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Roy S, Bhattacharya S. An in silico approach to evaluate the bindings of natural flavonoids and RNA-DNA hybrids. J Biomol Struct Dyn 2023:1-8. [PMID: 37922129 DOI: 10.1080/07391102.2023.2275184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/20/2023] [Indexed: 11/05/2023]
Abstract
Flavonoids, low molecular weight polyphenolic compounds, are important natural products that belong to plant secondary metabolites. They have diverse biomedical applications such as antioxidative, anti-inflammatory, enzyme inhibitory, antimutagenic, anticarcinogenic, aromatase inhibitory effects, etc. Some of the flavonoids have been exported for bindings with certain DNA and tRNA structures both experimentally and computationally. RNA-DNA hybrid (RDH) falls into an important category of noncanonical nucleic acid structures that have many important biological functions. We have investigated the interaction of RDH structures with some of the dietary flavonoids with the aid of computational methods such as docking and molecular dynamics simulation. The presence of the - OH group on the ligand and the availability of a proper binding pocket in the macromolecule are the two main factors driving the binding preference. Thus, this computationally guided report explains the binding of the flavonoids with RDH structures to assist the researchers in designing noncanonical nucleic acid-targeted drug molecules.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Soma Roy
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata, India
| | - Santanu Bhattacharya
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata, India
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, India
- Department of Chemistry, Indian Institute of Science, Education & Research, Tirupati, India
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2
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A DNA packaging motor inchworms along one strand allowing it to adapt to alternative double-helical structures. Nat Commun 2021; 12:3439. [PMID: 34103515 PMCID: PMC8187434 DOI: 10.1038/s41467-021-23725-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 04/22/2021] [Indexed: 01/29/2023] Open
Abstract
Ring ATPases that translocate disordered polymers possess lock-washer architectures that they impose on their substrates during transport via a hand-over-hand mechanism. Here, we investigate the operation of ring motors that transport ordered, helical substrates, such as the bacteriophage ϕ29 dsDNA packaging motor. This pentameric motor alternates between an ATP loading dwell and a hydrolysis burst wherein it packages one turn of DNA in four steps. When challenged with DNA-RNA hybrids and dsRNA, the motor matches its burst to the shorter helical pitches, keeping three power strokes invariant while shortening the fourth. Intermittently, the motor loses grip on the RNA-containing substrates, indicating that it makes optimal load-bearing contacts with dsDNA. To rationalize these observations, we propose a helical inchworm translocation mechanism in which, during each cycle, the motor increasingly adopts a lock-washer structure during the ATP loading dwell and successively regains its planar form with each power stroke during the burst. Ring ATPase translocases that operate on disordered substrates adopt lockwasher architectures and use a hand-over-hand mechanism. By challenging the dsDNA packaging motor of bacteriophage ϕ29 with hybrid and dsRNA, the authors propose that the motor cycles between planar and lock-washer structures.
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Liu T, Yu T, Zhang S, Wang Y, Zhang W. Thermodynamic and kinetic properties of a single base pair in A-DNA and B-DNA. Phys Rev E 2021; 103:042409. [PMID: 34005973 DOI: 10.1103/physreve.103.042409] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 03/27/2021] [Indexed: 11/07/2022]
Abstract
Double stranded DNA can adopt different forms, the so-called A-, B-, and Z-DNA, which play different biological roles. In this work, the thermodynamic and the kinetic parameters for the base-pair closing and opening in A-DNA and B-DNA were calculated by all-atom molecular dynamics simulations at different temperatures. The thermodynamic parameters of the base pair in B-DNA were in good agreement with the experimental results. The free energy barrier of breaking a single base stack results from the enthalpy increase ΔH caused by the disruption of hydrogen bonding and base-stacking interactions, as well as water and base interactions. The free energy barrier of base pair closing comes from the unfavorable entropy loss ΔS caused by the restriction of torsional angles and hydration. It was found that the enthalpy change ΔH and the entropy change ΔS for the base pair in A-DNA are much larger than those in B-DNA, and the transition rates between the opening and the closing state for the base pair in A-DNA are much slower than those in B-DNA. The large difference of the enthalpy and entropy change for forming the base pair in A-DNA and B-DNA results from different hydration in A-DNA and B-DNA. The hydration pattern observed around DNA is an accompanying process for forming the base pair, rather than a follow-up of the conformation.
