1
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Iwakawa HO. The clade-specific target recognition mechanisms of plant RISCs. Nucleic Acids Res 2024; 52:6662-6673. [PMID: 38621714 PMCID: PMC11194062 DOI: 10.1093/nar/gkae257] [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: 01/03/2024] [Revised: 03/04/2024] [Accepted: 04/01/2024] [Indexed: 04/17/2024] Open
Abstract
Eukaryotic Argonaut proteins (AGOs) assemble RNA-induced silencing complexes (RISCs) with guide RNAs that allow binding to complementary RNA sequences and subsequent silencing of target genes. The model plant Arabidopsis thaliana encodes 10 different AGOs, categorized into three distinct clades based on amino acid sequence similarity. While clade 1 and 2 RISCs are known for their roles in post-transcriptional gene silencing, and clade 3 RISCs are associated with transcriptional gene silencing in the nucleus, the specific mechanisms of how RISCs from each clade recognize their targets remain unclear. In this study, I conducted quantitative binding analyses between RISCs and target nucleic acids with mismatches at various positions, unveiling distinct target binding characteristics unique to each clade. Clade 1 and 2 RISCs require base pairing not only in the seed region but also in the 3' supplementary region for stable target RNA binding, with clade 1 exhibiting a higher stringency. Conversely, clade 3 RISCs tolerate dinucleotide mismatches beyond the seed region. Strikingly, they bind to DNA targets with an affinity equal to or surpassing that of RNA, like prokaryotic AGO complexes. These insights challenge existing views on plant RNA silencing and open avenues for exploring new functions of eukaryotic AGOs.
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Affiliation(s)
- Hiro-oki Iwakawa
- Department of Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo 171-8501, Japan
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2
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Ratajczyk EJ, Šulc P, Turberfield AJ, Doye JPK, Louis AA. Coarse-grained modeling of DNA-RNA hybrids. J Chem Phys 2024; 160:115101. [PMID: 38497475 DOI: 10.1063/5.0199558] [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: 11/17/2023] [Accepted: 01/26/2024] [Indexed: 03/19/2024] Open
Abstract
We introduce oxNA, a new model for the simulation of DNA-RNA hybrids that is based on two previously developed coarse-grained models-oxDNA and oxRNA. The model naturally reproduces the physical properties of hybrid duplexes, including their structure, persistence length, and force-extension characteristics. By parameterizing the DNA-RNA hydrogen bonding interaction, we fit the model's thermodynamic properties to experimental data using both average-sequence and sequence-dependent parameters. To demonstrate the model's applicability, we provide three examples of its use-calculating the free energy profiles of hybrid strand displacement reactions, studying the resolution of a short R-loop, and simulating RNA-scaffolded wireframe origami.
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Affiliation(s)
- Eryk J Ratajczyk
- Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
- Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Petr Šulc
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, Arizona 85281, USA
- School of Natural Sciences, Department of Bioscience, Technical University Munich, 85748 Garching, Germany
| | - Andrew J Turberfield
- Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
- Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, United Kingdom
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3
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Dohnalová H, Matoušková E, Lankaš F. Temperature-dependent elasticity of DNA, RNA, and hybrid double helices. Biophys J 2024; 123:572-583. [PMID: 38340722 PMCID: PMC10938081 DOI: 10.1016/j.bpj.2024.01.032] [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: 10/08/2023] [Revised: 12/19/2023] [Accepted: 01/26/2024] [Indexed: 02/12/2024] Open
Abstract
Nucleic acid double helices in their DNA, RNA, and DNA-RNA hybrid form play a fundamental role in biology and are main building blocks of artificial nanostructures, but how their properties depend on temperature remains poorly understood. Here, we report thermal dependence of dynamic bending persistence length, twist rigidity, stretch modulus, and twist-stretch coupling for DNA, RNA, and hybrid duplexes between 7°C and 47°C. The results are based on all-atom molecular dynamics simulations using different force field parameterizations. We first demonstrate that unrestrained molecular dynamics can reproduce experimentally known mechanical properties of the duplexes at room temperature. Beyond experimentally known features, we also infer the twist rigidity and twist-stretch coupling of the hybrid duplex. As for the temperature dependence, we found that increasing temperature softens all the duplexes with respect to bending, twisting, and stretching. The relative decrease of the stretch moduli is 0.003-0.004/°C, similar for all the duplex variants despite their very different stretching stiffness, whereas RNA twist stiffness decreases by 0.003/°C, and smaller values are found for the other elastic moduli. The twist-stretch couplings are nearly unaffected by temperature. The stretching, bending, and twisting stiffness all include an important entropic component. Relation of our results to the two-state model of DNA flexibility is discussed. Our work provides temperature-dependent elasticity of nucleic acid duplexes at the microsecond scale relevant for initial stages of protein binding.
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Affiliation(s)
- Hana Dohnalová
- Department of Informatics and Chemistry, University of Chemistry and Technology Prague, Praha 6, Czech Republic
| | - Eva Matoušková
- Department of Informatics and Chemistry, University of Chemistry and Technology Prague, Praha 6, Czech Republic
| | - Filip Lankaš
- Department of Informatics and Chemistry, University of Chemistry and Technology Prague, Praha 6, Czech Republic.
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4
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Park SJ, Callaghan KL, Ellis AV. Role of helicity in the nonenzymatic template-directed primer extension of DNA. Org Biomol Chem 2023; 21:6702-6706. [PMID: 37555399 DOI: 10.1039/d3ob01179h] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
Complexing a DNA primer with an RNA template showed improved nonenzymatic template-directed primer extension, attributed to a shift in the DNA helicity from a B-type towards an A-type helix. A 2-fold (deoxyadenosine) and 4.5-fold (deoxycytidine) increase in conversion from initial DNA primer to a primer + 1 nucleotide product was observed.
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Affiliation(s)
- Sung Joon Park
- School of Chemical and Biomedical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Kimberley Laura Callaghan
- School of Chemical and Biomedical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Amanda Vera Ellis
- School of Chemical and Biomedical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia.
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5
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Genna V, Iglesias-Fernández J, Reyes-Fraile L, Villegas N, Guckian K, Seth P, Wan B, Cabrero C, Terrazas M, Brun-Heath I, González C, Sciabola S, Villalobos A, Orozco M. Controlled sulfur-based engineering confers mouldability to phosphorothioate antisense oligonucleotides. Nucleic Acids Res 2023; 51:4713-4725. [PMID: 37099382 PMCID: PMC10250214 DOI: 10.1093/nar/gkad309] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 04/04/2023] [Accepted: 04/24/2023] [Indexed: 04/27/2023] Open
Abstract
Phosphorothioates (PS) have proven their effectiveness in the area of therapeutic oligonucleotides with applications spanning from cancer treatment to neurodegenerative disorders. Initially, PS substitution was introduced for the antisense oligonucleotides (PS ASOs) because it confers an increased nuclease resistance meanwhile ameliorates cellular uptake and in-vivo bioavailability. Thus, PS oligonucleotides have been elevated to a fundamental asset in the realm of gene silencing therapeutic methodologies. But, despite their wide use, little is known on the possibly different structural changes PS-substitutions may provoke in DNA·RNA hybrids. Additionally, scarce information and significant controversy exists on the role of phosphorothioate chirality in modulating PS properties. Here, through comprehensive computational investigations and experimental measurements, we shed light on the impact of PS chirality in DNA-based antisense oligonucleotides; how the different phosphorothioate diastereomers impact DNA topology, stability and flexibility to ultimately disclose pro-Sp S and pro-Rp S roles at the catalytic core of DNA Exonuclease and Human Ribonuclease H; two major obstacles in ASOs-based therapies. Altogether, our results provide full-atom and mechanistic insights on the structural aberrations PS-substitutions provoke and explain the origin of nuclease resistance PS-linkages confer to DNA·RNA hybrids; crucial information to improve current ASOs-based therapies.
