1
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Tosti Guerra F, Poppleton E, Šulc P, Rovigatti L. ANNaMo: Coarse-grained modeling for folding and assembly of RNA and DNA systems. J Chem Phys 2024; 160:205102. [PMID: 38814009 DOI: 10.1063/5.0202829] [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: 02/07/2024] [Accepted: 05/04/2024] [Indexed: 05/31/2024] Open
Abstract
The folding of RNA and DNA strands plays crucial roles in biological systems and bionanotechnology. However, studying these processes with high-resolution numerical models is beyond current computational capabilities due to the timescales and system sizes involved. In this article, we present a new coarse-grained model for investigating the folding dynamics of nucleic acids. Our model represents three nucleotides with a patchy particle and is parameterized using well-established nearest-neighbor models. Thanks to the reduction of degrees of freedom and to a bond-swapping mechanism, our model allows for simulations at timescales and length scales that are currently inaccessible to more detailed models. To validate the performance of our model, we conducted extensive simulations of various systems: We examined the thermodynamics of DNA hairpins, capturing their stability and structural transitions, the folding of an MMTV pseudoknot, which is a complex RNA structure involved in viral replication, and also explored the folding of an RNA tile containing a k-type pseudoknot. Finally, we evaluated the performance of the new model in reproducing the melting temperatures of oligomers and the dependence on the toehold length of the displacement rate in toehold-mediated displacement processes, a key reaction used in molecular computing. All in all, the successful reproduction of experimental data and favorable comparisons with existing coarse-grained models validate the effectiveness of the new model.
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Affiliation(s)
- F Tosti Guerra
- Department of Physics, Sapienza University of Rome, Roma, Italy
| | - E Poppleton
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, USA
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - P Šulc
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, USA
- Department of Bioscience, School of Natural Sciences, Technical University Munich, Munich, Germany
| | - L Rovigatti
- Department of Physics, Sapienza University of Rome, Roma, Italy
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2
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Shulgina Y, Trinidad MI, Langeberg CJ, Nisonoff H, Chithrananda S, Skopintsev P, Nissley AJ, Patel J, Boger RS, Shi H, Yoon PH, Doherty EE, Pande T, Iyer AM, Doudna JA, Cate JHD. RNA language models predict mutations that improve RNA function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.05.588317. [PMID: 38617247 PMCID: PMC11014562 DOI: 10.1101/2024.04.05.588317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Structured RNA lies at the heart of many central biological processes, from gene expression to catalysis. While advances in deep learning enable the prediction of accurate protein structural models, RNA structure prediction is not possible at present due to a lack of abundant high-quality reference data. Furthermore, available sequence data are generally not associated with organismal phenotypes that could inform RNA function. We created GARNET (Gtdb Acquired RNa with Environmental Temperatures), a new database for RNA structural and functional analysis anchored to the Genome Taxonomy Database (GTDB). GARNET links RNA sequences derived from GTDB genomes to experimental and predicted optimal growth temperatures of GTDB reference organisms. This enables construction of deep and diverse RNA sequence alignments to be used for machine learning. Using GARNET, we define the minimal requirements for a sequence- and structure-aware RNA generative model. We also develop a GPT-like language model for RNA in which triplet tokenization provides optimal encoding. Leveraging hyperthermophilic RNAs in GARNET and these RNA generative models, we identified mutations in ribosomal RNA that confer increased thermostability to the Escherichia coli ribosome. The GTDB-derived data and deep learning models presented here provide a foundation for understanding the connections between RNA sequence, structure, and function.