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Affiliation(s)
- Taigang Liu
- Department of Physics Wuhan University, Wuhan 430072, China.,School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China
| | - Ting Yu
- Department of Physics Wuhan University, Wuhan 430072, China
| | - Shuhao Zhang
- Department of Physics Wuhan University, Wuhan 430072, China
| | - Yujie Wang
- Department of Physics Wuhan University, Wuhan 430072, China.,Department of Physics and Telecommunication Engineering, Zhoukou Normal University, Zhoukou 466000, China
| | - Wenbing Zhang
- Department of Physics Wuhan University, Wuhan 430072, China
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4
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Krupkin M, Jackson LN, Ha B, Puglisi EV. Advances in understanding the initiation of HIV-1 reverse transcription. Curr Opin Struct Biol 2020; 65:175-183. [PMID: 32916568 PMCID: PMC9973426 DOI: 10.1016/j.sbi.2020.07.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/12/2020] [Accepted: 07/21/2020] [Indexed: 01/18/2023]
Abstract
Many viruses, including Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and Human Immunodeficiency Virus (HIV), use RNA as their genetic material. How viruses harness RNA structure and RNA-protein interactions to control their replication remains obscure. Recent advances in the characterization of HIV-1 reverse transcriptase, the enzyme that converts its single-stranded RNA genome into a double-stranded DNA copy, reveal how the reverse transcription complex evolves during initiation. Here we highlight these advances in HIV-1 structural biology and discuss how they are furthering our understanding of HIV and related ribonucleoprotein complexes implicated in viral disease.
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Affiliation(s)
- Miri Krupkin
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lynnette Nthenya Jackson
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Betty Ha
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Elisabetta Viani Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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5
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Yang D, Liu W, Deng X, Xie W, Chen H, Zhong Z, Ma J. GC-Content Dependence of Elastic and Overstretching Properties of DNA:RNA Hybrid Duplexes. Biophys J 2020; 119:852-861. [PMID: 32738216 DOI: 10.1016/j.bpj.2020.06.034] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 05/22/2020] [Accepted: 06/18/2020] [Indexed: 01/25/2023] Open
Abstract
DNA:RNA hybrid duplex plays important roles in various biological processes. Both its structural stability and interactions with proteins are highly sequence dependent. In this study, we utilize homebuilt optical tweezers to investigate how GC contents in the sequence influence the structural and mechanical properties of DNA:RNA hybrid by measuring its contour length, elasticities, and overstretching dynamics. Our results support that the DNA:RNA hybrid adopts a conformation between the A- and B-form helix, and the GC content does not affect its structural and elastic parameters obviously when varying from 40 to 60% before the overstretching transition of DNA:RNA hybrid occurs. In the overstretching transition, however, our study unravels significant heterogeneity and strong sequence dependence, suggesting the presence of a highly dynamic competition between the two processes, namely the S-form duplex formation (nonhysteretic) and the unpeeling (hysteretic). Analyzing the components left in DNA:RNA hybrid after the overstretching transition suggests that the RNA strand is more easily unpeeled than the DNA strand, whereas an increase in the GC content from 40 to 60% can significantly reduce unpeeling. Large hysteresis is observed between the stretching and relaxation processes, which is also quantitatively correlated with the percentage of unpeeling in the DNA:RNA duplex. Increasing in both the salt concentration and GC content can effectively reduce the hysteresis with the latter being more significant. Together, our study reveals that the mechanical properties of DNA:RNA hybrid duplexes are significantly different from double-stranded DNA and double-stranded RNA, and its overstretching behavior is highly sequence dependent. These results should be taken into account in the future studies on DNA:RNA-hybrid-related functional structures and motor proteins.
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Affiliation(s)
- Dongni Yang
- School of Physics, Sun Yat-sen University, Guangzhou, Guangdong, China; State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Wenzhao Liu
- School of Physics, Sun Yat-sen University, Guangzhou, Guangdong, China; State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiangyu Deng
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Wei Xie
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Hu Chen
- Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Department of Physics, Xiamen University, Xiamen, Fujian, China
| | - Zhensheng Zhong
- School of Physics, Sun Yat-sen University, Guangzhou, Guangdong, China; State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou, Guangdong, China.
| | - Jie Ma
- School of Physics, Sun Yat-sen University, Guangzhou, Guangdong, China; State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou, Guangdong, China.