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Affiliation(s)
- Vito Genna
- Mechanisms of Diseases, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain
- NBD | Nostrum Biodiscovery, Baldiri Reixac 10, Barcelona 08028, Spain
| | | | - Laura Reyes-Fraile
- Mechanisms of Diseases, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain
| | - Nuria Villegas
- Mechanisms of Diseases, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain
| | | | - Punit Seth
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Brad Wan
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Cristina Cabrero
- Instituto de Química Física Rocasolano, C/ Serrano 119, Madrid 28006, Spain
| | - Montserrat Terrazas
- Mechanisms of Diseases, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain
- Department of Inorganic and Organic Chemistry, Section of Organic Chemistry, IBUB, University of Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
| | - Isabelle Brun-Heath
- Mechanisms of Diseases, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain
| | - Carlos González
- Instituto de Química Física Rocasolano, C/ Serrano 119, Madrid 28006, Spain
| | | | | | - Modesto Orozco
- Mechanisms of Diseases, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain
- Department of Biochemistry and Biomedicine, University of Barcelona, Barcelona 08028, Spain
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6
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Sharma R, Patelli AS, Bruin LD, Maddocks JH. cgNA+web : A visual interface to the cgNA+ sequence-dependent statistical mechanics model of double-stranded nucleic acids. J Mol Biol 2023. [DOI: 10.1016/j.jmb.2023.167978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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7
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Pan X, Huang LF. Multi-omics to characterize the functional relationships of R-loops with epigenetic modifications, RNAPII transcription and gene expression. Brief Bioinform 2022; 23:6618633. [DOI: 10.1093/bib/bbac238] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 05/19/2022] [Accepted: 05/21/2022] [Indexed: 12/12/2022] Open
Abstract
Abstract
Abnormal accumulation of R-loops results in replication stress, genome instability, chromatin alterations and gene silencing. Little research has been done to characterize functional relationships among R-loops, histone marks, RNA polymerase II (RNAPII) transcription and gene regulation. We built extremely randomized trees (ETs) models to predict the genome-wide R-loops using RNAPII and multiple histone modifications chromatin immunoprecipitation (ChIP)-seq, DNase-seq, Global Run-On sequencing (GRO-seq) and R-loop profiling data. We compared the performance of ET models to multiple machine learning approaches, and the proposed ET models achieved the best and extremely robust performances. Epigenetic profiles are highly predictive of R-loops genome-widely and they are strongly associated with R-loop formation. In addition, the presence of R-loops is significantly correlated with RNAPII transcription activity, H3K4me3 and open chromatin around the transcription start site, and H3K9me1 and H3K9me3 around the transcription termination site. RNAPII pausing defects were correlated with 5′R-loops accumulation, and transcriptional termination defects and read-throughs were correlated with 3′R-loops accumulation. Furthermore, we found driver genes with 5′R-loops and RNAPII pausing defects express significantly higher and genes with 3′R-loops and read-through transcription express significantly lower than genes without R-loops. These driver genes are enriched with chromosomal instability, Hippo–Merlin signaling Dysregulation, DNA damage response and TGF-β pathways, indicating R-loops accumulating at the 5′ end of genes play oncogenic roles, whereas at the 3′ end of genes play tumor-suppressive roles in tumorigenesis.
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Affiliation(s)
- Xingxin Pan
- Division of Experimental Hematology and Cancer Biology , Brain Tumor Center, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229 , USA
| | - L Frank Huang
- Division of Experimental Hematology and Cancer Biology , Brain Tumor Center, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229 , USA
- Department of Pediatrics, University of Cincinnati College of Medicine , Cincinnati, OH 45229 , USA
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8
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Afanasyev AY, Onufriev AV. Stretching of Long Double-Stranded DNA and RNA Described by the Same Approach. J Chem Theory Comput 2022; 18:3911-3920. [PMID: 35544776 DOI: 10.1021/acs.jctc.1c01221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We propose an approach to help interpret polymer force-extension curves that exhibit plateau regimes. When coupled to a bead-spring dynamic model, the approach accurately reproduces a variety of experimental force-extension curves of long double-stranded DNA and RNA, including torsionally constrained and unconstrained DNA and negatively supercoiled DNA. A key feature of the model is a specific nonconvex energy function of the spring. We provide an algorithm to obtain the five required parameters of the model from experimental force-extension curves. The applicability of the approach to the force-extension curves of double-stranded (ds) DNA of variable GC content as well as to a DNA/RNA hybrid structure is explored and confirmed. We use the approach to explain counterintuitive sequence-dependent trends and make predictions. In the plateau region of the force-extension curves, our molecular dynamics simulations show that the polymer separates into a mix of weakly and strongly stretched states without forming macroscopically distinct phases. The distribution of these states is predicted to depend on the sequence.
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Affiliation(s)
- Alexander Y Afanasyev
- Department of Biomedical Engineering and Mechanics, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Alexey V Onufriev
- Departments of Computer Science and Physics, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
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9
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Ma Q, Li SFY. Enzyme- and label-free fluorescence microRNA biosensor based on the distance-dependent photoinduced electron transfer of DNA/Cu nanoparticles. Microchem J 2021. [DOI: 10.1016/j.microc.2020.105646] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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10
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Muniz MI, Lackey HH, Heemstra JM, Weber G. DNA/TNA mesoscopic modeling of melting temperatures suggests weaker hydrogen bonding of CG than in DNA/RNA. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137413] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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11
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Liu JH, Xi K, Zhang X, Bao L, Zhang X, Tan ZJ. Structural Flexibility of DNA-RNA Hybrid Duplex: Stretching and Twist-Stretch Coupling. Biophys J 2019; 117:74-86. [PMID: 31164196 PMCID: PMC6626833 DOI: 10.1016/j.bpj.2019.05.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 04/25/2019] [Accepted: 05/17/2019] [Indexed: 12/21/2022] Open
Abstract
DNA-RNA hybrid (DRH) duplexes play essential roles during the replication of DNA and the reverse transcription of RNA viruses, and their flexibility is important for their biological functions. Recent experiments indicated that A-form RNA and B-form DNA have a strikingly different flexibility in stretching and twist-stretch coupling, and the structural flexibility of DRH duplex is of great interest, especially in stretching and twist-stretch coupling. In this work, we performed microsecond all-atom molecular dynamics simulations with new AMBER force fields to characterize the structural flexibility of DRH duplex in stretching and twist-stretch coupling. We have calculated all the helical parameters, stretch modulus, and twist-stretch coupling parameters for the DRH duplex. First, our analyses on structure suggest that the DRH duplex exhibits an intermediate conformation between A- and B-forms and closer to A-form, which can be attributed to the stronger rigidity of the RNA strand than the DNA strand. Second, our calculations show that the DRH duplex has the stretch modulus of 834 ± 34 pN and a very weak twist-stretch coupling. Our quantitative analyses indicate that, compared with DNA and RNA duplexes, the different flexibility of the DRH duplex in stretching and twist-stretch coupling is mainly attributed to its apparently different basepair inclination in the helical structure.
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Affiliation(s)
- Ju-Hui Liu
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Kun Xi
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Xi Zhang
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Lei Bao
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Xinghua Zhang
- College of Life Science, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan, China.
| | - Zhi-Jie Tan
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China.
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12
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13
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de Oliveira Martins E, Basílio Barbosa V, Weber G. DNA/RNA hybrid mesoscopic model shows strong stability dependence with deoxypyrimidine content and stacking interactions similar to RNA/RNA. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2018.11.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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14
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Zhang C, Fu H, Yang Y, Zhou E, Tan Z, You H, Zhang X. The Mechanical Properties of RNA-DNA Hybrid Duplex Stretched by Magnetic Tweezers. Biophys J 2018; 116:196-204. [PMID: 30635125 DOI: 10.1016/j.bpj.2018.12.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 12/05/2018] [Accepted: 12/07/2018] [Indexed: 12/25/2022] Open
Abstract
RNA can anneal to its DNA template to generate an RNA-DNA hybrid (RDH) duplex and a displaced DNA strand, termed R-loop. RDH duplex occupies up to 5% of the mammalian genome and plays important roles in many biological processes. The functions of RDH duplex are affected by its mechanical properties, including the elasticity and the conformation transitions. The mechanical properties of RDH duplex, however, are still unclear. In this work, we studied the mechanical properties of RDH duplex using magnetic tweezers in comparison with those of DNA and RNA duplexes with the same sequences. We report that the contour length of RDH duplex is ∼0.30 nm/bp, and the stretching modulus of RDH duplex is ∼660 pN, neither of which is sensitive to NaCl concentration. The persistence length of RDH duplex depends on NaCl concentration, decreasing from ∼63 nm at 1 mM NaCl to ∼49 nm at 500 mM NaCl. Under high tension of ∼60 pN, the end-opened RDH duplex undergoes two distinct overstretching transitions; at high salt in which the basepairs are stable, it undergoes the nonhysteretic transition, leading to a basepaired elongated structure, whereas at low salt, it undergoes a hysteretic peeling transition, leading to the single-stranded DNA strand under force and the single-stranded RNA strand coils. The peeled RDH is difficult to reanneal back to the duplex conformation, which may be due to the secondary structures formed in the coiled single-stranded RNA strand. These results help us understand the full picture of the structures and mechanical properties of nucleic acid duplexes in solution and provide a baseline for studying the interaction of RDH with proteins at the single-molecule level.
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Affiliation(s)
- Chen Zhang
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan, China
| | - Hang Fu
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan, China
| | - Yajun Yang
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan, China
| | - Erchi Zhou
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan, China
| | - Zhijie Tan
- School of Physics and Technology, Wuhan University, Wuhan, China
| | - Huijuan You
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xinghua Zhang
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan, China.
