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Jakhlal J, Denhez C, Coantic-Castex S, Martinez A, Harakat D, Douki T, Guillaume D, Clivio P. SN- and NS-puckered sugar conformers are precursors of the (6-4) photoproduct in thymine dinucleotide. Org Biomol Chem 2022; 20:2300-2307. [PMID: 35253821 DOI: 10.1039/d2ob00044j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Some amount of furanose in a southern conformation, possibly in both, but certainly in one of the two adjacent nucleotides of a dipyrimidine site, is necessary for (6-4) photoproduct formation in oligonucleotides. To explore the necessity, role, and most favorable location of each South sugar conformer in the formation of the (6-4) adduct in the thymine dinucleotide TpT, the photochemical behavior of two synthetic analogues, in which the South sugar conformation is prohibited for one of their two sugars, has been examined. Herein, we experimentally demonstrate that the presence of one sugar presenting some amount of South puckering, at any of the extremities, is sufficient to trigger (6-4) adduct formation. Nonetheless, the photochemical behavior of the dinucleotide with a South-puckered conformation at the 5'-end, mimics more closely that of TpT. In addition, using the 5' North 3' South-dilocked dinucleotide, we demonstrate that the flexibility of the South pucker at the 3'-end has little influence on the (6-4) adduct formation.
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Affiliation(s)
- Jouda Jakhlal
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51100 Reims, France.
| | - Clément Denhez
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51100 Reims, France.
- MaSCA, P3M, UFR des Sciences Exactes et Naturelles, 51100 Reims, France
| | - Stéphanie Coantic-Castex
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51100 Reims, France.
| | - Agathe Martinez
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR des Sciences Exactes et Naturelles, 51100 Reims, France
| | - Dominique Harakat
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR des Sciences Exactes et Naturelles, 51100 Reims, France
| | - Thierry Douki
- Université Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, 38000 Grenoble, France
| | - Dominique Guillaume
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51100 Reims, France.
| | - Pascale Clivio
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51100 Reims, France.
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Teng D, Wei X, Li J, Gao H, Zhang M, Zong Z. One‐pot Facile Synthesis of Multifunctional Conjugated Microporous Polymers
via
Suzuki‐Miyaura Coupling Reaction. ChemistrySelect 2020. [DOI: 10.1002/slct.201904303] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Dao‐Guang Teng
- Key Laboratory of Coal Processing and Efficient UtilizationMinistry of EducationChina University of Mining & Technology Xuzhou 221116 Jiangsu China
| | - Xian‐Yong Wei
- Key Laboratory of Coal Processing and Efficient UtilizationMinistry of EducationChina University of Mining & Technology Xuzhou 221116 Jiangsu China
| | - Jia‐Hao Li
- Key Laboratory of Coal Processing and Efficient UtilizationMinistry of EducationChina University of Mining & Technology Xuzhou 221116 Jiangsu China
| | - Hua‐Shuai Gao
- Key Laboratory of Coal Processing and Efficient UtilizationMinistry of EducationChina University of Mining & Technology Xuzhou 221116 Jiangsu China
| | - Min Zhang
- Key Laboratory of Coal Processing and Efficient UtilizationMinistry of EducationChina University of Mining & Technology Xuzhou 221116 Jiangsu China
| | - Zhi‐Min Zong
- Key Laboratory of Coal Processing and Efficient UtilizationMinistry of EducationChina University of Mining & Technology Xuzhou 221116 Jiangsu China
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3
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Jing Z, Qi R, Thibonnier M, Ren P. Molecular Dynamics Study of the Hybridization between RNA and Modified Oligonucleotides. J Chem Theory Comput 2019; 15:6422-6432. [PMID: 31553600 PMCID: PMC6889957 DOI: 10.1021/acs.jctc.9b00519] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
MicroRNAs (miRNAs) are attractive drug candidates for many diseases as they can modulate the expression of gene networks. Recently, we discovered that DNAs targeting microRNA-22-3p (miR-22-3p) hold the potential for treating obesity and related metabolic disorders (type 2 diabetes mellitus, hyperlipidemia, and nonalcoholic fatty liver disease (NAFLD)) by turning fat-storing white adipocytes into fat-burning adipocytes. In this work, we explored the effects of chemical modifications, including phosphorothioate (PS), locked nucleic acid (LNA), and peptide nucleic acid (PNA), on the structure and energy of DNA analogs by using molecular dynamics (MD) simulations. To achieve a reliable prediction of the hybridization free energy, the AMOEBA polarizable force field and the free energy perturbation technique were employed. The calculated hybridization free energies are generally compatible with previous experiments. For LNA and PNA, the enhanced duplex stability can be explained by the preorganization mechanism, i.e., the single strands adopt stable helical structures similar to those in the duplex. For PS, the S and R isomers (Sp and Rp) have preferences for C2'-endo and C3'-endo sugar puckering conformations, respectively, and therefore Sp is less stable than Rp in DNA/RNA hybrids. In addition, the solvation penalty of Rp accounts for its destabilization effect. PS-LNA is similar to LNA as the sugar puckering is dominated by the locked sugar ring. This work demonstrated that MD simulations with polarizable force fields are useful for the understanding and design of modified nucleic acids.
