RNA nanoring systems.
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Affiliation(s)
- Christina J Bayard
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, NC, USA
| | - Yaroslava G Yingling
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, NC, USA.
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Zhang D, Li Y, Zhong Q, Wang A, Weng J, Gong L, Li G. Ribonucleic Acid Folding Prediction Based on Iterative Multiscale Simulation. J Phys Chem Lett 2022; 13:9957-9966. [PMID: 36260782 DOI: 10.1021/acs.jpclett.2c01342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
RNA folding prediction is a challenge. Currently, many RNA folding models are coarse-grained (CG) with the potential derived from the known RNA structures. However, this potential is not suitable for modified and entirely new RNA. It is also not suitable for the folding simulation of RNA in the real cellular environment, including many kinds of molecular interactions. In contrast, our proposed model has the potential to address these issues, which is a multiscale simulation scheme based on all-atom (AA) force fields. We fit the CG force field using the trajectories generated by the AA force field and then iteratively perform molecular dynamics (MD) simulations of the two scales. The all-atom molecular dynamics (AAMD) simulation is mainly responsible for the correction of RNA structure, and the CGMD simulation is mainly responsible for efficient conformational sampling. On the basis of this scheme, we can successfully fold three RNAs belonging to a hairpin, a pseudoknot, and a four-way junction.
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Affiliation(s)
- Dinglin Zhang
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, P. R. China
- Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing100049, P. R. China
| | - Yan Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, P. R. China
| | - Qinglu Zhong
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, P. R. China
| | - Anhui Wang
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, P. R. China
| | - Junben Weng
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, P. R. China
- Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing100049, P. R. China
| | - Lidong Gong
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian116029, China
| | - Guohui Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, P. R. China
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Kolev SK, St. Petkov P, Milenov TI, Vayssilov GN. Sodium and Magnesium Ion Location at the Backbone and at the Nucleobase of RNA: Ab Initio Molecular Dynamics in Water Solution. ACS OMEGA 2022; 7:23234-23244. [PMID: 35847262 PMCID: PMC9280761 DOI: 10.1021/acsomega.2c01327] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The interactions between Na+ or Mg2+ ions with different parts of single-stranded RNA molecules, namely, the oxygen atoms from the phosphate groups or the guanine base, in water solution have been studied using first-principles molecular dynamics. Sodium ions were found to be much more mobile than Mg2+ ions and readily underwent transitions between a state directly bonded to RNA oxygen atoms and a completely solvated state. The inner solvation shell of Na+ ions fluctuated stochastically at a femtosecond timescale coordinating on average 5 oxygen atoms for bonded Na+ ions and 5.5 oxygen atoms for solvated Na+ ions. In contrast, the inner solvation shell of Mg2+ ions was stable in both RNA-bonded and completely solvated states. In both cases, Mg2+ ions coordinated 6 oxygen atoms from the inner solvation shell. Consistent with their stable solvation shells, Mg2+ ions were more effective than Na+ ions in stabilizing the RNA backbone conformation. The exclusion zones between the first and second solvation shells, solvation shell widths, and angles for binding to carbonyl oxygen of guanine for solvated Na+ or Mg2+ ions exhibited a number of quantitative differences when compared with RNA crystallographic data. The presented results support the distinct capacity of Mg2+ ions to support the RNA structure not only in the crystal phase but also in the dynamic water environment both on the side of the phosphate moiety and on the side of the nucleobase.
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Affiliation(s)
- Stefan K. Kolev
- Institute
of Electronics, Bulgarian Academy of Sciences, 72 Tzarigradsko Chaussee Blvd., Sofia 1784, Bulgaria
| | - Petko St. Petkov
- Faculty
of Chemistry and Pharmacy, University of
Sofia, Boulevard James
Bouchier 1, Sofia 1126, Bulgaria
| | - Teodor I. Milenov
- Institute
of Electronics, Bulgarian Academy of Sciences, 72 Tzarigradsko Chaussee Blvd., Sofia 1784, Bulgaria
| | - Georgi N. Vayssilov
- Faculty
of Chemistry and Pharmacy, University of
Sofia, Boulevard James
Bouchier 1, Sofia 1126, Bulgaria
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Zhang D, Chen SJ, Zhou R. Modeling Noncanonical RNA Base Pairs by a Coarse-Grained IsRNA2 Model. J Phys Chem B 2021; 125:11907-11915. [PMID: 34694128 DOI: 10.1021/acs.jpcb.1c07288] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Noncanonical base pairs contribute crucially to the three-dimensional architecture of large RNA molecules; however, how to accurately model them remains an open challenge in RNA 3D structure prediction. Here, we report a promising coarse-grained (CG) IsRNA2 model to predict noncanonical base pairs in large RNAs through molecular dynamics simulations. By introducing a five-bead per nucleotide CG representation to reserve the three interacting edges of nucleobases, IsRNA2 accurately models various base-pairing interactions, including both canonical and noncanonical base pairs. A benchmark test indicated that IsRNA2 achieves a comparable performance to the atomic model in de novo modeling of noncanonical RNA structures. In addition, IsRNA2 was able to refine the 3D structure predictions for large RNAs in RNA-puzzle challenges. Finally, the graphics processing unit acceleration was introduced to speed up the sampling efficiency in IsRNA2 for very large RNA molecules. Therefore, the CG IsRNA2 model reported here offers a reliable approach to predict the structures and dynamics of large RNAs.
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Affiliation(s)
- Dong Zhang
- College of Life Sciences and Institute of Quantitative Biology, Zhejiang University, Hangzhou 310058, China
| | - Shi-Jie Chen
- Department of Physics, Department of Biochemistry, and Institute of Data Science and Informatics, University of Missouri, Columbia, Missouri 65211, United States
| | - Ruhong Zhou
- College of Life Sciences and Institute of Quantitative Biology, Zhejiang University, Hangzhou 310058, China
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Largy E, König A, Ghosh A, Ghosh D, Benabou S, Rosu F, Gabelica V. Mass Spectrometry of Nucleic Acid Noncovalent Complexes. Chem Rev 2021; 122:7720-7839. [PMID: 34587741 DOI: 10.1021/acs.chemrev.1c00386] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.
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Affiliation(s)
- Eric Largy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Alexander König
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Anirban Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Debasmita Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Sanae Benabou
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Frédéric Rosu
- Univ. Bordeaux, CNRS, INSERM, IECB, UMS 3033, F-33600 Pessac, France
| | - Valérie Gabelica
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
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Šulc P. The Multiscale Future of RNA Modeling. Biophys J 2020; 119:1270-1272. [PMID: 32941784 PMCID: PMC7462927 DOI: 10.1016/j.bpj.2020.08.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/14/2020] [Accepted: 08/25/2020] [Indexed: 11/28/2022] Open
Affiliation(s)
- Petr Šulc
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona.
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