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15
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Uppuladinne MVN, Sonavane UB, Deka RC, Joshi RR. Structural insight into antisense gapmer-RNA oligomer duplexes through molecular dynamics simulations. J Biomol Struct Dyn 2018; 37:2823-2836. [PMID: 30284504 DOI: 10.1080/07391102.2018.1498390] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
There is an extensive research carrying out on antisense technology and the molecules entering into clinical trials are increasing rapidly. Phosphorothioate (PS) is a chemical modification in which nonbridged oxygen is replaced with a sulfur, consequently providing resistance against nuclease activity. The 2'-4' conformationally restricted nucleoside has the structural features of both 2'-O-methoxy ethyl RNA (MOE), which shows good toxicity profile, and locked nucleic acid (LNA), which shows good binding affinity towards the target RNA. These modifications have been studied and suggested that they can be a potential therapeutic agents in antisense therapy. Mipomersen (ISIS 301012), which contains the novel nucleoside modification has been used to target to apolipoprotein (Apo B), which reduces LDL cholesterol by 6-41%. In this study, classical molecular dynamics (MD) simulations were performed on six different antisense gapmer/target-RNA oligomer duplexes (LNA-PS-LNA/RNA, RcMOE-PS-RcMOE/RNA, ScMOE-PS-ScMOE/RNA, MOE-PS-MOE/RNA, PS-DNA/RNA and DNA/RNA) to investigate the structural dynamics, stability and solvation properties. The LNA, MOE nucleotides present in respective duplexes are showing the structure of A-form and the PS-DNA nucleotides resemble the structure of B-form helix with respect to some of the helical parameters. Free energy calculations suggest that the oligomer, which contains LNA binds to the RNA strongly than other modifications as shown in experimental results. The MOE modified nucleotide, which although had a lower binding affinity but higher solvent accessible surface area (SASA) compared to the other modifications, may be influencing the toxicity and hence may be used it in Mipomersen, the second antisense molecule which is approved by FDA. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mallikarjunachari V N Uppuladinne
- a High Performance Computing - Medical and Bioinformatics Applications Group , Centre for Development of Advanced Computing (C-DAC) , Pune , India
| | - Uddhavesh B Sonavane
- a High Performance Computing - Medical and Bioinformatics Applications Group , Centre for Development of Advanced Computing (C-DAC) , Pune , India
| | - Ramesh Ch Deka
- b Department of Chemical Sciences , Tezpur University , Napaam , Sonitpur , India
| | - Rajendra R Joshi
- a High Performance Computing - Medical and Bioinformatics Applications Group , Centre for Development of Advanced Computing (C-DAC) , Pune , India
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16
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Lu S, Wang S, Zhao J, Sun J, Yang X. Fluorescence Light-Up Biosensor for MicroRNA Based on the Distance-Dependent Photoinduced Electron Transfer. Anal Chem 2017; 89:8429-8436. [DOI: 10.1021/acs.analchem.7b01900] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Shasha Lu
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute
of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
- University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Shuang Wang
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute
of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
- University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jiahui Zhao
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute
of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Sun
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute
of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Xiurong Yang
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute
of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
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17
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Nascent Connections: R-Loops and Chromatin Patterning. Trends Genet 2016; 32:828-838. [PMID: 27793359 DOI: 10.1016/j.tig.2016.10.002] [Citation(s) in RCA: 148] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 10/03/2016] [Accepted: 10/06/2016] [Indexed: 11/22/2022]
Abstract
RNA molecules, such as long noncoding RNAs (lncRNAs), have critical roles in regulating gene expression, chromosome architecture, and the modification states of chromatin. Recent developments suggest that RNA also influences gene expression and chromatin patterns through the interaction of nascent transcripts with their DNA template via the formation of co-transcriptional R-loop structures. R-loop formation over specific, conserved, hotspots occurs at thousands of genes in mammalian genomes and represents an important and dynamic feature of mammalian chromatin. Here, focusing primarily on mammalian systems, I describe the accumulating connections and possible mechanisms linking R-loop formation and chromatin patterning. The possible contribution of aberrant R-loops to pathological conditions is also discussed.
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18
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Sanz LA, Hartono SR, Lim YW, Steyaert S, Rajpurkar A, Ginno PA, Xu X, Chédin F. Prevalent, Dynamic, and Conserved R-Loop Structures Associate with Specific Epigenomic Signatures in Mammals. Mol Cell 2016; 63:167-78. [PMID: 27373332 DOI: 10.1016/j.molcel.2016.05.032] [Citation(s) in RCA: 365] [Impact Index Per Article: 45.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 01/11/2016] [Accepted: 05/23/2016] [Indexed: 11/28/2022]
Abstract
R-loops are three-stranded nucleic acid structures formed upon annealing of an RNA strand to one strand of duplex DNA. We profiled R-loops using a high-resolution, strand-specific methodology in human and mouse cell types. R-loops are prevalent, collectively occupying up to 5% of mammalian genomes. R-loop formation occurs over conserved genic hotspots such as promoter and terminator regions of poly(A)-dependent genes. In most cases, R-loops occur co-transcriptionally and undergo dynamic turnover. Detailed epigenomic profiling revealed that R-loops associate with specific chromatin signatures. At promoters, R-loops associate with a hyper-accessible state characteristic of unmethylated CpG island promoters. By contrast, terminal R-loops associate with an enhancer- and insulator-like state and define a broad class of transcription terminators. Together, this suggests that the retention of nascent RNA transcripts at their site of expression represents an abundant, dynamic, and programmed component of the mammalian chromatin that affects chromatin patterning and the control of gene expression.
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Affiliation(s)
- Lionel A Sanz
- Department of Molecular and Cellular Biology and Genome Center, 1 Shields Avenue, University of California, Davis, Davis, CA 95616, USA
| | - Stella R Hartono
- Department of Molecular and Cellular Biology and Genome Center, 1 Shields Avenue, University of California, Davis, Davis, CA 95616, USA
| | - Yoong Wearn Lim
- Department of Molecular and Cellular Biology and Genome Center, 1 Shields Avenue, University of California, Davis, Davis, CA 95616, USA
| | - Sandra Steyaert
- Department of Mathematical Modeling, Statistics, and Bioinformatics, University of Ghent, Ghent 9000, Belgium
| | - Aparna Rajpurkar
- Department of Molecular and Cellular Biology and Genome Center, 1 Shields Avenue, University of California, Davis, Davis, CA 95616, USA
| | - Paul A Ginno
- Department of Molecular and Cellular Biology and Genome Center, 1 Shields Avenue, University of California, Davis, Davis, CA 95616, USA
| | - Xiaoqin Xu
- Department of Molecular and Cellular Biology and Genome Center, 1 Shields Avenue, University of California, Davis, Davis, CA 95616, USA
| | - Frédéric Chédin
- Department of Molecular and Cellular Biology and Genome Center, 1 Shields Avenue, University of California, Davis, Davis, CA 95616, USA.
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19
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Goldsmith G, Rathinavelan T, Yathindra N. Selective Preference of Parallel DNA Triplexes Is Due to the Disruption of Hoogsteen Hydrogen Bonds Caused by the Severe Nonisostericity between the G*GC and T*AT Triplets. PLoS One 2016; 11:e0152102. [PMID: 27010368 PMCID: PMC4807104 DOI: 10.1371/journal.pone.0152102] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 03/08/2016] [Indexed: 12/14/2022] Open
Abstract
Implications of DNA, RNA and RNA.DNA hybrid triplexes in diverse biological functions, diseases and therapeutic applications call for a thorough understanding of their structure-function relationships. Despite exhaustive studies mechanistic rationale for the discriminatory preference of parallel DNA triplexes with G*GC & T*AT triplets still remains elusive. Here, we show that the highest nonisostericity between the G*GC & T*AT triplets imposes extensive stereochemical rearrangements contributing to context dependent triplex destabilisation through selective disruption of Hoogsteen scheme of hydrogen bonds. MD simulations of nineteen DNA triplexes with an assortment of sequence milieu reveal for the first time fresh insights into the nature and extent of destabilization from a single (non-overlapping), double (overlapping) and multiple pairs of nonisosteric base triplets (NIBTs). It is found that a solitary pair of NIBTs, feasible either at a G*GC/T*AT or T*AT/G*GC triplex junction, does not impinge significantly on triplex stability. But two overlapping pairs of NIBTs resulting from either a T*AT or a G*GC interruption disrupt Hoogsteen pair to a noncanonical mismatch destabilizing the triplex by ~10 to 14 kcal/mol, implying that their frequent incidence in multiples, especially, in short sequences could even hinder triplex formation. The results provide (i) an unambiguous and generalised mechanistic rationale for the discriminatory trait of parallel triplexes, including those studied experimentally (ii) clarity for the prevalence of antiparallel triplexes and (iii) comprehensive perspectives on the sequence dependent influence of nonisosteric base triplets useful in the rational design of TFO's against potential triplex target sites.