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6
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7
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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 DOI: 10.1016/j.bpj.2019.05.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [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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8
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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: 28] [Impact Index Per Article: 4.7] [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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9
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Hara RI, Maeda Y, Fujimaki H, Wada T. Enhancement in RNase H activity of a DNA/RNA hybrid duplex using artificial cationic oligopeptides. Chem Commun (Camb) 2018; 54:8526-8529. [DOI: 10.1039/c8cc04082f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
This study assessed the effects of artificial cationic oligopeptides on a DNA/RNA hybrid duplex.
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Affiliation(s)
- Rintaro Iwata Hara
- Faculty of Pharmaceutical Sciences
- Tokyo University of Science
- Noda
- Japan
- Department of Neurology and Neurological Science
| | - Yusuke Maeda
- Faculty of Pharmaceutical Sciences
- Tokyo University of Science
- Noda
- Japan
| | - Haruna Fujimaki
- Graduate School of Frontier Sciences
- The University of Tokyo
- Kashiwa
- Japan
| | - Takeshi Wada
- Faculty of Pharmaceutical Sciences
- Tokyo University of Science
- Noda
- Japan
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10
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Understanding B-DNA to A-DNA transition in the right-handed DNA helix: Perspective from a local to global transition. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017; 128:63-73. [DOI: 10.1016/j.pbiomolbio.2017.05.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 04/16/2017] [Accepted: 05/23/2017] [Indexed: 01/19/2023]
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11
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Anosova I, Kowal EA, Dunn MR, Chaput JC, Van Horn WD, Egli M. The structural diversity of artificial genetic polymers. Nucleic Acids Res 2015; 44:1007-21. [PMID: 26673703 PMCID: PMC4756832 DOI: 10.1093/nar/gkv1472] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 11/30/2015] [Indexed: 11/13/2022] Open
Abstract
Synthetic genetics is a subdiscipline of synthetic biology that aims to develop artificial genetic polymers (also referred to as xeno-nucleic acids or XNAs) that can replicate in vitro and eventually in model cellular organisms. This field of science combines organic chemistry with polymerase engineering to create alternative forms of DNA that can store genetic information and evolve in response to external stimuli. Practitioners of synthetic genetics postulate that XNA could be used to safeguard synthetic biology organisms by storing genetic information in orthogonal chromosomes. XNA polymers are also under active investigation as a source of nuclease resistant affinity reagents (aptamers) and catalysts (xenozymes) with practical applications in disease diagnosis and treatment. In this review, we provide a structural perspective on known antiparallel duplex structures in which at least one strand of the Watson-Crick duplex is composed entirely of XNA. Currently, only a handful of XNA structures have been archived in the Protein Data Bank as compared to the more than 100 000 structures that are now available. Given the growing interest in xenobiology projects, we chose to compare the structural features of XNA polymers and discuss their potential to access new regions of nucleic acid fold space.
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Affiliation(s)
- Irina Anosova
- The Biodesign Institute, Virginia G. Piper Center for Personalized Diagnostics, School of Molecular Sciences, Magnetic Resonance Research Center, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Ewa A Kowal
- Department of Biochemistry, Center for Structural Biology, and Vanderbilt Ingram Cancer Center, Vanderbilt University, School of Medicine, Nashville, TN 37232-0146, USA
| | - Matthew R Dunn
- Department of Pharmaceutical Sciences, University of California-Irvine, Irvine, CA 92697, USA
| | - John C Chaput
- Department of Pharmaceutical Sciences, University of California-Irvine, Irvine, CA 92697, USA
| | - Wade D Van Horn
- The Biodesign Institute, Virginia G. Piper Center for Personalized Diagnostics, School of Molecular Sciences, Magnetic Resonance Research Center, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Martin Egli
- Department of Biochemistry, Center for Structural Biology, and Vanderbilt Ingram Cancer Center, Vanderbilt University, School of Medicine, Nashville, TN 37232-0146, USA
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12
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Davis RR, Shaban NM, Perrino FW, Hollis T. Crystal structure of RNA-DNA duplex provides insight into conformational changes induced by RNase H binding. Cell Cycle 2015; 14:668-73. [PMID: 25664393 DOI: 10.4161/15384101.2014.994996] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
RNA-DNA hybrids play essential roles in a variety of biological processes, including DNA replication, transcription, and viral integration. Ribonucleotides incorporated within DNA are hydrolyzed by RNase H enzymes in a removal process that is necessary for maintaining genomic stability. In order to understand the structural determinants involved in recognition of a hybrid substrate by RNase H we have determined the crystal structure of a dodecameric non-polypurine/polypyrimidine tract RNA-DNA duplex. A comparison to the same sequence bound to RNase H, reveals structural changes to the duplex that include widening of the major groove to 12.5 Å from 4.2 Å and decreasing the degree of bending along the axis which may play a crucial role in the ribonucleotide recognition and cleavage mechanism within RNase H. This structure allows a direct comparison to be made about the conformational changes induced in RNA-DNA hybrids upon binding to RNase H and may provide insight into how dysfunction in the endonuclease causes disease.