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Affiliation(s)
- Zhifeng Jing
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712
| | - Rui Qi
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712
| | | | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712
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4
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The ability of locked nucleic acid oligonucleotides to pre-structure the double helix: A molecular simulation and binding study. PLoS One 2019; 14:e0211651. [PMID: 30753192 PMCID: PMC6372149 DOI: 10.1371/journal.pone.0211651] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 01/17/2019] [Indexed: 02/07/2023] Open
Abstract
Locked nucleic acid (LNA) oligonucleotides bind DNA target sequences forming Watson-Crick and Hoogsteen base pairs, and are therefore of interest for medical applications. To be biologically active, such an oligonucleotide has to efficiently bind the target sequence. Here we used molecular dynamics simulations and electrophoresis mobility shift assays to elucidate the relation between helical structure and affinity for LNA-containing oligonucleotides. In particular, we have studied how LNA substitutions in the polypyrimidine strand of a duplex (thus forming a hetero duplex, i.e. a duplex with a DNA polypurine strand and an LNA/DNA polypyrimidine strand) enhance triplex formation. Based on seven polypyrimidine single strand oligonucleotides, having LNAs in different positions and quantities, we show that alternating LNA with one or more non-modified DNA nucleotides pre-organizes the hetero duplex toward a triple-helical-like conformation. This in turn promotes triplex formation, while consecutive LNAs distort the duplex structure disfavoring triplex formation. The results support the hypothesis that a pre-organization in the hetero duplex structure enhances the binding of triplex forming oligonucleotides. Our findings may serve as a criterion in the design of new tools for efficient oligonucleotide hybridization.
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5
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Nilsson L, Villa A. Modeling and Simulation of Oligonucleotide Hybrids: Outlining a Strategy. Methods Mol Biol 2019; 2036:113-126. [PMID: 31410793 DOI: 10.1007/978-1-4939-9670-4_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Molecular dynamics simulations with a state-of-the-art force field provide an atomistic detailed description of the structural and thermodynamic features of biomolecules. Effects of chemical modifications and of the environment such as sequence, solvent, and ionic strength can explicitly be taken into account. Molecular simulation techniques can also provide insight in change in binding affinity, in protonation (pKa shift) and tautomeric propensity due to changes in the environment or in the molecular system. The quality and reliability of a simulation depend on the quality of the force field and on the reproducibility of the data, and validation depends on the availability of suitable experimental data. Here, we describe the workflow to investigate oligonucleotide hybrids using molecular simulation including hardware and software information.
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Affiliation(s)
- Lennart Nilsson
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Alessandra Villa
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.
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Abstract
BACKGROUND Numerous different types of variations can occur in DNA and have diverse effects and consequences. The Variation Ontology (VariO) was developed for systematic descriptions of variations and their effects at DNA, RNA and protein levels. RESULTS VariO use and terms for DNA variations are described in depth. VariO provides systematic names for variation types and detailed descriptions for changes in DNA function, structure and properties. The principles of VariO are presented along with examples from published articles or databases, most often in relation to human diseases. VariO terms describe local DNA changes, chromosome number and structure variants, chromatin alterations, as well as genomic changes, whether of genetic or non-genetic origin. CONCLUSIONS DNA variation systematics facilitates unambiguous descriptions of variations and their effects and further reuse and integration of data from different sources by both human and computers.
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Affiliation(s)
- Mauno Vihinen
- Department of Experimental Medical Science, Lund University, BMC B13, SE-22184, Lund, Sweden.