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Affiliation(s)
- Gunaseelan Goldsmith
- Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronics City Phase I, Bangalore, India
- Manipal University, Manipal, India
| | | | - Narayanarao Yathindra
- Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronics City Phase I, Bangalore, India
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20
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Martínez-Montero S, Deleavey GF, Dierker-Viik A, Lindovska P, Ilina T, Portella G, Orozco M, Parniak MA, González C, Damha MJ. Synthesis and properties of 2'-deoxy-2',4'-difluoroarabinose-modified nucleic acids. J Org Chem 2015; 80:3083-91. [PMID: 25723361 PMCID: PMC4484724 DOI: 10.1021/jo502948t] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We report the synthesis, thermal stability, and RNase H substrate activity of 2'-deoxy-2',4'-difluoroarabino-modified nucleic acids. 2'-Deoxy-2',4'-difluoroarabinouridine (2,'4'-diF-araU) was prepared in a stereoselective way in six steps from 2'-deoxy-2'-fluoroarabinouridine (2'-F-araU). NMR analysis and quantum mechanical calculations at the nucleoside level reveal that introduction of 4'-fluorine introduces a strong bias toward the North conformation, despite the presence of the 2'-βF, which generally steers the sugar pucker toward the South/East conformation. Incorporation of the novel monomer into DNA results on a neutral to slightly stabilizing thermal effect on DNA-RNA hybrids. Insertion of 2',4'-diF-araU nucleotides in the DNA strand of a DNA-RNA hybrid decreases the rate of both human and HIV reverse transcriptase-associated RNase H-mediated cleavage of the complement RNA strand compared to that for an all-DNA strand or a DNA strand containing the corresponding 2'-F-araU nucleotide units, consistent with the notion that a 4'-fluorine in 2'-F-araU switches the preferred sugar conformation from DNA-like (South/East) to RNA-like (North).
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Affiliation(s)
- Saúl Martínez-Montero
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
| | - Glen F. Deleavey
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
| | - Arden Dierker-Viik
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
| | - Petra Lindovska
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
| | - Tatiana Ilina
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, 450 Technology Drive, Pittsburgh, Pennsylvania 15219-3143, United States
| | - Guillem Portella
- Joint IRB–BSC program on Computational Biology, Institute for Research in Biomedicine, Barcelona Supercomputing Center, and Department of Biochemistry, University of Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Modesto Orozco
- Joint IRB–BSC program on Computational Biology, Institute for Research in Biomedicine, Barcelona Supercomputing Center, and Department of Biochemistry, University of Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Michael A. Parniak
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, 450 Technology Drive, Pittsburgh, Pennsylvania 15219-3143, United States
| | - Carlos González
- Instituto de Química Física Rocasolano, CSIC, C/Serrano 119, 28006 Madrid, Spain
| | - Masad J. Damha
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
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21
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Wons E, Mruk I, Kaczorowski T. Relaxed specificity of prokaryotic DNA methyltransferases results in DNA site-specific modification of RNA/DNA heteroduplexes. J Appl Genet 2015; 56:539-546. [PMID: 25787880 DOI: 10.1007/s13353-015-0279-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 02/27/2015] [Accepted: 03/02/2015] [Indexed: 01/18/2023]
Abstract
RNA/DNA hybrid duplexes regularly occur in nature, for example in transcriptional R loops. Their susceptibility to modification by DNA-specific or RNA-specific enzymes is, thus, a biologically relevant question, which, in addition, has possible biotechnological implications. In this study, we investigated the activity of four isospecific DNA methyltransferases (M.EcoVIII, M.LlaCI, M.HindIII, M.BstZ1II) toward an RNA/DNA duplex carrying one 5'-AAGCUU-3'/3'-TTCGAA-5' target sequence. The analyzed enzymes belong to the β-group of adenine N6-methyltransferases and recognize the palindromic DNA sequence 5'-AAGCTT-3'/3'-TTCGAA-5'. Under standard conditions, none of these isospecific enzymes could detectibly methylate the RNA/DNA duplex. However, the addition of agents that generally relax specificity, such as dimethyl sulfoxide (DMSO) and glycerol, resulted in substantial methylation of the RNA/DNA duplex by M.EcoVIII and M.LlaCI. Only the DNA strand of the RNA/DNA duplex was methylated. The same was not observed for M.HindIII or M.BstZ1II. This is, to our knowledge, the first report that demonstrates such activity by prokaryotic DNA methyltransferases. Possible applications of these findings in a laboratory practice are also discussed.
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Affiliation(s)
- Ewa Wons
- Department of Microbiology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland
| | - Iwona Mruk
- Department of Microbiology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland
| | - Tadeusz Kaczorowski
- Department of Microbiology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland.
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22
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Tolokh IS, Pabit SA, Katz AM, Chen Y, Drozdetski A, Baker N, Pollack L, Onufriev AV. Why double-stranded RNA resists condensation. Nucleic Acids Res 2014; 42:10823-31. [PMID: 25123663 PMCID: PMC4176364 DOI: 10.1093/nar/gku756] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The addition of small amounts of multivalent cations to solutions containing double-stranded DNA leads to inter-DNA attraction and eventual condensation. Surprisingly, the condensation is suppressed in double-stranded RNA, which carries the same negative charge as DNA, but assumes a different double helical form. Here, we combine experiment and atomistic simulations to propose a mechanism that explains the variations in condensation of short (25 base-pairs) nucleic acid (NA) duplexes, from B-like form of homopolymeric DNA, to mixed sequence DNA, to DNA:RNA hybrid, to A-like RNA. Circular dichroism measurements suggest that duplex helical geometry is not the fundamental property that ultimately determines the observed differences in condensation. Instead, these differences are governed by the spatial variation of cobalt hexammine (CoHex) binding to NA. There are two major NA-CoHex binding modes--internal and external--distinguished by the proximity of bound CoHex to the helical axis. We find a significant difference, up to 5-fold, in the fraction of ions bound to the external surfaces of the different NA constructs studied. NA condensation propensity is determined by the fraction of CoHex ions in the external binding mode.
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Affiliation(s)
- Igor S Tolokh
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA
| | - Suzette A Pabit
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853-3501, USA
| | - Andrea M Katz
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853-3501, USA
| | - Yujie Chen
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853-3501, USA
| | | | - Nathan Baker
- Applied Statistics and Computational Modeling Group, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853-3501, USA
| | - Alexey V Onufriev
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA Department of Physics, Virginia Tech, Blacksburg, VA 24061, USA
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23
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Suresh G, Priyakumar UD. Atomistic investigation of the effect of incremental modification of deoxyribose sugars by locked nucleic acid (β-D-LNA and α-L-LNA) moieties on the structures and thermodynamics of DNA-RNA hybrid duplexes. J Phys Chem B 2014; 118:5853-63. [PMID: 24845216 DOI: 10.1021/jp5014779] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Chemically modified oligonucleotides offer many possibilities in utilizing their special features for a vast number of applications in nucleic acid based therapies and synthetic molecular biology. Locked nucleic acid analogues (α-/β-LNA) are modifications having an extra ring of 2'-O,4'-C-methylene group in the furanose sugar. LNA strands have been shown to exhibit high binding affinity toward RNA and DNA strands, and the resultant duplexes show significantly high melting temperatures. In the present study, molecular dynamics (MD) simulations were performed on DNA-RNA hybrid duplexes by systematically modifying their deoxyribose sugars with locked nucleic acid analogues. Several geometrical and energetic analyses were performed using principal component (PCA) analysis and binding free energy methods to understand the consequence of incorporated isomeric LNA modifications on the structure, dynamics, and stability of DNA-RNA hybrid duplex. The β-modification systematically changes the conformation of the DNA-RNA hybrid duplex whereas drastic changes are observed for α-modification. The fully modified duplexes have distinct properties compared to partial and unmodified duplexes, and the partly modified duplexes have properties intermediate to full strand and unmodified duplexes. The distribution of BI versus BII populations suggests that backbone rearrangement is minimal for β-LNA modification in order to accommodate it in duplexes whereas extensive backbone rearrangement is necessary in order to incorporate α-LNA modification which subsequently alters the energetic and structural properties of the duplexes. The simulation results also suggest that the alteration of DNA-RNA hybrid properties depends on the position of modification and the gap between the modifications.
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Affiliation(s)
- Gorle Suresh
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology , Hyderabad 500 032, India
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24
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Vuković L, Koh HR, Myong S, Schulten K. Substrate recognition and specificity of double-stranded RNA binding proteins. Biochemistry 2014; 53:3457-66. [PMID: 24801449 PMCID: PMC4051425 DOI: 10.1021/bi500352s] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Recognition of double-stranded (ds)
RNA is an important part of many cellular pathways, including RNA
silencing, viral recognition, RNA editing, processing, and transport.
dsRNA recognition is often achieved by dsRNA binding domains (dsRBDs).
