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Mixed guanine, adenine base quartets: possible roles of protons and metal ions in their stabilization. J Biol Inorg Chem 2017; 23:41-49. [PMID: 29218641 PMCID: PMC5756560 DOI: 10.1007/s00775-017-1507-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 10/18/2017] [Indexed: 11/17/2022]
Abstract
Structural variations of the well-known guanine quartet (G4) motif in nucleic acid structures, namely substitution of two guanine bases (G) by two adenine (A) nucleobases in mutual trans positions, are discussed and studied by density functional theory (DFT) methods. This work was initiated by three findings, namely (1) that GA mismatches are compatible with complementary pairing patterns in duplex-DNA structures and can, in principle, be extended to quartet structures, (2) that GA pairs can come in several variations, including with a N1 protonated adeninium moiety (AH), and (3) that cross-linking of the major donor sites of purine nucleobases (N1 and N7) by transition metal ions of linear coordination geometries produces planar purine quartets, as demonstrated by some of us in the past. Here, possible structures of mixed AGAG quartets both in the presence of protons and alkali metal ions are discussed, and in particular, the existence of a putative four-purine, two-metal motif.
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Bansal M, Jayaram B, Mittal A. Nucleic acids in disease and disorder: Understanding the language of life emerging from the ‘ABC’ of DNA. J Biosci 2012; 37:375-8. [DOI: 10.1007/s12038-012-9226-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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3
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Galeone A, Mayol L, Randazzo A, Virgilio A, Virno A. Effect of the introduction of an A-residue into a quadruplex forming oligonucleotide containing a 5'-5' polarity of inversion site. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2008; 26:1151-4. [PMID: 18058555 DOI: 10.1080/15257770701527034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Preliminary NMR studies on structure formed by sequence 3'-TGA-5'-5'-GGT-3' are described. We proposed the formation of a tetramolecular quadruplex in which strands are equivalent to each other and three G-tetrads are present. The possibility of the occurrence of an A-tetrad also is discussed.
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Affiliation(s)
- A Galeone
- Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli Federico II, Napoli, Italy.
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Affiliation(s)
- N Srinivasan
- Molecular Biophysics Unit; Indian Institute of Science; Bangalore 560 012; India
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Amo-Ochoa P, Sanz Miguel PJ, Lax P, Alonso I, Roitzsch M, Zamora F, Lippert B. Models of Putative (AH)G(AH)G Nucleobase Quartets. Angew Chem Int Ed Engl 2005; 44:5670-4. [PMID: 16086347 DOI: 10.1002/anie.200500896] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Pilar Amo-Ochoa
- Departamento de Tecnología Industrial, Universidad Alfonso X El Sabio, 28691 Villanueva de la Cañada, 28049 Madrid, Spain
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Amo-Ochoa P, Sanz Miguel PJ, Lax P, Alonso I, Roitzsch M, Zamora F, Lippert B. Modelle möglicher (AH)G(AH)G-Nucleobasenquartette. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200500896] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Chowdhury S, Bansal M. Modelling studies on neurodegenerative disease-causing triplet repeat sequences d(GGC/GCC)n and d(CAG/CTG)n. J Biosci 2001; 26:649-65. [PMID: 11807295 DOI: 10.1007/bf02704763] [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: 01/29/2023]
Abstract
Model building and molecular mechanics studies have been carried out to examine the potential structures for d(GGC/GCC)5 and d(CAG/CTG)5 that might relate to their biological function and association with triplet repeat expansion diseases. Model building studies suggested that hairpin and quadruplex structures could be formed with these repeat sequences. Molecular mechanics studies have demonstrated that the hairpin and hairpin dimer structures of triplet repeat sequences formed by looping out of the two strands are as favourable as the corresponding B-DNA type hetero duplex structures. Further, at high salt condition, Greek key type quadruplex structures are energetically comparable with hairpin dimer and B-DNA type duplex structures. All tetrads in the quadruplex structures are well stacked and provide favourable stacking energy values. Interestingly, in the energy minimized hairpin dimer and Greek key type quadruplex structures, all the bases even in the non-G tetrads are cyclically hydrogen bonded, even though the A, C and T-tetrads were not hydrogen bonded in the starting structures.