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Hartono YD, Xu Y, Karshikoff A, Nilsson L, Villa A. Modeling p K Shift in DNA Triplexes Containing Locked Nucleic Acids. J Chem Inf Model 2018. [PMID: 29537270 DOI: 10.1021/acs.jcim.7b00741] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The protonation states for nucleic acid bases are difficult to assess experimentally. In the context of DNA triplex, the protonation state of cytidine in the third strand is particularly important, because it needs to be protonated in order to form Hoogsteen hydrogen bonds. A sugar modification, locked nucleic acid (LNA), is widely used in triplex forming oligonucleotides to target sites in the human genome. In this study, the parameters for LNA are developed in line with the CHARMM nucleic acid force field and validated toward the available structural experimental data. In conjunction, two computational methods were used to calculate the protonation state of the third strand cytidine in various DNA triplex environments: λ-dynamics and multiple pH regime. Both approaches predict p K of this cytidine shifted above physiological pH when cytidine is in the third strand in a triplex environment. Both methods show an upshift due to cytidine methylation, and a small downshift when the sugar configuration is locked. The predicted p K values for cytidine in DNA triplex environment can inform the design of better-binding oligonucleotides.
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Affiliation(s)
- Yossa Dwi Hartono
- Department of Biosciences and Nutrition , Karolinska Institutet , SE-141 83 Huddinge , Sweden.,Division of Structural Biology and Biochemistry, School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , Singapore 637551
| | - You Xu
- Department of Biosciences and Nutrition , Karolinska Institutet , SE-141 83 Huddinge , Sweden
| | - Andrey Karshikoff
- Department of Biosciences and Nutrition , Karolinska Institutet , SE-141 83 Huddinge , Sweden
| | - Lennart Nilsson
- Department of Biosciences and Nutrition , Karolinska Institutet , SE-141 83 Huddinge , Sweden
| | - Alessandra Villa
- Department of Biosciences and Nutrition , Karolinska Institutet , SE-141 83 Huddinge , Sweden
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8
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Xu Y, Villa A, Nilsson L. The free energy of locking a ring: Changing a deoxyribonucleoside to a locked nucleic acid. J Comput Chem 2017; 38:1147-1157. [PMID: 28101966 PMCID: PMC5434909 DOI: 10.1002/jcc.24692] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 11/01/2016] [Accepted: 11/08/2016] [Indexed: 01/09/2023]
Abstract
Locked nucleic acid (LNA), a modified nucleoside which contains a bridging group across the ribose ring, improves the stability of DNA/RNA duplexes significantly, and therefore is of interest in biotechnology and gene therapy applications. In this study, we investigate the free energy change between LNA and DNA nucleosides. The transformation requires the breaking of the bridging group across the ribose ring, a problematic transformation in free energy calculations. To address this, we have developed a 3-step (easy to implement) and a 1-step protocol (more efficient, but more complicated to setup), for single and dual topologies in classical molecular dynamics simulations, using the Bennett Acceptance Ratio method to calculate the free energy. We validate the approach on the solvation free energy difference for the nucleosides thymidine, cytosine, and 5-methyl-cytosine. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
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Affiliation(s)
- You Xu
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, SE-141 83, Sweden
| | - Alessandra Villa
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, SE-141 83, Sweden
| | - Lennart Nilsson
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, SE-141 83, Sweden
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Suresh G, Padhi S, Patil I, Priyakumar UD. Urea Mimics Nucleobases by Preserving the Helical Integrity of B-DNA Duplexes via Hydrogen Bonding and Stacking Interactions. Biochemistry 2016; 55:5653-5664. [DOI: 10.1021/acs.biochem.6b00309] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Gorle Suresh
- Center for Computational
Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500032, India
| | - Siladitya Padhi
- Center for Computational
Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500032, India
| | - Indrajit Patil
- Center for Computational
Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500032, India
| | - U. Deva Priyakumar
- Center for Computational
Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500032, India
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10
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Suresh G, Srinivasan H, Nanda S, Priyakumar UD. Ligand-Induced Stabilization of a Duplex-like Architecture Is Crucial for the Switching Mechanism of the SAM-III Riboswitch. Biochemistry 2016; 55:3349-60. [PMID: 27249101 DOI: 10.1021/acs.biochem.5b00973] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Riboswitches are structured RNA motifs that control gene expression by sensing the concentrations of specific metabolites and make up a promising new class of antibiotic targets. S-Adenosylmethionine (SAM)-III riboswitch, mainly found in lactic acid bacteria, is involved in regulating methionine and SAM biosynthetic pathways. SAM-III riboswitch regulates the gene expression by switching the translation process on and off with respect to the absence and presence of the SAM ligand, respectively. In this study, an attempt is made to understand the key conformational transitions involved in ligand binding using atomistic molecular dynamics (MD) simulations performed in an explicit solvent environment. G26 is found to recognize the SAM ligand by forming hydrogen bonds, whereas the absence of the ligand leads to opening of the binding pocket. Consistent with experimental results, the absence of the SAM ligand weakens the base pairing interactions between the nucleobases that are part of the Shine-Dalgarno (SD) and anti-Shine-Dalgarno (aSD) sequences, which in turn facilitates recognition of the SD sequence by ribosomes. Detailed analysis reveals that a duplex-like structure formed by nucleotides from different parts of the RNA and the adenine base of the ligand is crucial for the stability of the completely folded state in the presence of the ligand. Previous experimental studies have shown that the SAM-III riboswitch exists in equilibrium between the unfolded and partially folded states in the absence of the ligand, which completely folds upon binding of the ligand. Comparison of the results presented here to the available experimental data indicates the structures obtained using the MD simulations resemble the partially folded state. Thus, this study provides a detailed understanding of the fully and partially folded structures of the SAM-III riboswitch in the presence and absence of the ligand, respectively. This study hypothesizes a dual role for the SAM ligand, which facilitates conformational switching between partially and fully folded states by forming a stable duplex-like structure and strengthening the interactions between SD and aSD nucleotides.