We use atomistic molecular dynamics simulations to examine the binding
interface of the transactivation response RNA binding protein (TRBP)
dsRBDs to dsRNA substrates. Our results explain the exclusive selectivity
of dsRBDs toward dsRNA and against DNA–RNA hybrid and dsDNA
duplexes. We also provide corresponding experimental evidence. The
dsRNA duplex is recognized by dsRBDs through the A-form of three duplex
grooves and by the chemical properties of RNA bases, which have 2′-hydroxyl
groups on their sugar rings. Our simulations show that TRBP dsRBD
discriminates dsRNA- from DNA-containing duplexes primarily through
interactions at two duplex grooves. The simulations also reveal that
the conformation of the DNA–RNA duplex can be altered by dsRBD
proteins, resulting in a weak binding of dsRBDs to DNA–RNA
hybrids. Our study reveals the structural and molecular basis of protein–RNA
interaction that gives rise to the observed substrate specificity
of dsRNA binding proteins.
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Affiliation(s)
- Lela Vuković
- Department of Physics, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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25
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Vik ES, Nawaz MS, Strøm Andersen P, Fladeby C, Bjørås M, Dalhus B, Alseth I. Endonuclease V cleaves at inosines in RNA. Nat Commun 2014; 4:2271. [PMID: 23912683 PMCID: PMC3741635 DOI: 10.1038/ncomms3271] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 07/09/2013] [Indexed: 01/05/2023] Open
Abstract
Endonuclease V orthologues are highly conserved proteins found in all kingdoms of life. While the prokaryotic enzymes are DNA repair proteins for removal of deaminated adenosine (inosine) from the genome, no clear role for the eukaryotic counterparts has hitherto been described. Here we report that human endonuclease V (ENDOV) and also Escherichia coli endonuclease V are highly active ribonucleases specific for inosine in RNA. Inosines are normal residues in certain RNAs introduced by specific deaminases. Adenosine-to-inosine editing is essential for proper function of these transcripts and defects are linked to various human disease. Here we show that human ENDOV cleaves an RNA substrate containing inosine in a position corresponding to a biologically important site for deamination in the Gabra-3 transcript of the GABA(A) neurotransmitter. Further, human ENDOV specifically incises transfer RNAs with inosine in the wobble position. This previously unknown RNA incision activity may suggest a role for endonuclease V in normal RNA metabolism.
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Affiliation(s)
- Erik Sebastian Vik
- Department of Microbiology, Oslo University Hospital HF and University of Oslo, Rikshospitalet, PO Box 4950 Nydalen, 0424 Oslo, Norway
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26
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Suresh G, Priyakumar UD. DNA–RNA hybrid duplexes with decreasing pyrimidine content in the DNA strand provide structural snapshots for the A- to B-form conformational transition of nucleic acids. Phys Chem Chem Phys 2014; 16:18148-55. [DOI: 10.1039/c4cp02478h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A gradual increase in the deoxypyrimidine content in DNA–RNA hybrids leads to B- to A-form nucleic acid transition. Possible factors that govern nuclease activity on hybrid duplexes are presented.
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Affiliation(s)
- Gorle Suresh
- Centre for Computational Natural Sciences and Bioinformatics
- International Institute of Information Technology
- Hyderabad 500 032, India
| | - U. Deva Priyakumar
- Centre for Computational Natural Sciences and Bioinformatics
- International Institute of Information Technology
- Hyderabad 500 032, India
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27
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Wright DW, Deuzing IP, Flandre P, van den Eede P, Govaert M, Setiawan L, Coveney PV, Marcelin AG, Calvez V, Boucher CAB, Beerens N. A polymorphism at position 400 in the connection subdomain of HIV-1 reverse transcriptase affects sensitivity to NNRTIs and RNaseH activity. PLoS One 2013; 8:e74078. [PMID: 24098331 PMCID: PMC3788777 DOI: 10.1371/journal.pone.0074078] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 07/26/2013] [Indexed: 11/19/2022] Open
Abstract
Reverse transcriptase (RT) plays an essential role in HIV-1 replication, and inhibition of this enzyme is a key component of HIV-treatment. However, the use of RT inhibitors can lead to the emergence of drug-resistant variants. Until recently, most clinically relevant resistance mutations were found in the polymerase domain of RT. Lately, an increasing number of resistance mutations has been identified in the connection and RNaseH domain. To further explore the role of these domains we analyzed the complete RT sequence of HIV-1 subtype B patients failing therapy. Position A/T400 in the connection subdomain is polymorphic, but the proportion of T400 increases from 41% in naïve patients to 72% in patients failing therapy. Previous studies suggested a role for threonine in conferring resistance to nucleoside RT inhibitors. Here we report that T400 also mediates resistance to non-nucleoside RT inhibitors. The susceptibility to NVP and EFV was reduced 5-fold and 2-fold, respectively, in the wild-type subtype B NL4.3 background. We show that substitution A400T reduces the RNaseH activity. The changes in enzyme activity are remarkable given the distance to both the polymerase and RNaseH active sites. Molecular dynamics simulations were performed, which provide a novel atomistic mechanism for the reduction in RNaseH activity induced by T400. Substitution A400T was found to change the conformation of the RNaseH primer grip region. Formation of an additional hydrogen bond between residue T400 and E396 may play a role in this structural change. The slower degradation of the viral RNA genome may provide more time for dissociation of the bound NNRTI from the stalled RT-template/primer complex, after which reverse transcription can resume.
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Affiliation(s)
- David W. Wright
- Centre for Computational Science, Department of Chemistry, University College London, United Kingdom
| | - Ilona P. Deuzing
- Department of Virology, ViroscienceLab, Erasmus MC, Rotterdam, The Netherlands
| | - Philippe Flandre
- Institut National de la Santé et de la Recherche Médicale UMR-S 943 and Université Pierre and Marie Curie, Paris, France
| | | | | | - Laurentia Setiawan
- Department of Virology, ViroscienceLab, Erasmus MC, Rotterdam, The Netherlands
| | - Peter V. Coveney
- Centre for Computational Science, Department of Chemistry, University College London, United Kingdom
| | - Anne-Geneviève Marcelin
- Institut National de la Santé et de la Recherche Médicale UMR-S 943 and Université Pierre and Marie Curie, Paris, France
| | - Vincent Calvez
- Institut National de la Santé et de la Recherche Médicale UMR-S 943 and Université Pierre and Marie Curie, Paris, France
| | | | - Nancy Beerens
- Department of Virology, ViroscienceLab, Erasmus MC, Rotterdam, The Netherlands
- * E-mail:
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28
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Suresh G, Priyakumar UD. Structures, dynamics, and stabilities of fully modified locked nucleic acid (β-D-LNA and α-L-LNA) duplexes in comparison to pure DNA and RNA duplexes. J Phys Chem B 2013; 117:5556-64. [PMID: 23617391 DOI: 10.1021/jp4016068] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Locked nucleic acid (LNA) is a chemical modification which introduces a -O-CH2- linkage in the furanose sugar of nucleic acids and blocks its conformation in a particular state. Two types of modifications, namely, 2'-O,4'-C-methylene-β-D-ribofuranose (β-D-LNA) and 2'-O,4'-C-methylene-α-L-ribofuranose (α-L-LNA), have been shown to yield RNA and DNA duplex-like structures, respectively. LNA modifications lead to increased melting temperatures of DNA and RNA duplexes, and have been suggested as potential therapeutic agents in antisense therapy. In this study, molecular dynamics (MD) simulations were performed on fully modified LNA duplexes and pure DNA and RNA duplexes sharing a similar sequence to investigate their structure, stabilities, and solvation properties. Both LNA duplexes undergo unwinding of the helical structure compared to the pure DNA and RNA duplexes. Though the α-LNA substituent has been proposed to mimic deoxyribose sugar in its conformational properties, the fully modified duplex was found to exhibit unique structural and dynamic properties with respect to the other three nucleic acid structures. Free energy calculations accurately capture the enhanced stabilization of the LNA duplex structures compared to DNA and RNA molecules as observed in experiments. π-stacking interaction between bases from complementary strands is shown to be one of the contributors to enhanced stabilization upon LNA substitution. A combination of two factors, namely, nature of the -O-CH2- linkage in the LNAs vs their absence in the pure duplexes and similar conformations of the sugar rings in DNA and α-LNA vs the other two, is suggested to contribute to the stark differences among the four duplexes studied here in terms of their structural, dynamic, and energetic properties.