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Affiliation(s)
- Yekaterina Shulgina
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
| | - Marena I Trinidad
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Conner J Langeberg
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
| | - Hunter Nisonoff
- Center for Computational Biology, University of California, Berkeley, CA, United States
| | - Seyone Chithrananda
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, USA
| | - Petr Skopintsev
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
| | - Amos J Nissley
- Department of Chemistry, University of California, Berkeley, CA, USA
| | - Jaymin Patel
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Ron S Boger
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Biophysics Graduate Program, University of California, Berkeley, CA, USA
| | - Honglue Shi
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Peter H Yoon
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
| | - Erin E Doherty
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
| | - Tara Pande
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, USA
| | - Aditya M Iyer
- Department of Physics, University of California, Berkeley, CA, USA
| | - Jennifer A Doudna
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jamie H D Cate
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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3
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de Oliveira Martins E, Weber G. Nearest-neighbour parametrization of DNA single, double and triple mismatches at low sodium concentration. Biophys Chem 2024; 306:107156. [PMID: 38157701 DOI: 10.1016/j.bpc.2023.107156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/27/2023] [Accepted: 12/17/2023] [Indexed: 01/03/2024]
Abstract
DNA mismatches, that is, base pairs different from the canonical AT and CG, are involved in numerous biological processes and can be a problem for technological applications such as PCR amplification. The nearest-neighbour (NN) model is the standard approach for predicting melting temperatures and is used in methods of secondary structure predictions and modelling of hybridization kinetics. However, despite its biological and technological importance, existing NN parameters that include DNA mismatches are incomplete, and those available were obtained from a limited set of melting temperature at high sodium concentration. To our knowledge, there is currently no NN set of parameters for up to three mismatches covering all configurations at low sodium concentrations. Here, we are applying the NN model to a large set of 4096 published melting temperatures, covering all combinations of single, double and triple mismatches. Dealing with such a large set of temperature is challenging in several ways, bringing new methodological problems. Here, optimizing a large number of 252 independent parameters has required the development of a new method where we readjust the seed parameters using the definition of the Gibbs free energy. The new parameters predict the training set within 1.1 °C and the validation set to 2.7 °C.
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Affiliation(s)
- Erik de Oliveira Martins
- Departamento de Física, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, MG, Brazil; Escola Politécnica, Centro Universitário Católica do Leste de Minas Gerais, 35170-056 Coronel Fabriciano, MG, Brazil
| | - Gerald Weber
- Departamento de Física, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, MG, Brazil.
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4
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Schroeder SJ. Insights into nucleic acid helix formation from infrared spectroscopy. Biophys J 2024; 123:115-117. [PMID: 38130057 PMCID: PMC10808036 DOI: 10.1016/j.bpj.2023.12.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/09/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023] Open
Affiliation(s)
- Susan J Schroeder
- Department of Chemistry and Biochemistry, School of Biological Sciences, University of Oklahoma, Norman, Oklahoma.
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5
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Arteaga S, Dolenz BJ, Znosko BM. Competitive Influence of Alkali Metals in the Ion Atmosphere on Nucleic Acid Duplex Stability. ACS OMEGA 2024; 9:1287-1297. [PMID: 38222622 PMCID: PMC10785066 DOI: 10.1021/acsomega.3c07563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/04/2023] [Accepted: 12/11/2023] [Indexed: 01/16/2024]
Abstract
The nonspecific atmosphere around nucleic acids, often termed the ion atmosphere, encompasses a collection of weak ion-nucleic acid interactions. Although nonspecific, the ion atmosphere has been shown to influence nucleic acid folding and structural stability. Studies investigating the composition of the ion atmosphere have shown competitive occupancy of the atmosphere between metal ions in the same solution. Many studies have investigated single ion effects on nucleic acid secondary structure stability; however, no comprehensive studies have investigated how the competitive occupancy of mixed ions in the ion atmosphere influences nucleic acid secondary structure stability. Here, six oligonucleotides were optically melted in buffers containing molar quantities, or mixtures, of either XCl (X = Li, K, Rb, or Cs) or NaCl. A correction factor was developed to better predict RNA duplex stability in solutions containing mixed XCl/NaCl. For solutions containing a 1:1 mixture of XCl/NaCl, one alkali metal chloride contributed more to duplex stability than the other. Overall, there was a 54% improvement in predictive capabilities with the correction factor compared with the standard 1.0 M NaCl nearest-neighbor models. This correction factor can be used in models to better predict RNA secondary structure in solutions containing mixed XCl/NaCl.