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Affiliation(s)
- Ryan R Davis
- a Department of Biochemistry; Center for Structural Biology ; Wake Forest School of Medicine ; Winston-Salem , NC USA
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13
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Sun Y, Borbat PP, Grigoryants VM, Myers WK, Freed JH, Scholes CP. Pulse dipolar ESR of doubly labeled mini TAR DNA and its annealing to mini TAR RNA. Biophys J 2015; 108:893-902. [PMID: 25692594 DOI: 10.1016/j.bpj.2014.12.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 11/07/2014] [Accepted: 12/03/2014] [Indexed: 12/27/2022] Open
Abstract
Pulse dipolar electron-spin resonance in the form of double electron electron resonance was applied to strategically placed, site-specifically attached pairs of nitroxide spin labels to monitor changes in the mini TAR DNA stem-loop structure brought on by the HIV-1 nucleocapsid protein NCp7. The biophysical structural evidence was at Ångstrom-level resolution under solution conditions not amenable to crystallography or NMR. In the absence of complementary TAR RNA, double labels located in both the upper and the lower stem of mini TAR DNA showed in the presence of NCp7 a broadened distance distribution between the points of attachment, and there was evidence for several conformers. Next, when equimolar amounts of mini TAR DNA and complementary mini TAR RNA were present, NCp7 enhanced the annealing of their stem-loop structures to form duplex DNA-RNA. When duplex TAR DNA-TAR RNA formed, double labels initially located 27.5 Å apart at the 3'- and 5'-termini of the 27-base mini TAR DNA relocated to opposite ends of a 27 bp RNA-DNA duplex with 76.5 Å between labels, a distance which was consistent with the distance between the two labels in a thermally annealed 27-bp TAR DNA-TAR RNA duplex. Different sets of double labels initially located 26-27 Å apart in the mini TAR DNA upper stem, appropriately altered their interlabel distance to ~35 Å when a 27 bp TAR DNA-TAR RNA duplex formed, where the formation was caused either through NCp7-induced annealing or by thermal annealing. In summary, clear structural evidence was obtained for the fraying and destabilization brought on by NCp7 in its biochemical function as an annealing agent and for the detailed structural change from stem-loop to duplex RNA-DNA when complementary RNA was present.
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Affiliation(s)
- Yan Sun
- Department of Chemistry, University at Albany, State University of New York, Albany, New York
| | - Peter P Borbat
- Department of Chemistry and Chemical Biology and ACERT, Cornell University, Ithaca, New York
| | - Vladimir M Grigoryants
- Department of Chemistry, University at Albany, State University of New York, Albany, New York
| | - William K Myers
- Department of Chemistry, University at Albany, State University of New York, Albany, New York
| | - Jack H Freed
- Department of Chemistry and Chemical Biology and ACERT, Cornell University, Ithaca, New York
| | - Charles P Scholes
- Department of Chemistry, University at Albany, State University of New York, Albany, New York.
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14
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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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15
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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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16
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Johnson CN, Spring AM, Sergueev D, Shaw BR, Germann MW. Structural basis of the RNase H1 activity on stereo regular borano phosphonate DNA/RNA hybrids. Biochemistry 2011; 50:3903-12. [PMID: 21443203 DOI: 10.1021/bi200083d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Numerous DNA chemistries for improving oligodeoxynucleotide (ODN)-based RNA targeting have been explored. The majority of the modifications render the ODN/RNA target insensitive to RNase H1. Borano phosphonate ODN's are among the few modifications that are tolerated by RNase H1. To understand the effect of the stereochemistry of the BH(3) modification on the nucleic acid structure and RNase H1 enzyme activity, we have investigated two DNA/RNA hybrids containing either a R(P) or S(P) BH(3) modification by nuclear magnetic resonance (NMR) spectroscopy. T(M) studies show that the stabilities of R(P) and S(P) modified DNA/RNA hybrids are essentially identical (313.8 K) and similar to that of an unmodified control (312.9 K). The similarity is also reflected in the imino proton spectra. To characterize such similar structures, we used a large number of NMR restraints (including dipolar couplings and backbone torsion angles) to determine structural features that were important for RNase H1 activity. The final NMR structures exhibit excellent agreement with the data (total R(x) values of <6%) with helical properties between those of an A and B helix. Subtle backbone variations are observed in the DNA near the modification, while the RNA strands are relatively unperturbed. In the case of the S(P) modification, for which more perturbations are recorded, a slightly narrower minor groove is also obtained. Unique NOE base contacts localize the S(P) BH(3) group in the major groove while the R(P) BH(3) group points away from the DNA. However, this creates a potential clash of the R(P) BH(3) groups with important RNase H1 residues in a complex, while the S(P) BH(3) groups could be tolerated. We therefore predict that on the basis of our NMR structures a fully R(P) BH(3) DNA/RNA hybrid would not be a substrate for RNase H1.
