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Ng C, Samanta A, Mandrup OA, Tsang E, Youssef S, Klausen LH, Dong M, Nijenhuis MAD, Gothelf KV. Folding Double-Stranded DNA into Designed Shapes with Triplex-Forming Oligonucleotides. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2302497. [PMID: 37311656 DOI: 10.1002/adma.202302497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/07/2023] [Indexed: 06/15/2023]
Abstract
The compaction and organization of genomic DNA is a central mechanism in eukaryotic cells, but engineered architectural control over double-stranded DNA (dsDNA) is notably challenging. Here, long dsDNA templates are folded into designed shapes via triplex-mediated self-assembly. Triplex-forming oligonucleotides (TFOs) bind purines in dsDNA via normal or reverse Hoogsteen interactions. In the triplex origami methodology, these non-canonical interactions are programmed to compact dsDNA (linear or plasmid) into well-defined objects, which demonstrate a variety of structural features: hollow and raster-filled, single- and multi-layered, with custom curvatures and geometries, and featuring lattice-free, square-, or honeycomb-pleated internal arrangements. Surprisingly, the length of integrated and free-standing dsDNA loops can be modulated with near-perfect efficiency; from hundreds down to only six bp (2 nm). The inherent rigidity of dsDNA promotes structural robustness and non-periodic structures of almost 25.000 nt are therefore formed with fewer unique starting materials, compared to other DNA-based self-assembly methods. Densely triplexed structures also resist degradation by DNase I. Triplex-mediated dsDNA folding is methodologically straightforward and orthogonal to Watson-Crick-based methods. Moreover, it enables unprecedented spatial control over dsDNA templates.
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Affiliation(s)
- Cindy Ng
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Central Denmark Region, 8000, Denmark
| | - Anirban Samanta
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Central Denmark Region, 8000, Denmark
| | - Ole Aalund Mandrup
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Central Denmark Region, 8000, Denmark
| | - Emily Tsang
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Central Denmark Region, 8000, Denmark
| | - Sarah Youssef
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Central Denmark Region, 8000, Denmark
| | - Lasse Hyldgaard Klausen
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Central Denmark Region, 8000, Denmark
| | - Mingdong Dong
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Central Denmark Region, 8000, Denmark
| | - Minke A D Nijenhuis
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Central Denmark Region, 8000, Denmark
| | - Kurt V Gothelf
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Central Denmark Region, 8000, Denmark
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Yuan F, Liu X, Tan L. Binding and stabilization effect of arene ruthenium(Ⅱ) polypyridyl complexes toward the triple-helical RNA poly(U)•poly(A)⁎poly(U). Inorganica Chim Acta 2022. [DOI: 10.1016/j.ica.2022.121140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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3
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Kunkler CN, Schiefelbein GE, O'Leary NJ, McCown PJ, Brown JA. A single natural RNA modification can destabilize a U•A-T-rich RNA•DNA-DNA triple helix. RNA (NEW YORK, N.Y.) 2022; 28:1172-1184. [PMID: 35820700 PMCID: PMC9380742 DOI: 10.1261/rna.079244.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
Recent studies suggest noncoding RNAs interact with genomic DNA, forming RNA•DNA-DNA triple helices, as a mechanism to regulate transcription. One way cells could regulate the formation of these triple helices is through RNA modifications. With over 140 naturally occurring RNA modifications, we hypothesize that some modifications stabilize RNA•DNA-DNA triple helices while others destabilize them. Here, we focus on a pyrimidine-motif triple helix composed of canonical U•A-T and C•G-C base triples. We employed electrophoretic mobility shift assays and microscale thermophoresis to examine how 11 different RNA modifications at a single position in an RNA•DNA-DNA triple helix affect stability: 5-methylcytidine (m5C), 5-methyluridine (m5U or rT), 3-methyluridine (m3U), pseudouridine (Ψ), 4-thiouridine (s4U), N 6-methyladenosine (m6A), inosine (I), and each nucleobase with 2'-O-methylation (Nm). Compared to the unmodified U•A-T base triple, some modifications have no significant change in stability (Um•A-T), some have ∼2.5-fold decreases in stability (m5U•A-T, Ψ•A-T, and s4U•A-T), and some completely disrupt triple helix formation (m3U•A-T). To identify potential biological examples of RNA•DNA-DNA triple helices controlled by an RNA modification, we searched RMVar, a database for RNA modifications mapped at single-nucleotide resolution, for lncRNAs containing an RNA modification within a pyrimidine-rich sequence. Using electrophoretic mobility shift assays, the binding of DNA-DNA to a 22-mer segment of human lncRNA Al157886.1 was destabilized by ∼1.7-fold with the substitution of m5C at known m5C sites. Therefore, the formation and stability of cellular RNA•DNA-DNA triple helices could be influenced by RNA modifications.
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Affiliation(s)
- Charlotte N Kunkler
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Grace E Schiefelbein
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Nathan J O'Leary
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Phillip J McCown
- Michigan Medicine, Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Jessica A Brown
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
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Chen YL, He W, Kirmizialtin S, Pollack L. Insights into the structural stability of major groove RNA triplexes by WAXS-guided MD simulations. CELL REPORTS. PHYSICAL SCIENCE 2022; 3:100971. [PMID: 35936555 PMCID: PMC9351628 DOI: 10.1016/j.xcrp.2022.100971] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
RNA triple helices are commonly observed tertiary motifs that are associated with critical biological functions, including signal transduction. Because the recognition of their biological importance is relatively recent, their full range of structural properties has not yet been elucidated. The integration of solution wide-angle X-ray scattering (WAXS) with molecular dynamics (MD) simulations, described here, provides a new way to capture the structures of major-groove RNA triplexes that evade crystallographic characterization. This method yields excellent agreement between measured and computed WAXS profiles and allows for an atomically detailed visualization of these motifs. Using correlation maps, the relationship between well-defined features in the scattering profiles and real space characteristics of RNA molecules is defined, including the subtle conformational variations in the double-stranded RNA upon the incorporation of a third strand by base triples. This readily applicable approach has the potential to provide insight into interactions that stabilize RNA tertiary structure that enables function.
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Affiliation(s)
- Yen-Lin Chen
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
- These authors contributed equally
| | - Weiwei He
- Department of Chemistry, New York University, New York, NY 10003, USA
- Chemistry Program, Science Division, New York University Abu Dhabi, Abu Dhabi 129188, UAE
- These authors contributed equally
| | - Serdal Kirmizialtin
- Chemistry Program, Science Division, New York University Abu Dhabi, Abu Dhabi 129188, UAE
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
- Lead contact
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Substituent effects on the interactions of ruthenium(II) polypyridyl complexes [Ru(bpy)2(6-R-dppz)]2+ (R = hydroxy and fluorine) with the RNA triplex poly(rU)·poly(rA) × poly(rU). Polyhedron 2021. [DOI: 10.1016/j.poly.2021.115196] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Ruszkowska A, Ruszkowski M, Hulewicz JP, Dauter Z, Brown JA. Molecular structure of a U•A-U-rich RNA triple helix with 11 consecutive base triples. Nucleic Acids Res 2020; 48:3304-3314. [PMID: 31930330 PMCID: PMC7102945 DOI: 10.1093/nar/gkz1222] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 12/16/2019] [Accepted: 12/20/2019] [Indexed: 02/07/2023] Open
Abstract
Three-dimensional structures have been solved for several naturally occurring RNA triple helices, although all are limited to six or fewer consecutive base triples, hindering accurate estimation of global and local structural parameters. We present an X-ray crystal structure of a right-handed, U•A-U-rich RNA triple helix with 11 continuous base triples. Due to helical unwinding, the RNA triple helix spans an average of 12 base triples per turn. The double helix portion of the RNA triple helix is more similar to both the helical and base step structural parameters of A′-RNA rather than A-RNA. Its most striking features are its wide and deep major groove, a smaller inclination angle and all three strands favoring a C3′-endo sugar pucker. Despite the presence of a third strand, the diameter of an RNA triple helix remains nearly identical to those of DNA and RNA double helices. Contrary to our previous modeling predictions, this structure demonstrates that an RNA triple helix is not limited in length to six consecutive base triples and that longer RNA triple helices may exist in nature. Our structure provides a starting point to establish structural parameters of the so-called ‘ideal’ RNA triple helix, analogous to A-RNA and B-DNA double helices.