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Affiliation(s)
- Sebastian
J. Arteaga
- Department of Chemistry, Saint Louis University, Saint
Louis, Missouri 63103, United States
| | - Bruce J. Dolenz
- Department of Chemistry, Saint Louis University, Saint
Louis, Missouri 63103, United States
| | - Brent M. Znosko
- Department of Chemistry, Saint Louis University, Saint
Louis, Missouri 63103, United States
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6
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Dutta N, Sarzynska J, Deb I, Lahiri A. Predicting nearest neighbor free energies of modified RNA with LIE: results for pseudouridine and N1-methylpseudouridine within RNA duplexes. Phys Chem Chem Phys 2024; 26:992-999. [PMID: 38088148 DOI: 10.1039/d3cp02442c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
Pseudouridine (Ψ) and N1-methylpseudouridine (m1Ψ) are among the key modifications in the field of mRNA therapeutics and vaccine research. The accuracy of the design and development of therapeutic RNAs containing such modifications depends on the accuracy of the secondary structure prediction, which in turn depends on the nearest neighbor (NN) thermodynamic parameters for the standard and modified residues. Here, we propose a simple approach based on molecular dynamics simulations and linear interaction energy (LIE) approximation that is able to predict the NN free energy parameters for U-A, Ψ-A and m1Ψ-A pairs in reasonable agreement with the recent experimental reports. We report the NN thermodynamic parameters for different U, Ψ and m1Ψ base pairs, which might be helpful for a deeper understanding of the effect of these modifications in RNA. The predicted NN free energy parameters in this study are able to closely reproduce the folding free energies of duplexes containing internal Ψ for which the thermodynamic data were available. Additionally, we report the predicted folding free energies for the duplexes containing internal m1Ψ.
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Affiliation(s)
- Nivedita Dutta
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata 700009, West Bengal, India.
| | - Joanna Sarzynska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznan 61-704, Poland
| | - Indrajit Deb
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata 700009, West Bengal, India.
| | - Ansuman Lahiri
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata 700009, West Bengal, India.
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Metkar M, Pepin CS, Moore MJ. Tailor made: the art of therapeutic mRNA design. Nat Rev Drug Discov 2024; 23:67-83. [PMID: 38030688 DOI: 10.1038/s41573-023-00827-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2023] [Indexed: 12/01/2023]
Abstract
mRNA medicine is a new and rapidly developing field in which the delivery of genetic information in the form of mRNA is used to direct therapeutic protein production in humans. This approach, which allows for the quick and efficient identification and optimization of drug candidates for both large populations and individual patients, has the potential to revolutionize the way we prevent and treat disease. A key feature of mRNA medicines is their high degree of designability, although the design choices involved are complex. Maximizing the production of therapeutic proteins from mRNA medicines requires a thorough understanding of how nucleotide sequence, nucleotide modification and RNA structure interplay to affect translational efficiency and mRNA stability. In this Review, we describe the principles that underlie the physical stability and biological activity of mRNA and emphasize their relevance to the myriad considerations that factor into therapeutic mRNA design.
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8
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Wang F, Xia R, Su Y, Cai P, Xu X. Quantifying RNA structures and interactions with a unified reduced chain representation model. Int J Biol Macromol 2023; 253:127181. [PMID: 37793523 DOI: 10.1016/j.ijbiomac.2023.127181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/30/2023] [Accepted: 09/25/2023] [Indexed: 10/06/2023]
Abstract
RNA is a pivotal molecule that plays critical roles in various cellular processes. Quantifying RNA structures and interactions is essential to understanding RNA function and developing RNA-based therapeutics. Using a unified five-bead model and a non-redundant database, this paper investigates the structural features and interactions of five commonly occurring RNA motifs, i.e., double-stranded helices, hairpin loops, internal/bulge loops, multi-branched junctions, and single-stranded terminal tails. Analyzing detailed distributions of RNA local structural features and base-base interactions reveals a preference for helical structures in both local backbone structures and base orientations. The interactions between adjacent bases exhibit motif-specific and sequence-dependent characteristics, reflecting the distinct topological constraints imposed by different loop-helix connection modes and the varying pairing and stacking interactions among different sequences. These findings shed light on the stability of RNA helices, emphasizing their significance in providing dominant base pairing and stacking interactions for RNA structures and stability. The four non-helix motifs encompass unpaired nucleotide loops and exhibit diverse base-base interactions, contributing to the structural diversity observed in RNA. Overall, the complexity of RNA structure arises from the intricate interplay of base-base interactions.