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Affiliation(s)
- Gorle Suresh
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, India
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29
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Baker BA, Mahmoudabadi G, Milam VT. Using double-stranded DNA probes to promote specificity in target capture. Colloids Surf B Biointerfaces 2013; 102:884-90. [DOI: 10.1016/j.colsurfb.2012.09.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Revised: 08/10/2012] [Accepted: 09/10/2012] [Indexed: 12/30/2022]
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30
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Piperakis MM, Gaynor JW, Fisher J, Cosstick R. Thermal stabilisation of RNA·RNA duplexes and G-quadruplexes by phosphorothiolate linkages. Org Biomol Chem 2012; 11:966-74. [PMID: 23250349 DOI: 10.1039/c2ob26940f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The effect of 3'-S-phosphorothiolate linkages on the stability of RNA·RNA duplexes and G-quadruplex structures has been studied. 3'-Thio-2'-deoxyuridine was incorporated into RNA duplexes and thermal melting studies revealed that the resulting 3'-S-phosphorothiolate linkages increased the stability of the duplex to thermal denaturation. Additionally, and contrary to expectation, a similar effect on duplex stability was observed when the same thionucleoside was incorporated into the RNA strand of a RNA·DNA duplex. A suitably protected derivative of 3'-thio-2'-deoxyguanosine was prepared using an oxidation-reduction strategy and this residue also increased the thermal stability the [d(TGGGGT)](4) G-quadruplex when positioned centrally. The results are discussed in terms of the influence that the sulfur atom has on the conformation of the furanose ring and imply that the previously noted high thermal stability of parallel RNA quadruplexes is not derived from H-bonding interactions of the 2'-hydroxyl group, but can be attributed to conformational effects.
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31
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Deleavey GF, Damha MJ. Designing chemically modified oligonucleotides for targeted gene silencing. ACTA ACUST UNITED AC 2012; 19:937-54. [PMID: 22921062 DOI: 10.1016/j.chembiol.2012.07.011] [Citation(s) in RCA: 430] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2012] [Revised: 06/28/2012] [Accepted: 07/02/2012] [Indexed: 02/07/2023]
Abstract
Oligonucleotides (ONs), and their chemically modified mimics, are now routinely used in the laboratory as a means to control the expression of fundamentally interesting or therapeutically relevant genes. ONs are also under active investigation in the clinic, with many expressing cautious optimism that at least some ON-based therapies will succeed in the coming years. In this review, we will discuss several classes of ONs used for controlling gene expression, with an emphasis on antisense ONs (AONs), small interfering RNAs (siRNAs), and microRNA-targeting ONs (anti-miRNAs). This review provides a current and detailed account of ON chemical modification strategies for the optimization of biological activity and therapeutic application, while clarifying the biological pathways, chemical properties, benefits, and limitations of oligonucleotide analogs used in nucleic acids research.
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Affiliation(s)
- Glen F Deleavey
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, QC H3A 0B8, Canada.
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32
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Ivančić-Baće I, Al Howard J, Bolt EL. Tuning in to interference: R-loops and cascade complexes in CRISPR immunity. J Mol Biol 2012; 422:607-616. [PMID: 22743103 DOI: 10.1016/j.jmb.2012.06.024] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Revised: 06/13/2012] [Accepted: 06/16/2012] [Indexed: 12/26/2022]
Abstract
Stable RNA-DNA hybrids formed by invasion of an RNA strand into duplex DNA, termed R-loops, are notorious for provoking genome instability especially when they arise during transcription. However, in some instances (DNA replication and class switch recombination), R-loops are useful so long as their existence is carefully managed to avoid them persisting. A recent flow of research papers establishes a newly discovered use for R-loops as key intermediates in a prokaryotic immune system called CRISPR (Clustered Regularly Interspersed Short Palindromic Repeats). Structures and mechanism of ribonucleoprotein complexes ("Cascades") that form CRISPR R-loops highlight precision targeting of duplex DNA that has sequence characteristics marking it as foe, enabling nucleolytic destruction of DNA and recycling the Cascade. We review these significant recent breakthroughs in understanding targeting/interference stages of CRISPR immunity and discuss questions arising, including a possible link between targeting and adaptive immunity in prokaryotes.
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Affiliation(s)
- Ivana Ivančić-Baće
- Department of Molecular Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
| | - Jamieson Al Howard
- School of Biomedical Sciences, University of Nottingham Medical School, Queens Medical Centre, Nottingham NG7 2UH, UK
| | - Edward L Bolt
- School of Biomedical Sciences, University of Nottingham Medical School, Queens Medical Centre, Nottingham NG7 2UH, UK.
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33
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Abstract
DNA polymerase substrate specificity is fundamental to genome integrity and to polymerase applications in biotechnology. In the current paradigm, active site geometry is the main site of specificity control. Here, we describe the discovery of a distinct specificity checkpoint located over 25 Å from the active site in the polymerase thumb subdomain. In Tgo, the replicative DNA polymerase from Thermococcus gorgonarius, we identify a single mutation (E664K) within this region that enables translesion synthesis across a template abasic site or a cyclobutane thymidine dimer. In conjunction with a classic "steric-gate" mutation (Y409G) in the active site, E664K transforms Tgo DNA polymerase into an RNA polymerase capable of synthesizing RNAs up to 1.7 kb long as well as fully pseudouridine-, 5-methyl-C-, 2'-fluoro-, or 2'-azido-modified RNAs primed from a wide range of primer chemistries comprising DNA, RNA, locked nucleic acid (LNA), or 2'O-methyl-DNA. We find that E664K enables RNA synthesis by selectively increasing polymerase affinity for the noncognate RNA/DNA duplex as well as lowering the K(m) for ribonucleotide triphosphate incorporation. This gatekeeper mutation therefore identifies a key missing step in the adaptive path from DNA to RNA polymerases and defines a previously unknown postsynthetic determinant of polymerase substrate specificity with implications for the synthesis and replication of noncognate nucleic acid polymers.
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34
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Abstract
Seven-atom ring sugars, called septanoses, are increasingly the focus of scientific inquiries because of their potential biological activities. This article details the synthesis, conformational analysis, and protein-binding properties of septanose carbohydrates. A distinction is drawn between septanoses that are substituted in the 6-position of the ring and those that are not. When a C-6 substituent is absent, the structure is essentially that of an aldohexose in its septanose, rather than furanose or pyranose, ring form; they may play as-of-yet unexplored roles in glycobiology. Septanoses having a hydroxymethyl group at C-6, on the other hand, are ring-expanded analogues of pyranoses. Syntheses have moved beyond the preparation of seven-membered ring monosaccharides to the development of septanosyl donors. These donors have been used in the synthesis of novel di- and trisaccharides that contain septanoses as well as a variety of glycoconjugates. Low-energy conformations adopted by septanoses have been organized based on ring substitution and stereochemistry. Instances where septanoses have been demonstrated to bind to natural proteins are presented and analyzed. The major conclusion drawn in the chapter is that advances in the synthesis of septanose carbohydrates now enable a detailed investigation of their activity in a number of biological contexts.
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35
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Pramanik S, Nagatoishi S, Saxena S, Bhattacharyya J, Sugimoto N. Conformational flexibility influences degree of hydration of nucleic acid hybrids. J Phys Chem B 2011; 115:13862-72. [PMID: 21992117 DOI: 10.1021/jp207856p] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Four nucleic acid duplexes-DNA/RNA hybrid, RNA/DNA hybrid, RNA duplex, and DNA duplex-were studied under molecular crowding conditions of osmolytes. Destabilization of duplexes (ΔΔG°(25)) indicated that the ΔΔG°(25) values of hybrids were intermediate between those of DNA and RNA duplexes. In the presence of polyethylene glycol 200, the ΔΔG°(25) values were estimated to be +3.0, +3.5, +3.5, and +4.1 kcal mol(-1) for the DNA duplex, DNA/RNA hybrid, RNA/DNA hybrid, and RNA duplex, respectively. Differences in the number of water molecules taken up (-Δn(w)) upon duplex formations between 0 and 37 °C (Δ(-Δn(w))) were estimated to be 44.8 and 59.7 per duplex structure for the DNA/RNA and RNA/DNA hybrids, respectively. While the Δ(-Δn(w)) value for the DNA/RNA hybrid was intermediate between those of the DNA (26.1) and RNA (59.2) duplexes, the value for RNA/DNA hybrid was close to that of RNA duplex. These differences in the thermodynamic parameters and hydration are probably a consequence of the enhanced global flexibility of the RNA/DNA hybrid structure relative to the DNA/RNA hybrid structure observed in molecular dynamics simulations. This molecular crowding study provides information not only on hydration but also on the flexibility of the conformation of nucleic acid duplexes.
