Structural Properties of G,T-Parallel Duplexes
The structure of G,T-parallel-stranded duplexes of DNA carrying similar amounts of adenine and guanine residues is studied by means of molecular dynamics (MD) simulations and UV- and CD spectroscopies. In addition the impact of the substitution of adenine by 8-aminoadenine and guanine by 8-aminoguan...
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| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2010-01-01
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| Series: | Journal of Nucleic Acids |
| Online Access: | http://dx.doi.org/10.4061/2010/763658 |
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| _version_ | 1832567953275486208 |
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| author | Anna Aviñó Elena Cubero Raimundo Gargallo Carlos González Modesto Orozco Ramon Eritja |
| author_facet | Anna Aviñó Elena Cubero Raimundo Gargallo Carlos González Modesto Orozco Ramon Eritja |
| author_sort | Anna Aviñó |
| collection | DOAJ |
| description | The structure of G,T-parallel-stranded duplexes of DNA carrying similar amounts of adenine and guanine residues is studied by means of molecular dynamics (MD) simulations and UV- and CD spectroscopies. In addition the impact of the substitution of adenine by 8-aminoadenine and guanine by 8-aminoguanine is analyzed. The presence of 8-aminoadenine and 8-aminoguanine stabilizes the parallel duplex structure. Binding of these oligonucleotides to their target polypyrimidine sequences to form the corresponding G,T-parallel triplex was not observed. Instead, when unmodified parallel-stranded duplexes were mixed with their polypyrimidine target, an interstrand Watson-Crick duplex was formed. As predicted by theoretical calculations parallel-stranded duplexes carrying 8-aminopurines did not bind to their target. The preference for the parallel-duplex over the Watson-Crick antiparallel duplex is attributed to the strong stabilization of the parallel duplex produced by the 8-aminopurines. Theoretical studies show that the isomorphism of the triads is crucial for the stability of the parallel triplex. |
| format | Article |
| id | doaj-art-9e9cd70b0ba54ee7bb65308e1f9bbfa7 |
| institution | Kabale University |
| issn | 2090-021X |
| language | English |
| publishDate | 2010-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Journal of Nucleic Acids |
| spelling | doaj-art-9e9cd70b0ba54ee7bb65308e1f9bbfa72025-02-03T01:00:10ZengWileyJournal of Nucleic Acids2090-021X2010-01-01201010.4061/2010/763658763658Structural Properties of G,T-Parallel DuplexesAnna Aviñó0Elena Cubero1Raimundo Gargallo2Carlos González3Modesto Orozco4Ramon Eritja5Institute for Research in Biomedicine, IQAC-CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Edifici Helix, Baldiri Reixac 15, 08028 Barcelona, SpainJoint IRB-BSC Program on Computational Biology, Institute for Research in Biomedicine and Barcelona Supercomputing Center, Department of Biochemistry, University of Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, SpainDepartment of Analytical Chemistry, University of Barcelona, Diagonal 647, 08028 Barcelona, SpainDepartment of Spectroscopy and Molecular Structure, Instituto de Química Física Rocasolano, C.S.I.C. Serrano 119, 28006 Madrid, SpainJoint IRB-BSC Program on Computational Biology, Institute for Research in Biomedicine and Barcelona Supercomputing Center, Department of Biochemistry, University of Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, SpainInstitute for Research in Biomedicine, IQAC-CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Edifici Helix, Baldiri Reixac 15, 08028 Barcelona, SpainThe structure of G,T-parallel-stranded duplexes of DNA carrying similar amounts of adenine and guanine residues is studied by means of molecular dynamics (MD) simulations and UV- and CD spectroscopies. In addition the impact of the substitution of adenine by 8-aminoadenine and guanine by 8-aminoguanine is analyzed. The presence of 8-aminoadenine and 8-aminoguanine stabilizes the parallel duplex structure. Binding of these oligonucleotides to their target polypyrimidine sequences to form the corresponding G,T-parallel triplex was not observed. Instead, when unmodified parallel-stranded duplexes were mixed with their polypyrimidine target, an interstrand Watson-Crick duplex was formed. As predicted by theoretical calculations parallel-stranded duplexes carrying 8-aminopurines did not bind to their target. The preference for the parallel-duplex over the Watson-Crick antiparallel duplex is attributed to the strong stabilization of the parallel duplex produced by the 8-aminopurines. Theoretical studies show that the isomorphism of the triads is crucial for the stability of the parallel triplex.http://dx.doi.org/10.4061/2010/763658 |
| spellingShingle | Anna Aviñó Elena Cubero Raimundo Gargallo Carlos González Modesto Orozco Ramon Eritja Structural Properties of G,T-Parallel Duplexes Journal of Nucleic Acids |
| title | Structural Properties of G,T-Parallel Duplexes |
| title_full | Structural Properties of G,T-Parallel Duplexes |
| title_fullStr | Structural Properties of G,T-Parallel Duplexes |
| title_full_unstemmed | Structural Properties of G,T-Parallel Duplexes |
| title_short | Structural Properties of G,T-Parallel Duplexes |
| title_sort | structural properties of g t parallel duplexes |
| url | http://dx.doi.org/10.4061/2010/763658 |
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