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Affiliation(s)
- Agnieszka Ruszkowska
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556 USA
| | - Milosz Ruszkowski
- Synchrotron Radiation Research Section of MCL, National Cancer Institute, Argonne, IL 60439 USA
| | - Jacob P Hulewicz
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556 USA
| | - Zbigniew Dauter
- Synchrotron Radiation Research Section of MCL, National Cancer Institute, Argonne, IL 60439 USA
| | - Jessica A Brown
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556 USA
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Brown JA. Unraveling the structure and biological functions of RNA triple helices. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 11:e1598. [PMID: 32441456 PMCID: PMC7583470 DOI: 10.1002/wrna.1598] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 04/06/2020] [Accepted: 04/15/2020] [Indexed: 02/06/2023]
Abstract
It has been nearly 63 years since the first characterization of an RNA triple helix in vitro by Gary Felsenfeld, David Davies, and Alexander Rich. An RNA triple helix consists of three strands: A Watson–Crick RNA double helix whose major‐groove establishes hydrogen bonds with the so‐called “third strand”. In the past 15 years, it has been recognized that these major‐groove RNA triple helices, like single‐stranded and double‐stranded RNA, also mediate prominent biological roles inside cells. Thus far, these triple helices are known to mediate catalysis during telomere synthesis and RNA splicing, bind to ligands and ions so that metabolite‐sensing riboswitches can regulate gene expression, and provide a clever strategy to protect the 3′ end of RNA from degradation. Because RNA triple helices play important roles in biology, there is a renewed interest in better understanding the fundamental properties of RNA triple helices and developing methods for their high‐throughput discovery. This review provides an overview of the fundamental biochemical and structural properties of major‐groove RNA triple helices, summarizes the structure and function of naturally occurring RNA triple helices, and describes prospective strategies to isolate RNA triple helices as a means to establish the “triplexome”. This article is categorized under:RNA Structure and Dynamics > RNA Structure and Dynamics RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems
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Affiliation(s)
- Jessica A Brown
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
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Patro LPP, Kumar A, Kolimi N, Rathinavelan T. 3D-NuS: A Web Server for Automated Modeling and Visualization of Non-Canonical 3-Dimensional Nucleic Acid Structures. J Mol Biol 2017; 429:2438-2448. [PMID: 28652006 DOI: 10.1016/j.jmb.2017.06.013] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 06/15/2017] [Accepted: 06/15/2017] [Indexed: 10/19/2022]
Abstract
The inherent conformational flexibility of nucleic acids facilitates the formation of a range of conformations such as duplex, triplex, quadruplex, etc. that play crucial roles in biological processes. Elucidation of the influence of non-canonical base pair mismatches on DNA/RNA structures at different sequence contexts to understand the mismatch repair, misregulation of alternative splicing mechanisms and the sequence-dependent effect of RNA-DNA hybrid in relevance to antisense strategy demand their three-dimensional structural information. Furthermore, structural insights about nucleic acid triplexes, which are generally not tractable to structure determination by X-ray crystallography or NMR techniques, are essential to establish their biological function(s). A web server, namely 3D-NuS (http://iith.ac.in/3dnus/), has been developed to generate energy-minimized models of 80 different types of triplexes, 64 types of G-quadruplexes, left-handed Z-DNA/RNA duplexes, and RNA-DNA hybrid duplex along with inter- and intramolecular DNA or RNA duplexes comprising a variety of mismatches and their chimeric forms for any user-defined sequence and length. It also generates an ensemble of conformations corresponding to the modeled structure. These structures may serve as good starting models for docking proteins and small molecules with nucleic acids, NMR structure determination, cryo-electron microscope modeling, DNA/RNA nanotechnology applications and molecular dynamics simulation studies.
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Affiliation(s)
- L Ponoop Prasad Patro
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana State 502285, India
| | - Abhishek Kumar
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana State 502285, India
| | - Narendar Kolimi
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana State 502285, India
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Whelan DR, Hiscox TJ, Rood JI, Bambery KR, McNaughton D, Wood BR. Detection of an en masse and reversible B- to A-DNA conformational transition in prokaryotes in response to desiccation. J R Soc Interface 2014; 11:20140454. [PMID: 24898023 PMCID: PMC4208382 DOI: 10.1098/rsif.2014.0454] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 05/12/2014] [Indexed: 02/02/2023] Open
Abstract
The role that DNA conformation plays in the biochemistry of cells has been the subject of intensive research since DNA polymorphism was discovered. B-DNA has long been considered the native form of DNA in cells although alternative conformations of DNA are thought to occur transiently and along short tracts. Here, we report the first direct observation of a fully reversible en masse conformational transition between B- and A-DNA within live bacterial cells using Fourier transform infrared (FTIR) spectroscopy. This biospectroscopic technique allows for non-invasive and reagent-free examination of the holistic biochemistry of samples. For this reason, we have been able to observe the previously unknown conformational transition in all four species of bacteria investigated. Detection of this transition is evidence of a previously unexplored biological significance for A-DNA and highlights the need for new research into the role that A-DNA plays as a cellular defence mechanism and in stabilizing the DNA conformation. Such studies are pivotal in understanding the role of A-DNA in the evolutionary pathway of nucleic acids. Furthermore, this discovery demonstrates the exquisite capabilities of FTIR spectroscopy and opens the door for further investigations of cell biochemistry with this under-used technique.