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Affiliation(s)
- Christopher N Johnson
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302-3965, United States
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17
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Recognition of the unique structure of DNA:RNA hybrids. Biochimie 2008; 90:1026-39. [DOI: 10.1016/j.biochi.2008.04.011] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2008] [Accepted: 04/18/2008] [Indexed: 11/23/2022]
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18
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Affiliation(s)
- David M. Parish
- Departments of Chemistry and Structural Biology, State University of New York at Buffalo, Buffalo, New York 14260
| | - Thomas Szyperski
- Departments of Chemistry and Structural Biology, State University of New York at Buffalo, Buffalo, New York 14260
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19
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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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20
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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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21
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Juan ECM, Kondo J, Kurihara T, Ito T, Ueno Y, Matsuda A, Takénaka A. Crystal structures of DNA:DNA and DNA:RNA duplexes containing 5-(N-aminohexyl)carbamoyl-modified uracils reveal the basis for properties as antigene and antisense molecules. Nucleic Acids Res 2007; 35:1969-77. [PMID: 17341465 PMCID: PMC1874594 DOI: 10.1093/nar/gkl821] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Oligonucleotides containing 5-(N-aminohexyl)carbamoyl-modified uracils have promising features for applications as antigene and antisense therapies. Relative to unmodified DNA, oligonucleotides containing 5-(N-aminohexyl)carbamoyl-2′-deoxyuridine (NU) or 5-(N-aminohexyl)carbamoyl-2′-O-methyluridine (NUm), respectively exhibit increased binding affinity for DNA and RNA, and enhanced nuclease resistance. To understand the structural implications of NU and NUm substitutions, we have determined the X-ray crystal structures of DNA:DNA duplexes containing either NU or NUm and of DNA:RNA hybrid duplexes containing NUm. The aminohexyl chains are fixed in the major groove through hydrogen bonds between the carbamoyl amino groups and the uracil O4 atoms. The terminal ammonium cations on these chains could interact with the phosphate oxygen anions of the residues in the target strands. These interactions partly account for the increased target binding affinity and nuclease resistance. In contrast to NU, NUm decreases DNA binding affinity. This could be explained by the drastic changes in sugar puckering and in the minor groove widths and hydration structures seen in the NUm containing DNA:DNA duplex structure. The conformation of NUm, however, is compatible with the preferred conformation in DNA:RNA hybrid duplexes. Furthermore, the ability of NUm to render the duplexes with altered minor grooves may increase nuclease resistance and elicit RNase H activity.
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Affiliation(s)
| | | | | | - Takanori Ito
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan, Graduate School of Pharmaceutical Sciences, Hokkaido Universitym, Sapporo 060-0812, Japan and Faculty of Engineering, Gifu University, Gifu 501-1193, Japan
| | - Yoshihito Ueno
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan, Graduate School of Pharmaceutical Sciences, Hokkaido Universitym, Sapporo 060-0812, Japan and Faculty of Engineering, Gifu University, Gifu 501-1193, Japan
| | - Akira Matsuda
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan, Graduate School of Pharmaceutical Sciences, Hokkaido Universitym, Sapporo 060-0812, Japan and Faculty of Engineering, Gifu University, Gifu 501-1193, Japan
| | - Akio Takénaka
- *To whom correspondence should be addressed. +81 45 924 5709+81 45 924 5748
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22
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Noy A, Pérez A, Márquez M, Luque FJ, Orozco M. Structure, Recognition Properties, and Flexibility of the DNA·RNA Hybrid. J Am Chem Soc 2005; 127:4910-20. [PMID: 15796556 DOI: 10.1021/ja043293v] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Molecular dynamics is used to investigate the properties of the DNA.RNA hybrid in aqueous solution at room temperature. The structure of the hybrid is intermediate between A and B forms but, in general, closer to the canonical A-type helix. All the riboses exhibit North puckerings, while 2'-deoxyriboses exist in North, East, and South puckerings, the latter being the most populated one. The molecular recognition pattern of the DNA.RNA hybrid is a unique combination of those of normal DNA and RNA duplexes. Finally, the results obtained from essential dynamics and stiffness analysis demonstrate the large and very asymmetric flexibility of the hybrid and the strong predilection that each strand (DNA or RNA) has on the nature of their intrinsic motions in the corresponding homoduplexes. The implications of the unique structural and dynamic properties of the DNA.RNA hybrid on the mechanism of cleavage by RNase H are discussed.