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Affiliation(s)
- Smritimoy Pramanik
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Kobe 650-0047, Japan
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36
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Jore MM, Lundgren M, van Duijn E, Bultema JB, Westra ER, Waghmare SP, Wiedenheft B, Pul U, Wurm R, Wagner R, Beijer MR, Barendregt A, Zhou K, Snijders APL, Dickman MJ, Doudna JA, Boekema EJ, Heck AJR, van der Oost J, Brouns SJJ. Structural basis for CRISPR RNA-guided DNA recognition by Cascade. Nat Struct Mol Biol 2011; 18:529-36. [PMID: 21460843 DOI: 10.1038/nsmb.2019] [Citation(s) in RCA: 427] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Accepted: 01/24/2011] [Indexed: 12/17/2022]
Abstract
The CRISPR (clustered regularly interspaced short palindromic repeats) immune system in prokaryotes uses small guide RNAs to neutralize invading viruses and plasmids. In Escherichia coli, immunity depends on a ribonucleoprotein complex called Cascade. Here we present the composition and low-resolution structure of Cascade and show how it recognizes double-stranded DNA (dsDNA) targets in a sequence-specific manner. Cascade is a 405-kDa complex comprising five functionally essential CRISPR-associated (Cas) proteins (CasA(1)B(2)C(6)D(1)E(1)) and a 61-nucleotide CRISPR RNA (crRNA) with 5'-hydroxyl and 2',3'-cyclic phosphate termini. The crRNA guides Cascade to dsDNA target sequences by forming base pairs with the complementary DNA strand while displacing the noncomplementary strand to form an R-loop. Cascade recognizes target DNA without consuming ATP, which suggests that continuous invader DNA surveillance takes place without energy investment. The structure of Cascade shows an unusual seahorse shape that undergoes conformational changes when it binds target DNA.
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Affiliation(s)
- Matthijs M Jore
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, The Netherlands
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37
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Faustino I, Pérez A, Orozco M. Toward a consensus view of duplex RNA flexibility. Biophys J 2011; 99:1876-85. [PMID: 20858433 DOI: 10.1016/j.bpj.2010.06.061] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Revised: 06/22/2010] [Accepted: 06/25/2010] [Indexed: 11/25/2022] Open
Abstract
The structure and flexibility of the RNA duplex has been studied using extended molecular dynamics simulations on four diverse 18-mer oligonucleotides designed to contain many copies of the 10 unique dinucleotide steps in different sequence environments. Simulations were performed using the two most popular force fields for nucleic acids simulations (AMBER and CHARMM) in their latest versions, trying to arrive to a consensus picture of the RNA flexibility. Contrary to what was found for DNA duplex (DNA(2)), no clear convergence is found for the RNA duplex (RNA(2)), but one of the force field seems to agree better with experimental data. MD simulations performed with this force field were used to fully characterize, for the first time to our knowledge, the sequence-dependent elastic properties of RNA duplexes at different levels of resolutions. The flexibility pattern of RNA(2) shows similarities with DNA(2), but also surprising differences, which help us to understand the different biological functions of both molecules. A full mesoscopic model of RNA duplex at different resolution levels is derived to be used for genome-wide description of the flexibility of double-helical fragments of RNA.
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Affiliation(s)
- Ignacio Faustino
- Joint Institute of IRB/BSC Program on Computational Biology, Institute of Research in Biomedicine, Barcelona, Spain
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38
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Olimpo JT, DeStefano JJ. Duplex structural differences and not 2'-hydroxyls explain the more stable binding of HIV-reverse transcriptase to RNA-DNA versus DNA-DNA. Nucleic Acids Res 2010; 38:4426-35. [PMID: 20338878 PMCID: PMC2910049 DOI: 10.1093/nar/gkq169] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Human immunodeficiency virus reverse transcriptase (HIV-RT) binds more stably in binary complexes with RNA–DNA versus DNA–DNA. Current results indicate that only the -2 and -4 RNA nucleotides (-1 hybridized to the 3′ recessed DNA base) are required for stable binding to RNA–DNA, and even a single RNA nucleotide conferred significantly greater stability than DNA–DNA. Replacing 2′- hydroxyls on pivotal RNA bases with 2′-O-methyls did not affect stability, indicating that interactions between hydroxyls and RT amino acids do not stabilize binding. RT’s Kd (koff/kon) for DNA–DNA and RNA–DNA were similar, although koff differed almost 40-fold, suggesting a faster kon for DNA–DNA. Avian myeloblastosis and Moloney murine leukemia virus RTs also bound more stably to RNA–DNA, but the difference was less pronounced than with HIV-RT. We propose that the H- versus B-form structures of RNA–DNA and DNA–DNA, respectively, allow the former to conform more easily to HIV-RT’s binding cleft, leading to more stable binding. Biologically, the ability of RT to form a more stable complex on RNA–DNA may aid in degradation of RNA fragments that remain after DNA synthesis.
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Affiliation(s)
- Jeffrey T Olimpo
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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39
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Watts JK, Martín-Pintado N, Gómez-Pinto I, Schwartzentruber J, Portella G, Orozco M, González C, Damha MJ. Differential stability of 2'F-ANA*RNA and ANA*RNA hybrid duplexes: roles of structure, pseudohydrogen bonding, hydration, ion uptake and flexibility. Nucleic Acids Res 2010; 38:2498-511. [PMID: 20071751 PMCID: PMC2853132 DOI: 10.1093/nar/gkp1225] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Hybrids of RNA with arabinonucleic acids 2′F-ANA and ANA have very similar structures but strikingly different thermal stabilities. We now present a thorough study combining NMR and other biophysical methods together with state-of-the-art theoretical calculations on a fully modified 10-mer hybrid duplex. Comparison between the solution structure of 2′F-ANA•RNA and ANA•RNA hybrids indicates that the increased binding affinity of 2′F-ANA is related to several subtle differences, most importantly a favorable pseudohydrogen bond (2′F–purine H8) which contrasts with unfavorable 2′-OH–nucleobase steric interactions in the case of ANA. While both 2′F-ANA and ANA strands maintained conformations in the southern/eastern sugar pucker range, the 2′F-ANA strand’s structure was more compatible with the A-like structure of a hybrid duplex. No dramatic differences are found in terms of relative hydration for the two hybrids, but the ANA•RNA duplex showed lower uptake of counterions than its 2′F-ANA•RNA counterpart. Finally, while the two hybrid duplexes are of similar rigidities, 2′F-ANA single strands may be more suitably preorganized for duplex formation. Thus the dramatically increased stability of 2′F-ANA•RNA and ANA•RNA duplexes is caused by differences in at least four areas, of which structure and pseudohydrogen bonding are the most important.
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Affiliation(s)
- Jonathan K Watts
- Department of Chemistry, McGill University, Montreal, QC H3A 2K6, Canada
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40
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Abstract
The DNA x RNA hybrid duplexes are functionally important structures in gene expression that are underutilized as potential drug targets. Several tools are described here for the discovery and characterization of small molecules capable of the selective recognition of DNA x RNA hybrid structures. Competition dialysis and thermal denaturation of mixtures of polynucleotide structures can be used to identify small molecules that bind selectively to DNA x RNA hybrids. An assay that measures small molecule inhibition of RNase H can be used to measure a functional response to these ligands.
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Affiliation(s)
| | - Jonathan B. Chaires
- James Graham Brown Cancer Center, University of Louisville, 529 S. Jackson St., Louisville, KY 40202 USA
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41
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Utilizing RNA/DNA hybridization to directly quantify mRNA levels in microbial fermentation samples. J Microbiol Methods 2009; 79:205-10. [DOI: 10.1016/j.mimet.2009.09.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2009] [Revised: 09/01/2009] [Accepted: 09/02/2009] [Indexed: 11/22/2022]
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42
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Huang Y, Chen C, Russu IM. Dynamics and stability of individual base pairs in two homologous RNA-DNA hybrids. Biochemistry 2009; 48:3988-97. [PMID: 19296713 DOI: 10.1021/bi900070f] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Nuclear magnetic resonance spectroscopy and proton exchange have been used to characterize two RNA-DNA hybrids from the tR2 intrinsic transcription terminator site of phage lambda. The hybrids have the same base sequence [5'-GGCGCAGGCC(T/U)(T/U)CC-3'/5'-GGAAGGCC(T/U)GCGCC-3'] but differ from each other by an interchange of DNA and RNA strands. The opening of single base pairs in the two hybrids is characterized by measuring the rates of exchange of imino protons with solvent protons as a function of the concentration of a proton acceptor (ammonia base) at 10 degrees C. The free energy change in the opening reaction provides a measure of the stability of the base pair, while the rates of opening and closing define the base pair dynamics. The results demonstrate that, within the same base sequence context, dA-rU base pairs are less stable than dT-rA base pairs. The differences in stability are enhanced when two dA-rU base pairs are located next to each other in the hybrid structure. For the G-C base pairs, the rates of opening and closing and the stability are affected by the base sequence context and by the nature of the sugar moiety attached to the guanine. The dominant feature of the base sequence is the proximity of the dA-rU base pair, which destabilizes the G-C base pair when the guanine is located on the DNA strand. Two G-C base pairs (namely, those in the fourth and 10th positions) exhibit large differences in their opening and closing rates between the two hybrids, while maintaining the same stability. These results provide the first demonstration that, for RNA-DNA hybrid structures with the same base sequence, the opening dynamics and the stability of individual base pairs are strongly influenced by the chemical nature of each strand.