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Affiliation(s)
- Donna R Whelan
- Centre for Biospectroscopy, School of Chemistry, Monash University, Victoria 3800, Australia
| | - Thomas J Hiscox
- Department of Microbiology, School of Biomedical Sciences, Monash University, Victoria 3800, Australia
| | - Julian I Rood
- Department of Microbiology, School of Biomedical Sciences, Monash University, Victoria 3800, Australia
| | - Keith R Bambery
- Centre for Biospectroscopy, School of Chemistry, Monash University, Victoria 3800, Australia Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Don McNaughton
- Centre for Biospectroscopy, School of Chemistry, Monash University, Victoria 3800, Australia
| | - Bayden R Wood
- Centre for Biospectroscopy, School of Chemistry, Monash University, Victoria 3800, Australia
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Lin LJ, Lin SB, Wu CW, Kan LS. 1H NMR Study on the pH-Dependent Polymorphism of a DNA Triplex with Oligonucleoside Methylphosphonate Analogues. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.199500062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Kan LS, Ono A. Triplex Formation as Functions of Variation of Sequence and Chain Length of Deoxyoligonucleotides at Varied Concentrations of NaCl and MgCl2. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.199400120] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Ono A, Kan LS. Triplex Formation of Oligonucleotides Containing 2′-O-Methylurldine, 5-Bromo-2′-OMethyluridine and 2′-0-Methycytidine. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.199400119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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13
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Triplex DNA:RNA, 3′-to-5′ Inverted RNA and Protein Coding in Mitochondrial Genomes. J Comput Biol 2013; 20:660-71. [DOI: 10.1089/cmb.2012.0134] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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Overlapping genes coded in the 3′-to-5′-direction in mitochondrial genes and 3′-to-5′ polymerization of non-complementary RNA by an ‘invertase’. J Theor Biol 2012; 315:38-52. [DOI: 10.1016/j.jtbi.2012.08.044] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Revised: 08/17/2012] [Accepted: 08/30/2012] [Indexed: 11/23/2022]
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Cartwright RA, Graur D. The multiple personalities of Watson and Crick strands. Biol Direct 2011; 6:7. [PMID: 21303550 PMCID: PMC3055211 DOI: 10.1186/1745-6150-6-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Accepted: 02/08/2011] [Indexed: 11/18/2022] Open
Abstract
Background In genetics it is customary to refer to double-stranded DNA as containing a "Watson strand" and a "Crick strand." However, there seems to be no consensus in the literature on the exact meaning of these two terms, and the many usages contradict one another as well as the original definition. Here, we review the history of the terminology and suggest retaining a single sense that is currently the most useful and consistent. Proposal The Saccharomyces Genome Database defines the Watson strand as the strand which has its 5'-end at the short-arm telomere and the Crick strand as its complement. The Watson strand is always used as the reference strand in their database. Using this as the basis of our standard, we recommend that Watson and Crick strand terminology only be used in the context of genomics. When possible, the centromere or other genomic feature should be used as a reference point, dividing the chromosome into two arms of unequal lengths. Under our proposal, the Watson strand is standardized as the strand whose 5'-end is on the short arm of the chromosome, and the Crick strand as the one whose 5'-end is on the long arm. Furthermore, the Watson strand should be retained as the reference (plus) strand in a genomic database. This usage not only makes the determination of Watson and Crick unambiguous, but also allows unambiguous selection of reference stands for genomics. Reviewers This article was reviewed by John M. Logsdon, Igor B. Rogozin (nominated by Andrey Rzhetsky), and William Martin.
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Affiliation(s)
- Reed A Cartwright
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204-5001, USA.
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17
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Gfrörer A, Schnetter ME, Wolfrum J, Greulich KO. Double and Triple Helices of Nucleic Acid Polymers, Studied by UV-Resonance Raman Spectroscopy. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/bbpc.19930970203] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Xi H, Kumar S, Dosen-Micovic L, Arya DP. Calorimetric and spectroscopic studies of aminoglycoside binding to AT-rich DNA triple helices. Biochimie 2010; 92:514-29. [PMID: 20167243 PMCID: PMC3977217 DOI: 10.1016/j.biochi.2010.02.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2009] [Accepted: 02/08/2010] [Indexed: 11/21/2022]
Abstract
Calorimetric and fluorescence techniques were used to characterize the binding of aminoglycosides-neomycin, paromomycin, and ribostamycin, with 5'-dA(12)-x-dT(12)-x-dT(12)-3' intramolecular DNA triplex (x = hexaethylene glycol) and poly(dA).2poly(dT) triplex. Our results demonstrate the following features: (1) UV thermal analysis reveals that the T(m) for triplex decreases with increasing pH value in the presence of neomycin, while the T(m) for the duplex remains unchanged. (2) The binding affinity of neomycin decreases with increased pH, although there is an increase in observed binding enthalpy. (3) ITC studies conducted in two buffers (sodium cacodylate and MOPS) yield the number of protonated drug amino groups (Deltan) as 0.29 and 0.40 for neomycin and paromomycin interaction with 5'-dA(12)-x-dT(12)-x-dT(12)-3', respectively. (4) The specific heat capacity change (DeltaC(p)) determined by ITC studies is negative, with more negative values at lower salt concentrations. From 100 mM to 250 mM KCl, the DeltaC(p) ranges from -402 to -60 cal/(mol K) for neomycin. At pH 5.5, a more positive DeltaC(p) is observed, with a value of -98 cal/(mol K) at 100 mM KCl. DeltaC(p) is not significantly affected by ionic strength. (5) Salt dependence studies reveal that there are at least three amino groups of neomycin participating in the electrostatic interactions with the triplex. (6) FID studies using thiazole orange were used to derive the AC(50) (aminoglycoside concentration needed to displace 50% of the dye from the triplex) values. Neomycin shows a seven fold higher affinity than paromomycin and eleven fold higher affinity than ribostamycin at pH 6.8. (7) Modeling studies, consistent with UV and ITC results, show the importance of an additional positive charge in triplex recognition by neomycin. The modeling and thermodynamic studies indicate that neomycin binding to the DNA triplex depends upon significant contributions from charge as well as shape complementarity of the drug to the DNA triplex Watson-Hoogsteen groove.
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Affiliation(s)
- Hongjuan Xi
- Contribution from the Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634, USA
| | - Sunil Kumar
- Contribution from the Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634, USA
| | - Ljiljana Dosen-Micovic
- Contribution from the Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634, USA
| | - Dev P. Arya
- Contribution from the Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634, USA
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Montenay-Garestier T, Hélène C, Thuong NT. Design of sequence-specific bifunctional nucleic acid ligands. CIBA FOUNDATION SYMPOSIUM 2007; 158:147-57; discussion 204-12. [PMID: 1935419 DOI: 10.1002/9780470514085.ch10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Homopyrimidine oligodeoxynucleotides have been covalently linked to intercalating agents. These bifunctional nucleic acid ligands bind to the major groove of DNA at homopurine.homopyrimidine sequences, where they form triple helices. The homopyrimidine oligonucleotide binds parallel to the purine strand of the double helix. Two hydrogen bonds are formed between bases of the oligonucleotide and the purines engaged in Watson-Crick base pairs. The intercalating agent inserts its aromatic ring at the triplex-duplex junction, resulting in a strong stabilization of the triple helical structure. Bifunctional oligonucleotide-intercalator conjugates provide new tools for a selective control of gene expression. In addition, irreversible reactions can be targeted to the oligonucleotide recognition sequence. Cleavage reactions can be induced by a copper-phenanthroline chelate or an ellipticine derivative covalently linked to the triple helix-forming oligonucleotide.
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Affiliation(s)
- T Montenay-Garestier
- Laboratoire de Biophysique, INSERM U201, CNRS UA481, Muséum National d'Histoire Naturelle, Paris, France
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20
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Protoberberine Alkaloids: Physicochemical and Nucleic Acid Binding Properties. TOPICS IN HETEROCYCLIC CHEMISTRY 2007. [DOI: 10.1007/7081_2007_071] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Maiti M, Kumar GS. Molecular aspects on the interaction of protoberberine, benzophenanthridine, and aristolochia group of alkaloids with nucleic acid structures and biological perspectives. Med Res Rev 2007; 27:649-95. [PMID: 16894530 DOI: 10.1002/med.20087] [Citation(s) in RCA: 145] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Alkaloids occupy an important position in chemistry and pharmacology. Among the various alkaloids, berberine and coralyne of the protoberberine group, sanguinarine of the benzophenanthridine group, and aristololactam-beta-d-glucoside of the aristolochia group have potential to form molecular complexes with nucleic acid structures and have attracted recent attention for their prospective clinical and pharmacological utility. This review highlights (i) the physicochemical properties of these alkaloids under various environmental conditions, (ii) the structure and functional aspects of various forms of deoxyribonucleic acid (DNA) (B-form, Z-form, H(L)-form, protonated form, and triple helical form) and ribonucleic acid (RNA) (A-form, protonated form, and triple helical form), and (iii) the interaction of these alkaloids with various polymorphic DNA and RNA structures reported by several research groups employing various analytical techniques like absorbance, fluorescence, circular dichroism, and NMR spectroscopy; electrospray ionization mass spectrometry, thermal melting, viscosity, and DNase footprinting as well as molecular modeling and thermodynamic studies to provide detailed binding mechanism at the molecular level for structure-activity relationship. Nucleic acids binding properties of these alkaloids are interpreted in relation to their biological activity.