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Affiliation(s)
- Fengfei Wang
- Institute of Bioinformatics and Medical Engineering, School of Mathematics and Physics, Jiangsu University of Technology, Changzhou 213001, China
| | - Renjie Xia
- Institute of Bioinformatics and Medical Engineering, School of Mathematics and Physics, Jiangsu University of Technology, Changzhou 213001, China
| | - Yangyang Su
- Institute of Bioinformatics and Medical Engineering, School of Mathematics and Physics, Jiangsu University of Technology, Changzhou 213001, China
| | - Pinggen Cai
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China.
| | - Xiaojun Xu
- Institute of Bioinformatics and Medical Engineering, School of Mathematics and Physics, Jiangsu University of Technology, Changzhou 213001, China.
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9
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Kanarskaya MA, Pyshnyi DV, Lomzov AA. Diversity of Self-Assembled RNA Complexes: From Nanoarchitecture to Nanomachines. Molecules 2023; 29:10. [PMID: 38202593 PMCID: PMC10779776 DOI: 10.3390/molecules29010010] [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] [Received: 11/10/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 01/12/2024] Open
Abstract
New tool development for various nucleic acid applications is an essential task in RNA nanotechnology. Here, we determined the ability of self-limited complex formation by a pair of oligoribonucleotides carrying two pairwise complementary blocks connected by a linker of different lengths in each chain. The complexes were analyzed using UV melting, gel shift assay analysis, and molecular dynamics (MD) simulations. We have demonstrated the spontaneous formation of various self-limited and concatemer complexes. The linear concatemer complex is formed by a pair of oligomers without a linker in at least one of them. Longer linkers resulted in the formation of circular complexes. The self-limited complexes formation was confirmed using the toehold strand displacement. The MD simulations indicate the reliability of the complexes' structure and demonstrate their dynamics, which increase with the rise of complex size. The linearization of 2D circular complexes into 1D structures and a reverse cyclization process were demonstrated using a toehold-mediated approach. The approach proposed here for the construction and directed modification of the molecularity and shape of complexes will be a valuable tool in RNA nanotechnology, especially for the rational design of therapeutic nucleic acids with high target specificity and the programmable response of the immune system of organisms.
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Affiliation(s)
| | | | - Alexander A. Lomzov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia; (M.A.K.); (D.V.P.)
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10
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Escobar CA, Petersen RJ, Tonelli M, Fan L, Henzler-Wildman KA, Butcher SE. Solution Structure of Poly(UG) RNA. J Mol Biol 2023; 435:168340. [PMID: 37924862 PMCID: PMC10841838 DOI: 10.1016/j.jmb.2023.168340] [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] [Received: 09/14/2023] [Revised: 10/27/2023] [Accepted: 10/29/2023] [Indexed: 11/06/2023]
Abstract
Poly(UG) or "pUG" RNAs are UG or GU dinucleotide repeat sequences which are highly abundant in eukaryotes. Post-transcriptional addition of pUGs to RNA 3' ends marks mRNAs as vectors for gene silencing in C. elegans. We previously determined the crystal structure of pUG RNA bound to the ligand N-methyl mesoporphyrin IX (NMM), but the structure of free pUG RNA is unknown. Here we report the solution structure of the free pUG RNA (GU)12, as determined by nuclear magnetic resonance spectroscopy and small and wide-angle x-ray scattering (NMR-SAXS-WAXS). The low complexity sequence and 4-fold symmetry of the structure result in overlapped NMR signals that complicate chemical shift assignment. We therefore utilized single site-specific deoxyribose modifications which did not perturb the structure and introduced well-resolved methylene signals that are easily identified in NMR spectra. The solution structure ensemble has a root mean squared deviation (RMSD) of 0.62 Å and is a compact, left-handed quadruplex with a Z-form backbone, or "pUG fold." Overall, the structure agrees with the crystal structure of (GU)12 bound to NMM, indicating the pUG fold is unaltered by docking of the NMM ligand. The solution structure reveals conformational details that could not be resolved by x-ray crystallography, which explain how the pUG fold can form within longer RNAs.