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Affiliation(s)
- Gorle Suresh
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology , Hyderabad 500 032, India
| | - Harini Srinivasan
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology , Hyderabad 500 032, India
| | - Shivani Nanda
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology , Hyderabad 500 032, India
| | - U Deva Priyakumar
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology , Hyderabad 500 032, India
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11
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SURESH GORLE, PRIYAKUMAR UDEVA. Atomistic details of the molecular recognition of DNA-RNA hybrid duplex by ribonuclease H enzyme. J CHEM SCI 2015. [DOI: 10.1007/s12039-015-0942-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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12
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Niemietz C, Chandhok G, Schmidt H. Therapeutic Oligonucleotides Targeting Liver Disease: TTR Amyloidosis. Molecules 2015; 20:17944-75. [PMID: 26437390 PMCID: PMC6332041 DOI: 10.3390/molecules201017944] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 09/23/2015] [Accepted: 09/23/2015] [Indexed: 12/13/2022] Open
Abstract
The liver has become an increasingly interesting target for oligonucleotide therapy. Mutations of the gene encoding transthyretin (TTR), expressed in vast amounts by the liver, result in a complex degenerative disease, termed familial amyloid polyneuropathy (FAP). Misfolded variants of TTR are linked to the establishment of extracellular protein deposition in various tissues, including the heart and the peripheral nervous system. Recent progress in the chemistry and formulation of antisense (ASO) and small interfering RNA (siRNA) designed for a knockdown of TTR mRNA in the liver has allowed to address the issue of gene-specific molecular therapy in a clinical setting of FAP. The two therapeutic oligonucleotides bind to RNA in a sequence specific manner but exploit different mechanisms. Here we describe major developments that have led to the advent of therapeutic oligonucleotides for treatment of TTR-related disease.
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MESH Headings
- Amyloid Neuropathies, Familial/genetics
- Amyloid Neuropathies, Familial/therapy
- Animals
- Clinical Studies as Topic
- Drug Evaluation, Preclinical
- Gene Silencing
- Genetic Therapy
- Humans
- Liver Diseases/genetics
- Liver Diseases/therapy
- Mutation
- Oligonucleotides/administration & dosage
- Oligonucleotides/chemistry
- Oligonucleotides/genetics
- Oligonucleotides/therapeutic use
- Oligonucleotides, Antisense/administration & dosage
- Oligonucleotides, Antisense/chemistry
- Oligonucleotides, Antisense/genetics
- Oligonucleotides, Antisense/therapeutic use
- Prealbumin/genetics
- RNA Interference
- RNA, Small Interfering/administration & dosage
- RNA, Small Interfering/chemistry
- RNA, Small Interfering/genetics
- RNA, Small Interfering/therapeutic use
- Treatment Outcome
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Affiliation(s)
- Christoph Niemietz
- Klinik für Transplantationsmedizin, Universitätsklinikum Münster, Albert-Schweitzer-Campus 1, Gebäude A14, D-48149 Münster, Germany.
| | - Gursimran Chandhok
- Klinik für Transplantationsmedizin, Universitätsklinikum Münster, Albert-Schweitzer-Campus 1, Gebäude A14, D-48149 Münster, Germany.
| | - Hartmut Schmidt
- Klinik für Transplantationsmedizin, Universitätsklinikum Münster, Albert-Schweitzer-Campus 1, Gebäude A14, D-48149 Münster, Germany.
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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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