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Affiliation(s)
- Motilal Maiti
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, Kolkata 700 032, India.
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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: 54] [Impact Index Per Article: 2.8] [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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Noy A, Pérez A, Lankas F, Javier Luque F, Orozco M. Relative Flexibility of DNA and RNA: a Molecular Dynamics Study. J Mol Biol 2004; 343:627-38. [PMID: 15465050 DOI: 10.1016/j.jmb.2004.07.048] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2004] [Revised: 06/30/2004] [Accepted: 07/06/2004] [Indexed: 10/26/2022]
Abstract
State of the art molecular dynamics simulations are used to study the structure, dynamics, molecular interaction properties and flexibility of DNA and RNA duplexes in aqueous solution. Special attention is paid to the deformability of both types of structures, revisiting concepts on the relative flexibility of DNA and RNA duplexes. Our simulations strongly suggest that the concepts of flexibility, rigidity and deformability are much more complex than usually believed, and that it is not always true that DNA is more flexible than RNA.
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Affiliation(s)
- Agnes Noy
- Molecular Modeling and Bioinformatics Unit, Institut de Recerca Biomèdica, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain
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24
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Ojha RP, Tiwari RK. Triplex hydration: nanosecond molecular dynamics simulation of the solvated triplex formed by mixed sequences. Nucleic Acids Res 2003; 31:6373-80. [PMID: 14576325 PMCID: PMC275451 DOI: 10.1093/nar/gkg796] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A theoretical model for the hydration pattern and motion of ions around the triple helical DNA with mixed sequences d(GACTGGTGAC)d(GTCACCAGTC)*d(GACTGGTGAC) in solution, during MD simulation, using the particle mesh Ewald sum method, is elaborated here. The AMBER 5.0 force field has been used during the simulation in solvent. The simulation studies support a dynamically stable atmosphere around the DNA triplex in solution over the entire length of the trajectory. The results have been compared with Hoogsteen triplexes and examined in the context of the observed behaviour of hydration in crystallographic data of duplexes. The dynamical organization of counterions and water molecules around the triplex formed by mixed sequences is described here. It has been observed that cations prefer to bind between two adjoining purines of the second and the third strands. The idea of localized complexes (mobile counterions in unspecific electronegative pockets around the DNA triplex with water molecules) may have important implications for understanding the specificity of the interactions of nucleic acids with proteins and other ligands.
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Affiliation(s)
- Rajendra P Ojha
- Biophysics Unit, Department of Physics, DDU Gorakhpur University, Gorakhpur 273 009, India.
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25
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Rueda M, Kalko SG, Luque FJ, Orozco M. The structure and dynamics of DNA in the gas phase. J Am Chem Soc 2003; 125:8007-14. [PMID: 12823023 DOI: 10.1021/ja0300564] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The impact of the transfer from water to the vacuum in the duplex DNA has been explored by using long molecular dynamic simulations. In opposition to chemical intuition, it is found that vaporization of DNA, even at high temperatures, does not lead to a total disruption of the double helix. Rather, the DNA duplex preserves gross structural, energetic, and dynamic features of the conformation of the double helix in aqueous solution. Thus, the two strands remain bound, the global structure has a slight helicity, and the total number of DNA-DNA interactions is not dramatically different from that found in solution. The results provide detailed structural and dynamic information useful to complement current mass spectroscopy studies of DNA structures.
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Affiliation(s)
- Manuel Rueda
- Institut de Recerca Biomèdica, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain
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26
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Barbieri CM, Li TK, Guo S, Wang G, Shallop AJ, Pan W, Yang G, Gaffney BL, Jones RA, Pilch DS. Aminoglycoside complexation with a DNA.RNA hybrid duplex: the thermodynamics of recognition and inhibition of RNA processing enzymes. J Am Chem Soc 2003; 125:6469-77. [PMID: 12785787 DOI: 10.1021/ja021371d] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Spectroscopic and calorimetric techniques were employed to characterize and contrast the binding of the aminoglycoside paromomycin to three octamer nucleic acid duplexes of identical sequence but different strand composition (a DNA.RNA hybrid duplex and the corresponding DNA.DNA and RNA.RNA duplexes). In addition, the impact of paromomycin binding on both RNase H- and RNase A-mediated cleavage of the RNA strand in the DNA.RNA duplex was also determined. Our results reveal the following significant features: (i) Paromomycin binding enhances the thermal stabilities of the RNA.RNA and DNA.RNA duplexes to similar extents, with this thermal enhancement being substantially greater in magnitude than that of the DNA.DNA duplex. (ii) Paromomycin binding to the DNA.RNA hybrid duplex induces CD changes consistent with a shift from an A-like to a more canonical A-conformation. (iii) Paromomycin binding to all three octamer duplexes is linked to the uptake of a similar number of protons, with the magnitude of this number being dependent on pH. (iv) The affinity of paromomycin for the three host duplexes follows the hierarchy, RNA.RNA > DNA.RNA >> DNA.DNA. (v) The observed affinity of paromomycin for the RNA.RNA and DNA.RNA duplexes decreases with increasing pH. (vi) The binding of paromomycin to the DNA.RNA hybrid duplex inhibits both RNase H- and RNase A-mediated cleavage of the RNA strand. We discuss the implications of our combined results with regard to the specific targeting of DNA.RNA hybrid duplex domains and potential antiretroviral applications.
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Affiliation(s)
- Christopher M Barbieri
- Contribution from the Department of Pharmacology, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, 675 Hoes Lane, Piscataway, New Jersey 08854-5635, USA
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27
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Ojha RP, Tiwari RK. Molecular dynamics simulation study of DNA triplex formed by mixed sequences in solution. J Biomol Struct Dyn 2002; 20:107-26. [PMID: 12144358 DOI: 10.1080/07391102.2002.10506797] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The unrestrained molecular dynamics simulation of the triple helical DNA with mix sequences d(GACTGGTGAC).d(CTGACCACTG)*d (GACTGGTGAC), using the particle mesh Ewald sum, is presented here. The Ewald summation method effectively eliminates the usualcut-of of the long range interactions and allowed us to evaluate the full effect of the electrostatic forces. The AMBER5.0 force field has been used during the simulation in solvent. The MD results support a dynamically stable model of DNA triplex over the entire length of the trajectory. The duplex structure assumes the conformation, which is very close to B-DNA. In mixed sequences the purine bases occurs in both strand of DNA duplex. The bases of third strand do not favor the Hoogsteen or/and reverse Hoogsteen type of Hydrogen bonding but they form hydrogen bonds with the bases of both the strand of DNA duplex. The orientation of the third strand is parallel to one of the strand of duplex and all nucleotides (C, A, G & T) show isomorphic behavior with respect to the DNA duplex. The conformation of all the three strands is almost same except few exceptions. Due to interaction of third strand the conformational change in the duplex structure and a finite amount of displacement in the W-C base pairs have been observed. The conformational variation of the back bone torsion angles and helicoidal parameters, groove widths have been discussed. The sequence dependent effects on local conformation, helicoidal and morphological structure, width of the grooves of DNA helix may have important implication for understanding the functional energetics and specificity of interactions of DNA and its triplexes with proteins, pharmaceutical agents and other ligands.