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Affiliation(s)
- Yuegao Huang
- Department of Chemistry and Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut 06459, USA
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43
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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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44
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Goñi JR, Pérez A, Torrents D, Orozco M. Determining promoter location based on DNA structure first-principles calculations. Genome Biol 2008; 8:R263. [PMID: 18072969 PMCID: PMC2246265 DOI: 10.1186/gb-2007-8-12-r263] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2007] [Revised: 11/24/2007] [Accepted: 12/11/2007] [Indexed: 11/25/2022] Open
Abstract
A new method is presented which predicts promoter regions based on atomistic molecular dynamics simulations of small oligonucleotides, without requiring information on sequence conservation or features. A new method for the prediction of promoter regions based on atomic molecular dynamics simulations of small oligonucleotides has been developed. The method works independently of gene structure conservation and orthology and of the presence of detectable sequence features. Results obtained with our method confirm the existence of a hidden physical code that modulates genome expression.
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Affiliation(s)
- J Ramon Goñi
- Institute for Research in Biomedicine, Parc Científic de Barcelona, Josep Samitier, Barcelona 08028, Spain
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45
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Orozco M, Noy A, Pérez A. Recent advances in the study of nucleic acid flexibility by molecular dynamics. Curr Opin Struct Biol 2008; 18:185-93. [PMID: 18304803 DOI: 10.1016/j.sbi.2008.01.005] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2007] [Revised: 12/05/2007] [Accepted: 01/09/2008] [Indexed: 10/22/2022]
Abstract
The recent use of molecular dynamics (MD) simulations to study flexibility of nucleic acids has been reviewed from an analysis of the publications appearing in the past two years (from 2005 till date). Despite the existence of some unsolved problems in the methodologies, these years have been witness to major advances in the field. Based on a critical review of the most recent contributions, excitement exists on the expected evolution of the field in the next years.
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Affiliation(s)
- Modesto Orozco
- Joint IRB-BSC Program on Computational Biology, Institut de Recerca Biomèdica, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain.
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46
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Noy A, Luque FJ, Orozco M. Theoretical analysis of antisense duplexes: determinants of the RNase H susceptibility. J Am Chem Soc 2008; 130:3486-96. [PMID: 18298115 DOI: 10.1021/ja076734u] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The structure and dynamic properties of different antisense related duplexes (DNA x RNA, 2'O-Me-DNA x RNA, 2'F-ANA x RNA, C5(Y)-propynyl-DNA x RNA, ANA x RNA, and control duplexes DNA x DNA and RNA x RNA) have been determined by means of long molecular dynamics simulations (covering more than 0.5 micros of fully solvated unrestrained MD simulation). The massive analysis presented here allows us to determine the subtle differences between the different duplexes, which in all cases pertain to the same structural family. This analysis provides information on the molecular determinants that allow RNase H to recognize and degrade some of these duplexes, whereas others with apparently similar conformations are not affected. Subtle structural and deformability features define the key properties used by RNase H to discriminate between duplexes.
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Affiliation(s)
- Agnes Noy
- Joint IRB-BSC Research Program in Computational Biology, Institut de Recerca Biomèdica Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain
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47
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Pande V, Nilsson L. Insights into structure, dynamics and hydration of locked nucleic acid (LNA) strand-based duplexes from molecular dynamics simulations. Nucleic Acids Res 2008; 36:1508-16. [PMID: 18203740 PMCID: PMC2275159 DOI: 10.1093/nar/gkm1182] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Locked nucleic acid (LNA) is a chemically modified nucleic acid with its sugar ring locked in an RNA-like (C3′-endo) conformation. LNAs show extraordinary thermal stabilities when hybridized with DNA, RNA or LNA itself. We performed molecular dynamics simulations on five isosequential duplexes (LNA–DNA, LNA–LNA, LNA–RNA, RNA–DNA and RNA–RNA) in order to characterize their structure, dynamics and hydration. Structurally, the LNA–DNA and LNA–RNA duplexes are found to be similar to regular RNA–DNA and RNA–RNA duplexes, whereas the LNA–LNA duplex is found to have its helix partly unwound and does not resemble RNA–RNA duplex in a number of properties. Duplexes with an LNA strand have on average longer interstrand phosphate distances compared to RNA–DNA and RNA–RNA duplexes. Furthermore, intrastrand phosphate distances in LNA strands are found to be shorter than in DNA and slightly shorter than in RNA. In case of induced sugar puckering, LNA is found to tune the sugar puckers in partner DNA strand toward C3′-endo conformations more efficiently than RNA. The LNA–LNA duplex has lesser backbone flexibility compared to the RNA–RNA duplex. Finally, LNA is less hydrated compared to DNA or RNA but is found to have a well-organized water structure.
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Affiliation(s)
- Vineet Pande
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge SE-14157, Sweden
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48
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Priyakumar UD, Mackerell AD. Atomic detail investigation of the structure and dynamics of DNA.RNA hybrids: a molecular dynamics study. J Phys Chem B 2008; 112:1515-24. [PMID: 18197661 DOI: 10.1021/jp709827m] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA.RNA hybrid duplexes are biologically important molecules and are shown to have potential therapeutic properties. To investigate the relationship between structures, energetics, solvation and RNase H activity of hybrid duplexes in comparison with pure DNA and RNA duplexes, a molecular dynamics study using the CHARMM27 force field was undertaken. The structural properties of all four nucleic acids considered are in very good agreement with the experimental data. The backbone dihedral angles and the puckering of the (deoxy)ribose indicate that the purine rich strands retain their A-/B-like properties but the pyrimidine rich DNA strand undergoes A-B conformational transitions. The minor groove widths of the hybrid structures are narrower than those in the RNA duplex, a requirement for RNase H binding. In addition, sampling of noncanonical phosphodiester backbone dihedrals by the DNA strands, differential solvation properties and helical properties, most notably rise, are suggested to contribute to hybrids being RNase H substrates. Differential RNase H activity toward hybrids containing purine versus pyrimidine rich RNA strands is suggested to be due to sampling of values of the phosphodiester backbone dihedrals in the DNA strands. Notably, the present results indicate that hybrids have decreased flexibility as compared to RNA, in contrast to previous reports.
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Affiliation(s)
- U Deva Priyakumar
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, USA
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49
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Pérez A, Marchán I, Svozil D, Sponer J, Cheatham TE, Laughton CA, Orozco M. Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers. Biophys J 2007; 92:3817-29. [PMID: 17351000 PMCID: PMC1868997 DOI: 10.1529/biophysj.106.097782] [Citation(s) in RCA: 1775] [Impact Index Per Article: 104.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2006] [Accepted: 02/05/2007] [Indexed: 11/18/2022] Open
Abstract
We present here the parmbsc0 force field, a refinement of the AMBER parm99 force field, where emphasis has been made on the correct representation of the alpha/gamma concerted rotation in nucleic acids (NAs). The modified force field corrects overpopulations of the alpha/gamma = (g+,t) backbone that were seen in long (more than 10 ns) simulations with previous AMBER parameter sets (parm94-99). The force field has been derived by fitting to high-level quantum mechanical data and verified by comparison with very high-level quantum mechanical calculations and by a very extensive comparison between simulations and experimental data. The set of validation simulations includes two of the longest trajectories published to date for the DNA duplex (200 ns each) and the largest variety of NA structures studied to date (15 different NA families and 97 individual structures). The total simulation time used to validate the force field includes near 1 mus of state-of-the-art molecular dynamics simulations in aqueous solution.
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Affiliation(s)
- Alberto Pérez
- Molecular Modeling and Bioinformatics Unit, Institut de Recerca Biomèdica & Instituto Nacional de Bioinformática, Parc Científic de Barcelona, Barcelona 08028, Spain
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50
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Kawai K, Osakada Y, Sugimoto A, Fujitsuka M, Majima T. Hole Transfer Rates in A-Form DNA/2′-OMeRNA Hybrid. Chemistry 2007; 13:2386-91. [PMID: 17163564 DOI: 10.1002/chem.200601210] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The hole transfer rates in the DNA/DNA B-form duplex and DNA/2'-OMeRNA A-form duplex were measured which occurred in the time range of approximately 100 micros. The hole transfer rates in the A-form duplexes were slower and more strongly dependent on the temperature compared to those in the B-form duplexes, suggesting that the A-form is more rigid than the B-form duplex in this time scale.
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Affiliation(s)
- Kiyohiko Kawai
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan.
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