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Affiliation(s)
- Agnes Noy
- Molecular Modeling and Bioinformatics Unit, Parc Cientific de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain
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23
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Beloglazova NG, Fabani MM, Zenkova MA, Bichenkova EV, Polushin NN, Sil'nikov VV, Douglas KT, Vlassov VV. Sequence-specific artificial ribonucleases. I. Bis-imidazole-containing oligonucleotide conjugates prepared using precursor-based strategy. Nucleic Acids Res 2004; 32:3887-97. [PMID: 15273275 PMCID: PMC506794 DOI: 10.1093/nar/gkh702] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2004] [Revised: 06/24/2004] [Accepted: 06/24/2004] [Indexed: 11/14/2022] Open
Abstract
Antisense oligonucleotide conjugates, bearing constructs with two imidazole residues, were synthesized using a precursor-based technique employing post-synthetic histamine functionalization of oligonucleotides bearing methoxyoxalamido precursors at the 5'-termini. The conjugates were assessed in terms of their cleavage activities using both biochemical assays and conformational analysis by molecular modelling. The oligonucleotide part of the conjugates was complementary to the T-arm of yeast tRNA(Phe) (44-60 nt) and was expected to deliver imidazole groups near the fragile sequence C61-ACA-G65 of the tRNA. The conjugates showed ribonuclease activity at neutral pH and physiological temperature resulting in complete cleavage of the target RNA, mainly at the C63-A64 phosphodiester bond. For some constructs, cleavage was completed within 1-2 h under optimal conditions. Molecular modelling was used to determine the preferred orientation(s) of the cleaving group(s) in the complexes of the conjugates with RNA target. Cleaving constructs bearing two imidazole residues were found to be conformationally highly flexible, adopting no preferred specific conformation. No interactions other than complementary base pairing between the conjugates and the target were found to be the factors stabilizing the 'active' cleaving conformation(s).
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Affiliation(s)
- Natalia G Beloglazova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of the Russian Academy of Sciences, Novosibirsk 630090, Russian Federation
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24
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Gyi JI, Gao D, Conn GL, Trent JO, Brown T, Lane AN. The solution structure of a DNA*RNA duplex containing 5-propynyl U and C; comparison with 5-Me modifications. Nucleic Acids Res 2003; 31:2683-93. [PMID: 12736318 PMCID: PMC156038 DOI: 10.1093/nar/gkg356] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The addition of the propynyl group at the 5 position of pyrimidine nucleotides is highly stabilising. We have determined the thermodynamic stability of the DNA.RNA hybrid r(GAAGAGAAGC)*d(GC(p)U(p)U(p)C(p)U(p) C(p)U(p)U(p)C) where p is the propynyl group at the 5 position and compared it with that of the unmodified duplex and the effects of methyl substitutions. The incorporation of the propyne group at the 5 position gives rise to a very large stabilisation of the hybrid duplex compared with the analogous 5-Me modification. The duplexes have been characterised by gel electrophoresis and NMR spectroscopy, which indicate that methyl substitutions have a smaller influence on local and global conformation than the propynyl groups. The increased NMR spectral dispersion of the propyne-modified duplex allowed a larger number of experimental restraints to be measured. Restrained molecular dynamics in a fully solvated system showed that the propyne modification leads to substantial conformational rearrangements stabilising a more A-like structure. The propynyl groups occupy a large part of the major groove and make favourable van der Waals interactions with their nearest neighbours and the atoms of the rings. This enhanced overlap may account at least in part for the increased thermodynamic stability. Furthermore, the simulations show a spine of hydration in the major groove as well as in the minor groove involving the RNA hydroxyl groups.
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Affiliation(s)
- Jeffrey I Gyi
- Division of Molecular Structure, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
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