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Affiliation(s)
- R P Ojha
- Biophysics Unit, Department of Physics, DDU Gorakhpur University, India.
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28
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Teulade-Fichou MP, Perrin D, Boutorine A, Polverari D, Vigneron JP, Lehn JM, Sun JS, Garestier T, Helene C. Direct photocleavage of HIV-DNA by quinacridine derivatives triggered by triplex formation. J Am Chem Soc 2001; 123:9283-92. [PMID: 11562210 DOI: 10.1021/ja0109040] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amino-p-quinacridine compounds (PQs) have been shown to stabilize strongly and specifically triple-helical DNA. Moreover, these derivatives display photoactive properties that make them efficient DNA cleavage agents. We exploited these two properties (triplex-specific binding and photoactivity) to selectively cleave a double-stranded (ds)DNA sequence present in the HIV-1 genome. Cleavage was first carried out on a linearized plasmid (3300 bp) containing the HIV polypurine tract (PPT) that allowed targeting by a triplex-forming oligonucleotide (TFO). PQ(3)(), the most active compound of the series, efficiently cleaved double-stranded DNA in the vicinity of the PPT when this sequence had formed a triplex with a 16-mer TFO. Investigation of the cleavage at the molecular level was addressed on a short DNA fragment (56 bp); the photoinduced cleavage by PQ(3)() occurred only in the presence of the triple helix. Nevertheless, unusual cleavage patterns were observed: damage was observed at guanines located 6-9 bp away from the end of the triple helical site. This cleavage is very efficient (up to 60%), does not require alkaline treatment, and is observed on both strands. A quinacridine-TFO conjugate produced the same cleavage pattern. This observation, along with others, excludes the hypothesis of a triplex-induced allosteric binding site of PQ(3 )()adjacent to the damaged sequence and indicates that PQ(3 )()preferentially binds in the vicinity of the 5'-triplex junction. Irradiation in the presence of TFO-conjugates with acridine (an intercalative agent) and with the tripeptide lys-tryp-lys led to a complete inhibition of the photocleavage reaction. These results are interpreted in terms of competitive binding and of electron-transfer quenching. Together with the findings of simple mechanistic investigations, they led to the conclusion that the photoinduced damage proceeds through a direct electron transfer between the quinacridine and the guanines. This study addresses the chemical mechanism leading to strand breakage and characterizes the particular photosensitivity of the HIV-DNA target sequence which could be an oxidative hot spot for addressed photoinduced strand scission by photosensitizers.
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Affiliation(s)
- M P Teulade-Fichou
- Laboratoire de Chimie des Interactions Moléculaires, Collège de France, CNRS UPR 285, 11 place Marcelin Berthelot, 75005 Paris, France
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29
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Hatters DM, Wilson L, Atcliffe BW, Mulhern TD, Guzzo-Pernell N, Howlett GJ. Sedimentation analysis of novel DNA structures formed by homo-oligonucleotides. Biophys J 2001; 81:371-81. [PMID: 11423421 PMCID: PMC1301518 DOI: 10.1016/s0006-3495(01)75706-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sedimentation velocity analysis has been used to examine the base-specific structural conformations and unusual hydrogen bonding patterns of model oligonucleotides. Homo-oligonucleotides composed of 8-28 residues of dA, dT, or dC nucleotides in 100 mM sodium phosphate, pH 7.4, at 20 degrees C behave as extended monomers. Comparison of experimentally determined sedimentation coefficients with theoretical values calculated for assumed helical structures show that dT and dC oligonucleotides are more compact than dA oligonucleotides. For dA oligonucleotides, the average width (1.7 nm), assuming a cylindrical model, is smaller than for control duplex DNA whereas the average rise per base (0.34 nm) is similar to that of B-DNA. For dC and dT oligonucleotides, there is an increase in the average widths (1.8 nm and 2.1 nm, respectively) whereas the average rise per base is smaller (0.28 nm and 0.23 nm, respectively). A significant shape change is observed for oligo dC(28) at lower temperatures (10 degrees C), corresponding to a fourfold decrease in axial ratio. Optical density, circular dichroism, and differential scanning calorimetry data confirm this shape change, attributable from nuclear magnetic resonance analysis to i-motif formation. Sedimentation equilibrium studies of oligo dG(8) and dG(16) reveal extensive self-association and the formation of G-quadruplexes. Continuous distribution analysis of sedimentation velocity data for oligo dG(16) identifies the presence of discrete dimers, tetramers, and dodecamers. These studies distinguish the conformational and colligative properties of the individual bases in DNA and their inherent capacity to promote specific folding pathways.
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Affiliation(s)
- D M Hatters
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
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30
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Abstract
Several crystal structures of RNA fragments, alone or in complex with a specific protein, have been recently solved. In addition, the structures of an artificial ribozyme, the leadzyme, and the cleavage product of a human pathogen ribozyme, have extended the structural diversity of ribozyme architectures. The attained set of folding rules and motifs expand the repertoire seen previously in tRNA structures.
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Affiliation(s)
- E Westhof
- UPR9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg-Cedex, F-67084, France.
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31
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Vogtherr M, Kirchner R, Zuleeg T, Limmer S. Dimerization of double-stranded RNA possessing a 3'-overhanging single-stranded end. J Biomol Struct Dyn 1999; 17:355-65. [PMID: 10563584 DOI: 10.1080/07391102.1999.10508367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
A simple system derived from the acceptor stem of tRNA(Ala) is presented which undergoes a pH-dependent dimerization. This is brought about by formation of C+-G-C base triples of the pyrimidine motif type between protonated cytidines of the 3' single-stranded end and regularly paired G-C pairs in the double-helical stem. In addition, an unusual interaction between a protonated adenine and a regular G-C pair is suggested. The equilibrium between monomer and dimer forms can be monitored via NMR spectroscopy and UV melting curve analysis. A dimerization enthalpy of 159 kJ mol(-1) was found at pH 5.0. The system could serve as a model for inter- and intra-molecular association, respectively, of single-stranded and double-helical regions to enable optimal packing of large RNA molecules.
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Affiliation(s)
- M Vogtherr
- Max-Planck-Institut für Molekulare Genetik, Berlin-Dahlem, Germany
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32
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Abstract
DNA oligonucleotides can form multistranded helices through either the folding of a single strand or the association of two, three or four strands of DNA. Structures of several new DNA triplexes, G-quartet DNA quadruplexes and I-motif DNA quadruplexes have been reported recently. These structures provide new insights into helix stability and folding, loop conformations and cation interactions.
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Affiliation(s)
- D E Gilbert
- Department of Chemistry and Biochemistry, University of California, Los Angeles 90095-1569, USA
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33
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Soliva R, Luque FJ, Orozco M. Can G-C Hoogsteen-wobble pairs contribute to the stability of d(G. C-C) triplexes? Nucleic Acids Res 1999; 27:2248-55. [PMID: 10325411 PMCID: PMC148788 DOI: 10.1093/nar/27.11.2248] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Quantum mechanics, molecular dynamics and statistical mechanics methods are used to analyze the importance of neutral Hoogsteen-wobble G.C pairing in the stabilization of triple helices based on the poly-(G.C-C) trio at neutral pH and low ionic strength. In spite of the existence of a single hydrogen bond, the Hoogsteen-wobble G.C pair is found to be quite stable both in gas phase and solvated DNA. Molecular dynamics simulations of different triplexes based on the d(G.C-C) trio leads to stable structures if the neutral d(G.C-C) steps stabilized by Hoogsteen-wobble pairs are mixed with d(G.C-C+) steps. Finally, high level ab initio calculations and thermodynamic integration techniques are used to determine the relative stability of G.C wobble and G.C imino pairings. It is found that triplexes containing the imino pairing are slightly more stable structures than those with the wobble one, due mainly to a better stacking.