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Affiliation(s)
- Cristian A Escobar
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Riley J Petersen
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Marco Tonelli
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA; National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, USA
| | - Lixin Fan
- Basic Science Program, Frederick National Laboratory for Cancer Research, SAXS Core Facility of National Cancer Institute, Frederick, MD, USA
| | - Katherine A Henzler-Wildman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA; National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, USA
| | - Samuel E Butcher
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA; National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, USA.
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11
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Sieg JP, Jolley EA, Huot MJ, Babitzke P, Bevilacqua P. In vivo-like nearest neighbor parameters improve prediction of fractional RNA base-pairing in cells. Nucleic Acids Res 2023; 51:11298-11317. [PMID: 37855684 PMCID: PMC10639048 DOI: 10.1093/nar/gkad807] [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: 06/08/2023] [Revised: 09/11/2023] [Accepted: 09/27/2023] [Indexed: 10/20/2023] Open
Abstract
We conducted a thermodynamic analysis of RNA stability in Eco80 artificial cytoplasm, which mimics in vivo conditions, and compared it to transcriptome-wide probing of mRNA. Eco80 contains 80% of Escherichia coli metabolites, with biological concentrations of metal ions, including 2 mM free Mg2+ and 29 mM metabolite-chelated Mg2+. Fluorescence-detected binding isotherms (FDBI) were used to conduct a thermodynamic analysis of 24 RNA helices and found that these helices, which have an average stability of -12.3 kcal/mol, are less stable by ΔΔGo37 ∼1 kcal/mol. The FDBI data was used to determine a set of Watson-Crick free energy nearest neighbor parameters (NNPs), which revealed that Eco80 reduces the stability of three NNPs. This information was used to adjust the NN model using the RNAstructure package. The in vivo-like adjustments have minimal effects on the prediction of RNA secondary structures determined in vitro and in silico, but markedly improve prediction of fractional RNA base pairing in E. coli, as benchmarked with our in vivo DMS and EDC RNA chemical probing data. In summary, our thermodynamic and chemical probing analyses of RNA helices indicate that RNA secondary structures are less stable in cells than in artificially stable in vitro buffer conditions.
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Affiliation(s)
- Jacob P Sieg
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Elizabeth A Jolley
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Melanie J Huot
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Paul Babitzke
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Philip C Bevilacqua
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
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12
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Szabat M, Prochota M, Kierzek R, Kierzek E, Mathews DH. A Test and Refinement of Folding Free Energy Nearest Neighbor Parameters for RNA Including N 6-Methyladenosine. J Mol Biol 2022; 434:167632. [PMID: 35588868 DOI: 10.1016/j.jmb.2022.167632] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/29/2022] [Accepted: 05/07/2022] [Indexed: 12/26/2022]
Abstract
RNA folding free energy change parameters are widely used to predict RNA secondary structure and to design RNA sequences. These parameters include terms for the folding free energies of helices and loops. Although the full set of parameters has only been traditionally available for the four common bases and backbone, it is well known that covalent modifications of nucleotides are widespread in natural RNAs. Covalent modifications are also widely used in engineered sequences. We recently derived a full set of nearest neighbor terms for RNA that includes N6-methyladenosine (m6A). In this work, we test the model using 98 optical melting experiments, matching duplexes with or without N6-methylation of A. Most experiments place RRACH, the consensus site of N6-methylation, in a variety of contexts, including helices, bulge loops, internal loops, dangling ends, and terminal mismatches. For matched sets of experiments that include either A or m6A in the same context, we find that the parameters for m6A are as accurate as those for A. Across all experiments, the root mean squared deviation between estimated and experimental free energy changes is 0.67 kcal/mol. We used the new experimental data to refine the set of nearest neighbor parameter terms for m6A. These parameters enable prediction of RNA secondary structures including m6A, which can be used to model how N6-methylation of A affects RNA structure.
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Affiliation(s)
- Marta Szabat
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Martina Prochota
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Elzbieta Kierzek
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - David H Mathews
- Department of Biochemistry & Biophysics and Center for RNA Biology, 601 Elmwood Avenue, Box 712, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, United States.
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