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Affiliation(s)
- S Chowdhury
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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Chowdhury S, Bansal M. G-Quadruplex Structure Can Be Stable with Only Some Coordination Sites Being Occupied by Cations: A Six-Nanosecond Molecular Dynamics Study. J Phys Chem B 2001. [DOI: 10.1021/jp010929l] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shibasish Chowdhury
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012, India
| | - Manju Bansal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012, India
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Spacková N, Berger I, Sponer J. Structural dynamics and cation interactions of DNA quadruplex molecules containing mixed guanine/cytosine quartets revealed by large-scale MD simulations. J Am Chem Soc 2001; 123:3295-307. [PMID: 11457065 DOI: 10.1021/ja002656y] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Large-scale molecular dynamics (MD) simulations have been utilized to study G-DNA quadruplex molecules containing mixed GCGC and all-guanine GGGG quartet layers. Incorporation of mixed GCGC quartets into G-DNA stems substantially enhances their sequence variability. The mixed quadruplexes form rigid assemblies that require integral monovalent cations for their stabilization. The interaction of cations with the all-guanine quartets is the leading contribution for the stability of the four-stranded assemblies, while the mixed quartets are rather tolerated within the structure. The simulations predict that two cations are preferred to stabilize a four-layer quadruplex stem composed of two GCGC and two all-guanine quartets. The distribution of cations in the structure is influenced by the position of the GCGC quartets within the quadruplex, the presence and arrangement of thymidine loops connecting the guanine/cytosine stretches forming the stems, and the cation type present (Na(+) or K(+)). The simulations identify multiple nanosecond-scale stable arrangements of the thymidine loops present in the molecules investigated. In these thymidine loops, several structured pockets are identified capable of temporarily coordinating cations. However, no stable association of cations to a loop has been observed. The simulations reveal several paths through the thymidine loop regions that can be followed by the cations when exchanging between the central ion channel in the quadruplex stem and the surrounding solvent. We have carried out 20 independent simulations while the length of simulations reaches a total of 90 ns, rendering this study one of the most extensive MD investigations carried out on nucleic acids so far. The trajectories provide a largely converged characterization of the structural dynamics of these four-stranded G-DNA molecules.
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Affiliation(s)
- N Spacková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, and National Centre for Biomolecular Research, Královopolská 135, 612 65 Brno, Czech Republic
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Chowdhury S, Bansal M. A nanosecond molecular dynamics study of antiparallel d(G)7 quadruplex structures: effect of the coordinated cations. J Biomol Struct Dyn 2001; 18:647-69. [PMID: 11334103 DOI: 10.1080/07391102.2001.10506696] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Nanosecond scale molecular dynamics simulations have been performed on antiparallel Greek key type d(G7) quadruplex structures with different coordinated ions, namely Na+ and K+ ion, water and Na+ counter ions, using the AMBER force field and Particle Mesh Ewald technique for electrostatic interactions. Antiparallel structures are stable during the simulation, with root mean square deviation values of approximately 1.5 A from the initial structures. Hydrogen bonding patterns within the G-tetrads depend on the nature of the coordinated ion, with the G-tetrad undergoing local structural variation to accommodate different cations. However, alternating syn-anti arrangement of bases along a chain as well as in a quartet is maintained through out the MD simulation. Coordinated Na+ ions, within the quadruplex cavity are quite mobile within the central channel and can even enter or exit from the quadruplex core, whereas coordinated K+ ions are quite immobile. MD studies at 400K indicate that K+ ion cannot come out from the quadruplex core without breaking the terminal G-tetrads. Smaller grooves in antiparallel structures are better binding sites for hydrated counter ions, while a string of hydrogen bonded water molecules are observed within both the small and large grooves. The hydration free energy for the K+ ion coordinated structure is more favourable than that for the Na+ ion coordinated antiparallel quadruplex structure.