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Affiliation(s)
- R Soliva
- Departament de Bioquímica, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, Barcelona 08028, Spain
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34
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Mariappan SV, Catasti P, Silks LA, Bradbury EM, Gupta G. The high-resolution structure of the triplex formed by the GAA/TTC triplet repeat associated with Friedreich's ataxia. J Mol Biol 1999; 285:2035-52. [PMID: 9925783 DOI: 10.1006/jmbi.1998.2435] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Expansions of the triplet repeat, GAA/TTC, inside the first intron of the frataxin gene causes Friedreich's ataxia (FRDA). It was of interest to us to examine whether the FRDA repeat forms an unusual DNA structure, since formation of such structure during replication may cause its expansion. Here, we show that the FRDA repeat forms a triplex in which the TTC strand folds on either side of the same GAA strand. We have determined the high-resolution NMR structures of two intramolecularly folded FRDA triplexes, (GAA)2T4(TTC)2T4(CTT)2 and (GAA)2T4(TTC)2T2CT2(CTT)2 with T.A.T and C+.G.C triads. T4 represents a synthetic loop sequence, whereas T2CT2 is the natural loop-folding sequence of the TTC strand. We have also made use of site-specific 15N-labeling of the cytosine residues to investigate their protonation status and their interaction with other protons. We show that the cytosine residues of the Hoogsteen C+.G pairs in this triplex are protonated close to physiological pH. Therefore, it appears that the triplex formation offers a plausible explanation for the expansion of the GAA/TTC repeats in FRDA.
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Affiliation(s)
- S V Mariappan
- Life Sciences Division, LS-2 MS 880, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
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35
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Peptide nucleic acids. ACTA ACUST UNITED AC 1999. [DOI: 10.1016/s1874-5113(99)80009-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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36
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Exploring the Structural Repertoire of Guanine-Rich DNA Sequences: Computer Modelling Studies. ACTA ACUST UNITED AC 1999. [DOI: 10.1016/s1380-7323(99)80083-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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37
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Rothman JH, Richards WG. Novel Hoogsteen-like bases for configurational recognition of the T-A base pair by DNA triplex formation. Biopolymers 1998. [DOI: 10.1002/(sici)1097-0282(199612)39:6<795::aid-bip6>3.0.co;2-q] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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38
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Self BD, Moore DS. Nucleic acid vibrational circular dichroism, absorption, and linear dichroism spectra. II. A DeVoe theory approach. Biophys J 1998; 74:2249-58. [PMID: 9591652 PMCID: PMC1299568 DOI: 10.1016/s0006-3495(98)77934-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The DeVoe polarizability theory is used to calculate vibrational circular dichroism (VCD) and infrared (IR) absorption spectra of four polyribonucleotides: poly(rA) x poly(rU), poly(rU) x poly(rA) x poly(rU), poly(rG) x poly(rC), and poly(rC+) x poly(rI) x poly(rC). This is the first report on the use of the DeVoe theory to calculate VCD, oriented VCD, IR absorption, and IR linear dichroism (LD) spectra of double- and triple-stranded polyribonucleotides. Results are reported for DeVoe theory calculations--within the base-stretching 1750-1550 cm(-1) spectral region--on several proposed multistranded polyribonucleotide geometries. The calculated spectra obtained from these proposed geometries are compared with previously reported measured and calculated VCD and IR spectral results. Base-base hydrogen-bonding effects on the frequencies and magnitudes of the base carbonyl stretching modes are explicitly considered. The good agreements found between calculated and measured spectra are proposed to be further evidence of the usefulness of the DeVoe theory in drawing three-dimensional structural conclusions from measured polyribonucleotide VCD and IR spectra.
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Affiliation(s)
- B D Self
- Department of Chemistry, Howard University, Washington, DC 20059, USA
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39
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Sehlstedt U, Aich P, Bergman J, Vallberg H, Nordén B, Gräslund A. Interactions of the antiviral quinoxaline derivative 9-OH-B220 [2, 3-dimethyl-6-(dimethylaminoethyl)- 9-hydroxy-6H-indolo-[2, 3-b]quinoxaline] with duplex and triplex forms of synthetic DNA and RNA. J Mol Biol 1998; 278:31-56. [PMID: 9571032 DOI: 10.1006/jmbi.1998.1670] [Citation(s) in RCA: 100] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The binding of an antiviral quinoxaline derivative, 2,3-dimethyl- 6 - (dimethylaminoethyl) - 9 - hydroxy - 6H - indolo - [2,3 - b]quinoxaline (9-OH-B220), to synthetic double and triple helical DNA (poly(dA).poly(dT) and poly(dA).2poly(dT)) and RNA (poly(rA). poly(rU) and poly (rA).2poly(rU)) has been characterized using flow linear dichroism (LD), circular dichroism (CD), fluorescence spectroscopy, and thermal denaturation. When either of the DNA structures or the RNA duplex serve as host polymers a strongly negative LD is displayed, consistent with intercalation of the chromophoric ring system between the base-pairs/triplets of the nucleic acid structures. Evidence for this geometry also includes weak induced CD signals and strong increments of the fluorescence emission intensities upon binding of the drug to each of these polymer structures. In agreement with intercalative binding, 9-OH-B220 is found to effectively enhance the thermal stability of both the double and triple helical states of DNA as well as the RNA duplex. In the case of poly(dA).2poly(dT), the drug provides an unusually large stabilization of its triple helical state; upon binding of 9-OH-B220 the triplex-to-duplex equilibrium is shifted towards higher temperature by 52.5 deg. C in a 10 mM sodium cacodylate buffer (pH 7.0) containing 100 mM NaCl and 1 mM EDTA. When triplex RNA serves as host structure, LD indicates that the average orientation angle between the drug chromophore plane and the helix axis of the triple helical RNA is only about 60 to 65 degrees. Moreover, the thermal stabilizing capability, as well as the fluorescence increment, CD inducing power and perturbations of the absorption envelope, of 9-OH-B220 in complex with the RNA triplex are all less pronounced than those observed for the complexes with DNA and duplex RNA. These features indicate binding of 9-OH-B220 in the wide and shallow minor groove of poly(rA).2poly(rU). Based on the present results, some implications for the applications of this low-toxic, antiviral and easily administered drug in an antigene strategy, as well as its potential use as an antiretroviral agent, are discussed.
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Affiliation(s)
- U Sehlstedt
- Department of Biophysics, Stockholm University, Stockholm, S-106 91, Sweden
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40
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Liu M, Yang L, Deng W, Su M, Wang C, Lin SB, Kan LS, Bai C. Effect of selective substitution of 5-bromocytosine on conformation of DNA triple helices. J Biomol Struct Dyn 1998; 15:895-903. [PMID: 9619512 DOI: 10.1080/07391102.1998.10508211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Three triplex DNAs containing 5-bromocytosine[BrC] were studied by vibrational spectroscopy and molecular modelling. Firstly, three oligodeoxypyrimidines of 5'-(TC)3-T4-(BrCT)3 [CBrC], 5'-(TBrC)3-T4-(CT)3 [BrCC] and 5'-(TBrC)3-T4-(BrCT)3 [BrCBrC] were synthesized and then reacted with an oligodeoxypurine of 5'-(AG)3 at pH=4.5 in phosphate buffer respectively to form three comparative hairpin triplex named CY,YC and YY. The results of FT-Raman and IR revealed that YY is almost in A-like form, CY and YC are combinations of A-like form and B-like form, but A-form dominates in CY while B-form is equivalent as A-form in YC. The result is consistent with the theoretical analysis.
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Affiliation(s)
- M Liu
- Institute of Chemistry, Chinese Academy of Sciences, Beijing
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41
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Escudé C, Nguyen CH, Kukreti S, Janin Y, Sun JS, Bisagni E, Garestier T, Hélène C. Rational design of a triple helix-specific intercalating ligand. Proc Natl Acad Sci U S A 1998; 95:3591-6. [PMID: 9520410 PMCID: PMC19880 DOI: 10.1073/pnas.95.7.3591] [Citation(s) in RCA: 92] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
DNA triple helices offer new perspectives toward oligonucleotide-directed gene regulation. However, the poor stability of some of these structures might limit their use under physiological conditions. Specific ligands can intercalate into DNA triple helices and stabilize them. Molecular modeling and thermal denaturation experiments suggest that benzo[f]pyrido[3, 4-b]quinoxaline derivatives intercalate into triple helices by stacking preferentially with the Hoogsteen-paired bases. Based on this model, it was predicted that a benzo[f]quino[3,4-b]quinoxaline derivative, which possesses an additional aromatic ring, could engage additional stacking interactions with the pyrimidine strand of the Watson-Crick double helix upon binding of this pentacyclic ligand to a triplex structure. This compound was synthesized. Thermal denaturation experiments and inhibition of restriction enzyme cleavage show that this new compound can indeed stabilize triple helices with great efficiency and specificity and/or induce triple helix formation under physiological conditions.
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Affiliation(s)
- C Escudé
- Laboratoire de Biophysique, Muséum National d'Histoire Naturelle, Institut National de la Santé et de la Recherche Médicale U 201, Centre National de la Recherche Scientifique, Unité de Recherche Associ-ee 481, Paris, France
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42
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Nguyen CH, Marchand C, Delage S, Sun JS, Garestier T, Hélène C, Bisagni E. Synthesis of 13H-Benzo[6,7]- and 13H-Benzo[4,5]indolo[3,2-c]- quinolines: A New Series of Potent Specific Ligands for Triplex DNA. J Am Chem Soc 1998. [DOI: 10.1021/ja971707x] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Chi Hung Nguyen
- Contribution from the UMR 176 CNRS−Institut Curie, Section Recherche 15 rue Georges Clémenceau, 91405 Orsay, France, and Laboratoire de Biophysique, Muséum National d'Histoire Naturelle INSERM U 201 et CNRS URA 481 43 rue Cuvier, 75231 Paris Cedex 05, France
| | - Christophe Marchand
- Contribution from the UMR 176 CNRS−Institut Curie, Section Recherche 15 rue Georges Clémenceau, 91405 Orsay, France, and Laboratoire de Biophysique, Muséum National d'Histoire Naturelle INSERM U 201 et CNRS URA 481 43 rue Cuvier, 75231 Paris Cedex 05, France
| | - Stéphane Delage
- Contribution from the UMR 176 CNRS−Institut Curie, Section Recherche 15 rue Georges Clémenceau, 91405 Orsay, France, and Laboratoire de Biophysique, Muséum National d'Histoire Naturelle INSERM U 201 et CNRS URA 481 43 rue Cuvier, 75231 Paris Cedex 05, France
| | - Jian-Sheng Sun
- Contribution from the UMR 176 CNRS−Institut Curie, Section Recherche 15 rue Georges Clémenceau, 91405 Orsay, France, and Laboratoire de Biophysique, Muséum National d'Histoire Naturelle INSERM U 201 et CNRS URA 481 43 rue Cuvier, 75231 Paris Cedex 05, France
| | - Thérèse Garestier
- Contribution from the UMR 176 CNRS−Institut Curie, Section Recherche 15 rue Georges Clémenceau, 91405 Orsay, France, and Laboratoire de Biophysique, Muséum National d'Histoire Naturelle INSERM U 201 et CNRS URA 481 43 rue Cuvier, 75231 Paris Cedex 05, France
| | - Claude Hélène
- Contribution from the UMR 176 CNRS−Institut Curie, Section Recherche 15 rue Georges Clémenceau, 91405 Orsay, France, and Laboratoire de Biophysique, Muséum National d'Histoire Naturelle INSERM U 201 et CNRS URA 481 43 rue Cuvier, 75231 Paris Cedex 05, France
| | - Emile Bisagni
- Contribution from the UMR 176 CNRS−Institut Curie, Section Recherche 15 rue Georges Clémenceau, 91405 Orsay, France, and Laboratoire de Biophysique, Muséum National d'Histoire Naturelle INSERM U 201 et CNRS URA 481 43 rue Cuvier, 75231 Paris Cedex 05, France
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43
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Shafer RH. Stability and structure of model DNA triplexes and quadruplexes and their interactions with small ligands. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1998; 59:55-94. [PMID: 9427840 DOI: 10.1016/s0079-6603(08)61029-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
This review focuses on the structural and thermodynamic characterization of model DNA triplex and quadruplex structures, taking into account effects of stoichiometry and sequence. Methods such as gel electrophoresis, UV melting, and scanning calorimetry, and the results thereof, are described for determination of the thermodynamic stability of such systems. Three classes of triplexes are considered based on the composition of the third strand, while quadruplex systems are limited to those based on the guanine quartet. X-ray crystallography and high resolution NMR studies are also described for these two classes of unusual structures. Ligand binding to triplexes and quadruplexes is also reviewed, with emphasis on specific molecular recognition. The availability of three-dimensional structures for triplex and quadruplex species sets the stage for structure-based development of ligands capable of binding to them specifically. To this end, we consider the application of DOCK, a program for the discovery of small molecules that can recognize macromolecular structures, to the problem of recognizing folded quadruplex structures. Such studies may ultimately lead to pharmaceutically active compounds.
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Affiliation(s)
- R H Shafer
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco 94143, USA
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44
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Srinivasan AR, Olson WK. Molecular Models of Nucleic Acid Triple Helixes. I. DNA and RNA Backbone Complexes. J Am Chem Soc 1998. [DOI: 10.1021/ja972720k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- A. R. Srinivasan
- Contribution from the Department of Chemistry, Wright-Rieman Laboratories, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854-8087
| | - Wilma K. Olson
- Contribution from the Department of Chemistry, Wright-Rieman Laboratories, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854-8087
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45
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Ouali M, Gousset H, Geinguenaud F, Liquier J, Gabarro-Arpa J, Le Bret M, Taillandier E. Hydration of the dTn.dAn x dTn parallel triple helix: a Fourier transform infrared and gravimetric study correlated with molecular dynamics simulations. Nucleic Acids Res 1997; 25:4816-24. [PMID: 9365262 PMCID: PMC147119 DOI: 10.1093/nar/25.23.4816] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
We present a comparative analysis of the water organization around the dTn.dAn x dTn triple helix and the Watson-Crick double helix dTn.dAn respectively by means of gravimetric measurements, infrared spectroscopy and molecular dynamics simulations. The hydration per nucleotide determined by gravimetric and spectroscopic methods correlated with the molecular dynamics simulations shows that at high relative humidity (98% RH) the triple helix is less solvated than the duplex (17 +/- 2 water molecules per nucleotide instead of 21 +/-1). The experimental desorption curves are different for both structures and indicate that below 81% RH the triplex becomes more hydrated than the duplex. At this RH the FTIR spectra show the emergence of N-type sugars in the adenosine strand of the triplex. When the third strand is bound in the major groove of the Watson-Crick duplex molecular dynamics simulations show the formation of a spine of water molecules between the two thymidine strands.