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Affiliation(s)
- S Chowdhury
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore
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Stefl R, Spacková N, Berger I, Koca J, Sponer J. Molecular dynamics of DNA quadruplex molecules containing inosine, 6-thioguanine and 6-thiopurine. Biophys J 2001; 80:455-68. [PMID: 11159416 PMCID: PMC1301247 DOI: 10.1016/s0006-3495(01)76028-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The ability of the four-stranded guanine (G)-DNA motif to incorporate nonstandard guanine analogue bases 6-oxopurine (inosine, I), 6-thioguanine (tG), and 6-thiopurine (tI) has been investigated using large-scale molecular dynamics simulations. The simulations suggest that a G-DNA stem can incorporate inosines without any marked effect on its structure and dynamics. The all-inosine quadruplex stem d(IIII)(4) shows identical dynamical properties as d(GGGG)(4) on the nanosecond time scale, with both molecular assemblies being stabilized by monovalent cations residing in the channel of the stem. However, simulations carried out in the absence of these cations show dramatic differences in the behavior of d(GGGG)(4) and d(IIII)(4). Whereas vacant d(GGGG)(4) shows large fluctuations but does not disintegrate, vacant d(IIII)(4) is completely disrupted within the first nanosecond. This is a consequence of the lack of the H-bonds involving the N2 amino group that is not present in inosine. This indicates that formation of the inosine quadruplex could involve entirely different intermediate structures than formation of the guanosine quadruplex, and early association of cations in this process appears to be inevitable. In the simulations, the incorporation of 6-thioguanine and 6-thiopurine sharply destabilizes four-stranded G-DNA structures, in close agreement with experimental data. The main reason is the size of the thiogroup leading to considerable steric conflicts and expelling the cations out of the channel of the quadruplex stem. The G-DNA stem can accommodate a single thioguanine base with minor perturbations. Incorporation of a thioguanine quartet layer is associated with a large destabilization of the G-DNA stem whereas the all-thioguanine quadruplex immediately collapses.
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Affiliation(s)
- R Stefl
- Laboratory of Biomolecular Structure and Dynamics, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic
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Chowdhury S, Bansal M. Effect of coordinated ions on structure and flexiblity of parallel G-quandruplexes: a molecular dynamics study. J Biomol Struct Dyn 2000; 18:11-28. [PMID: 11021649 DOI: 10.1080/07391102.2000.10506581] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Single tract guanine residues can associate to form stable parallel quadruplex structures in the presence of certain cations. Nanosecond scale molecular dynamics simulations have been performed on fully solvated fibre model of parallel d(G7) quadruplex structures with Na+ or K+ ions coordinated in the cavity formed by the 06 atoms of the guanine bases. The AMBER 4.1 force field and Particle Mesh Ewald technique for electrostatic interactions have been used in all simulations. These quadruplex structures are stable during the simulation, with the middle four base tetrads showing root mean square deviation values between 0.5 to 0.8 A from the initial structure as well the high resolution crystal structure. Even in the absence of any coordinated ion in the initial structure, the G-quadruplex structure remains intact throughout the simulation. During the 1.1 ns MD simulation, one Na+ counter ion from the solvent as well as several water molecules enter the central cavity to occupy the empty coordination sites within the parallel quadruplex and help stabilize the structure. Hydrogen bonding pattern depends on the nature of the coordinated ion, with the G-tetrad undergoing local structural variation to accommodate cations of different sizes. In the absence of any coordinated ion, due to strong mutual repulsion, 06 atoms within G-tetrad are forced farther apart from each other, which leads to a considerably different hydrogen bonding scheme within the G-tetrads and very favourable interaction energy between the guanine bases constituting a G-tetrad. However, a coordinated ion between G-tetrads provides extra stacking energy for the G-tetrads and makes the quadruplex structure more rigid. Na+ ions, within the quadruplex cavity, are more mobile than coordinated K+ ions. A number of hydrogen bonded water molecules are observed within the grooves of all quadruplex structures.