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Affiliation(s)
- M Ouali
- Laboratoire CSSB, URA CNRS 1430, UFR Santé Médecine et Biologie Humaine, Université Paris XIII, 74 rue Marcel Cachin, 93017 Bobigny, France
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46
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Xu Z, Pilch DS, Srinivasan AR, Olson WK, Geacintov NE, Breslauer KJ. Modulation of nucleic acid structure by ligand binding: induction of a DNA.RNA.DNA hybrid triplex by DAPI intercalation. Bioorg Med Chem 1997; 5:1137-47. [PMID: 9222508 DOI: 10.1016/s0968-0896(97)00050-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The aromatic diamidine, DAPI (4',6-diamidino-2-phenylindole), is used as an important biological and cytological tool since it forms highly fluorescent complexes with nucleic acid duplexes via minor groove-directed/intercalative modes of interaction. In this study, we find that DAPI binding can induce the formation of an RNA-DNA hybrid triplex that would not otherwise form. More specifically, through application of a broad range of spectroscopic, viscometric, and molecular modeling techniques, we demonstrate that DAPI intercalation induces the formation of the poly(dT).poly(rA).poly(dT) hybrid triple helix, a structure which does not form in the absence of the ligand. Using UV mixing studies, we demonstrate that, in the presence of DAPI, the poly(rA).poly(dT) duplex and the poly(dT) single strand form a 1:1 complex (a triplex) that does not form in the absence of DAPI. Through temperature-dependent absorbance measurements, we show that the poly(dT).poly(rA).poly(dT) triplex melts via two distinct transitions: initial conversion of the triplex to the duplex state, with the DAPI remaining bound, followed by denaturation of the duplex-DAPI complex to its component single strands and free DAPI. Using optical melting profiles, we show that DAPI binding enhances the thermal stability of the poly(dT).poly(rA).poly(dT) triplex, an observation consistent with the preferential binding of the ligand to the triplex versus the duplex and single-stranded states. Our differential scanning calorimetric measurements reveal melting of the DAPI-saturated poly(dT).poly(rA).poly(dT) triplex to be associated with a lower enthalpy but greater cooperativity than melting of the corresponding DAPI-saturated poly(rA).poly(dT) duplex. Our flow linear dichroism and viscometric data are consistent with an intercalative mode of binding when DAPI interacts with both the poly(dT).poly(rA).poly(dT) triplex and the poly(rA).poly(dT) duplex. Finally, computer modeling studies suggest that a combination of both stacking and electrostatic interactions between the intercalated ligand and the host nucleic acid play important roles in the DAPI-induced stabilization of the poly(dT).poly(rA).poly(dT) triplex. In the aggregate, our results demonstrate that ligand binding can be used to induce the formation of triplex structures that do not form in the absence of the ligand. This triplex-inducing capacity has potentially important implications in the design of novel antisense, antigene, antiviral, and diagnostic strategies.
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Affiliation(s)
- Z Xu
- Department of Chemistry, Rutgers-The State University of New Jersey, New Brunswick 08903, USA
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47
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Lamm G, Pack GR. Calculation of Dielectric Constants near Polyelectrolytes in Solution. J Phys Chem B 1997. [DOI: 10.1021/jp9623453] [Citation(s) in RCA: 89] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gene Lamm
- UIC College of Medicine, 1601 Parkview Ave., Rockford, Illinois 61107
| | - George R. Pack
- UIC College of Medicine, 1601 Parkview Ave., Rockford, Illinois 61107
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48
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Yamaoka K, Yamamoto Y, Fujita Y, Ojima N. A Comparative Study on the Structure of Double-Stranded Antiparallel Poly(riboguanylic acid)·Poly(ribocytidylic acid) and Poly(deoxyriboguanylic acid)·Poly(deoxyribocytidylic acid) Helices in Solution by Pulsed Electric Linear Dichroism. J Phys Chem B 1997. [DOI: 10.1021/jp962590m] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kiwamu Yamaoka
- Department of Materials Science and Graduate Department of Gene Science, Faculty of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739, Japan
| | - Yutaka Yamamoto
- Department of Materials Science and Graduate Department of Gene Science, Faculty of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739, Japan
| | - Yoshimasa Fujita
- Department of Materials Science and Graduate Department of Gene Science, Faculty of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739, Japan
| | - Noriyuki Ojima
- Department of Materials Science and Graduate Department of Gene Science, Faculty of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739, Japan
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49
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Vovelle F, Prévost C, Durand M, Maurizot JC. Molecular modelling study of the netropsin complexation with a nucleic acid triple helix. J Biomol Struct Dyn 1996; 14:293-302. [PMID: 9016407 DOI: 10.1080/07391102.1996.10508125] [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: 02/03/2023]
Abstract
A detailed molecular mechanical study has been made on the complexes of netropsin with the double stranded oligonucleotide (dA)12.(dT)12 and with the triple helix (dA)12.(dT)12.(dT)12. The complexes were built using computer graphics and energy refined using JUMNA program. In agreement with circular dichroism experiments we have shown that 3 netropsins can bind the minor grooves of the triple helix and of the double helix. The groove geometry in the duplex and in the triplex is very similar. However a detailed analysis of the energetic terms shows, in agreement with thermal denaturation studies, that the affinity of netropsin toward the double helices is larger than towards triple helices.
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Affiliation(s)
- F Vovelle
- Centre de Biophysique Moléculaire, Orléans, France.
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50
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Rothman JH, Richards WG. Novel Hoogsteen-like bases for configurational recognition of the T-A base pair by DNA triplex formation. Biopolymers 1996; 39:795-812. [PMID: 8946801 DOI: 10.1002/(sici)1097-0282(199612)39:6%3c795::aid-bip6%3e3.0.co;2-q] [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: 02/03/2023]
Abstract
Effective sequence-specific recognition of duplex DNA is possible by triplex formation with natural oligonucleotides via Hoogsteen H-bonding. However, triplex formation is in practice limited to pyrimidine oligonucleotides binding duplex A-T or G-C base-pair DNA sequences specifically at homopurine sites in the major groove as T-A-T and C+.G-C triplets. Here we report the successful modeling of novel unnatural nucleosides that recognize the T-A DNA base pair by Hoogsteen interaction. Since the DNA triplex can be considered to assume an A-type or B-type conformation, these novel Hoogsteen nucleotides are tested within model A-type and B-type conformation triplex structures. A triplet consisting of the T-A base pair and one of the novel Hoogsteen nucleotides replaces the central T.A-T triplet in the triplex using the same deoxyribose-phosphodiester and base-deoxyribose dihedral angle configuration. The entire triplex is energy minimized and the presence of any structural or energetic perturbations due to the central triplet is assessed with respect to the unmodified energy-minimized (T.A-T)11 proposed starting structures. Incorporation of these novel triplets into both A-type and B-type natural tiplex structures provokes minimal change in the configuration of the central and adjacent triplets. The plan is to produce a series of Hoogsteen-like bases that preferentially bind the T-A major groove in either an A-type or B-type conformation. Selective recognition of the T-A major groove with respect to the G-C major groove, which presents similar keto and amine placement, is also assessed with configurational preference. Evaluation of the triplex solution structure by using these unnatural bases as binding conformational probes is a prerequisite to the further design of triplet forming bases.
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Affiliation(s)
- J H Rothman
- Physical and Theoretical, Chemistry Laboratory Oxford University, UK
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