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Affiliation(s)
- S Chowdhury
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore
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Gu J, Leszczynski J. A Remarkable Alteration in the Bonding Pattern: An HF and DFT Study of the Interactions between the Metal Cations and the Hoogsteen Hydrogen-Bonded G-Tetrad. J Phys Chem A 2000. [DOI: 10.1021/jp000591f] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Jiande Gu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 200031 P.R. China, and Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, Jackson, Mississippi 39217
| | - Jerzy Leszczynski
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 200031 P.R. China, and Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, Jackson, Mississippi 39217
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Gu J, Leszczynski J. Structures and Properties of Mixed DNA Bases Tetrads: Nonempirical ab Inito HF and DFT Studies. J Phys Chem A 2000. [DOI: 10.1021/jp992944k] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jiande Gu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 200031, P. R. China, and The Computational Center of Molecular Structure and Interactions, Department of Chemistry, Jackson State University, Jackson, Mississippi 39217
| | - Jerzy Leszczynski
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 200031, P. R. China, and The Computational Center of Molecular Structure and Interactions, Department of Chemistry, Jackson State University, Jackson, Mississippi 39217
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Gu J, Leszczynski J, Bansal M. A new insight into the structure and stability of Hoogsteen hydrogen-bonded G-tetrad: an ab initio SCF study. Chem Phys Lett 1999. [DOI: 10.1016/s0009-2614(99)00821-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Špačková N, Berger I, Šponer J. Nanosecond Molecular Dynamics Simulations of Parallel and Antiparallel Guanine Quadruplex DNA Molecules. J Am Chem Soc 1999. [DOI: 10.1021/ja984449s] [Citation(s) in RCA: 144] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Nad'a Špačková
- Contribution from the Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, Department of Physical Electronics, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic, and Institute for Molecular Biology and Biophysics, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Imre Berger
- Contribution from the Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, Department of Physical Electronics, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic, and Institute for Molecular Biology and Biophysics, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Jiří Šponer
- Contribution from the Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, Department of Physical Electronics, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic, and Institute for Molecular Biology and Biophysics, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
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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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Kiran MR, Bansal M. Molecular dynamics simulations on parallel and antiparallel C.G*G triplexes. J Biomol Struct Dyn 1998; 16:511-26. [PMID: 10052610 DOI: 10.1080/07391102.1998.10508266] [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
Molecular dynamics (MD) studies have been carried out on the Hoogsteen hydrogen bonded parallel and the reverse Hoogsteen hydrogen bonded antiparallel C.G*G triplexes. Earlier, the molecular mechanics studies had shown that the parallel structure was energetically more favourable than the antiparallel structure. To characterize the structural stability of the two triplexes and to investigate whether the antiparallel structure can transit to an energetically more favourable structure, due to the local fluctuations in the structure during the MD simulation, the two structures were subjected to 200ps of constant temperature vacuum MD simulations at 300K. Initially no constraints were applied to the structures and it was observed that for the antiparallel triplex, the structure showed a large root mean square deviation from the starting structure within the first 12ps and the N4-H41--O6 hydrogen bond in the WC duplex got distorted due to a high propeller twist and a moderate increase in the opening angle in the basepairs. Starting from an initial value of 30 degrees , helical twist of the average structure from this simulation had a value of 36 degrees , while the parallel structure stabilized at a twist of 33 degrees. In spite of the hydrogen bond distortions in the antiparallel triplex, it was energetically comparable to the parallel triplex. To examine the structural characteristics of an undistorted structure, another MD simulation was performed on the antiparallel triplex by constraining all the hydrogen bonds. This structure stabilized at an average twist of 33 degrees. In the course of the dynamics though the energy of the molecule - compared to the initial structure - improved, it did not become comparable to the parallel structure. Energy minimization studies performed in the presence of explicit water and counterions also showed the two structures to be equally favourable energetically. Together these results indicate that the parallel C.G*G triplex with Hoogsteen hydrogen bonds also represents a stereochemically and energetically favourable structure for this class of triplexes.
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Affiliation(s)
- M R Kiran
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore
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Salisbury SA, Wilson SE, Powell HR, Kennard O, Lubini P, Sheldrick GM, Escaja N, Alazzouzi E, Grandas A, Pedroso E. The bi-loop, a new general four-stranded DNA motif. Proc Natl Acad Sci U S A 1997; 94:5515-8. [PMID: 9159103 PMCID: PMC20809 DOI: 10.1073/pnas.94.11.5515] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The crystal structure of the cyclic octanucleotide d<pATTCATTC> contains two independent molecules that form a novel quadruplex by means of intermolecular Watson-Crick A.T pairs and base stacking. A virtually identical quadruplex composed of G.C pairs was found by earlier x-ray analysis of the linear heptamer d(GCATGCT), when the DNA was looped in the crystal. The close correspondence between these two structures of markedly dissimilar oligonucleotides suggests that they are both examples of a previously unrecognized motif. Their nucleotide sequences have little in common except for two separated 5'-purine-pyrimidine dinucleotides forming the quadruplex, and by implication these so-called "bi-loops" could occur widely in natural DNA. Such structures provide a mechanism for noncovalent linking of polynucleotides in vivo. Their capacity to associate by base stacking, demonstrated in the crystal structure of d(GCATGCT), creates a compact molecular framework made up of four DNA chains within which strand exchange could take place.
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Affiliation(s)
- S A Salisbury
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, United Kingdom
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