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Saneyoshi H, Mazzini S, Aviñó A, Portella G, González C, Orozco M, Marquez VE, Eritja R. Conformationally rigid nucleoside probes help understand the role of sugar pucker and nucleobase orientation in the thrombin-binding aptamer. Nucleic Acids Res 2009; 37:5589-601. [PMID: 19620215 PMCID: PMC2761269 DOI: 10.1093/nar/gkp598] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Modified thrombin-binding aptamers carrying 2′-deoxyguanine (dG) residues with locked North- or South-bicyclo[3.1.0]hexane pseudosugars were synthesized. Individual 2′-deoxyguanosines at positions dG5, dG10, dG14 and dG15 of the aptamer were replaced by these analogues where the North/anti and South/syn conformational states were confined. It was found that the global structure of the DNA aptamer was, for the most part, very accommodating. The substitution at positions 5, 10 and 14 with a locked South/syn-dG nucleoside produced aptamers with the same stability and global structure as the innate, unmodified one. Replacing position 15 with the same South/syn-dG nucleoside induced a strong destabilization of the aptamer, while the antipodal North/anti-dG nucleoside was less destabilizing. Remarkably, the insertion of a North/anti-dG nucleoside at position 14, where both pseudosugar conformation and glycosyl torsion angle are opposite with respect to the native structure, led to the complete disruption of the G-tetraplex structure as detected by NMR and confirmed by extensive molecular dynamics simulations. We conclude that conformationally locked bicyclo[3.1.0]hexane nucleosides appear to be excellent tools for studying the role of key conformational parameters that are critical for the formation of a stable, antiparallel G-tetrad DNA structures.
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Affiliation(s)
- Hisao Saneyoshi
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA, DISMA, Universita’ degli Studi di Milano. Via Celoria 2, I-20133 Milano, Italy, Institute for Research in Biomedicine, IQAC-CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Baldiri Reixac 15, E-08028 Barcelona, Joint IRB-BSC program on Computational Biology. Institute for Research in Biomedicine, Baldiri Reixac 10-12, E-08028 Barcelona and Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Department of Biochemistry, University of Barcelona, Diagonal 647, 08028 Barcelona, Instituto de Química Física Rocasolano. CSIC, C/Serrano, 119, 28006 Madrid, Spain
| | - Stefania Mazzini
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA, DISMA, Universita’ degli Studi di Milano. Via Celoria 2, I-20133 Milano, Italy, Institute for Research in Biomedicine, IQAC-CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Baldiri Reixac 15, E-08028 Barcelona, Joint IRB-BSC program on Computational Biology. Institute for Research in Biomedicine, Baldiri Reixac 10-12, E-08028 Barcelona and Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Department of Biochemistry, University of Barcelona, Diagonal 647, 08028 Barcelona, Instituto de Química Física Rocasolano. CSIC, C/Serrano, 119, 28006 Madrid, Spain
| | - Anna Aviñó
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA, DISMA, Universita’ degli Studi di Milano. Via Celoria 2, I-20133 Milano, Italy, Institute for Research in Biomedicine, IQAC-CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Baldiri Reixac 15, E-08028 Barcelona, Joint IRB-BSC program on Computational Biology. Institute for Research in Biomedicine, Baldiri Reixac 10-12, E-08028 Barcelona and Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Department of Biochemistry, University of Barcelona, Diagonal 647, 08028 Barcelona, Instituto de Química Física Rocasolano. CSIC, C/Serrano, 119, 28006 Madrid, Spain
| | - Guillem Portella
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA, DISMA, Universita’ degli Studi di Milano. Via Celoria 2, I-20133 Milano, Italy, Institute for Research in Biomedicine, IQAC-CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Baldiri Reixac 15, E-08028 Barcelona, Joint IRB-BSC program on Computational Biology. Institute for Research in Biomedicine, Baldiri Reixac 10-12, E-08028 Barcelona and Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Department of Biochemistry, University of Barcelona, Diagonal 647, 08028 Barcelona, Instituto de Química Física Rocasolano. CSIC, C/Serrano, 119, 28006 Madrid, Spain
| | - Carlos González
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA, DISMA, Universita’ degli Studi di Milano. Via Celoria 2, I-20133 Milano, Italy, Institute for Research in Biomedicine, IQAC-CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Baldiri Reixac 15, E-08028 Barcelona, Joint IRB-BSC program on Computational Biology. Institute for Research in Biomedicine, Baldiri Reixac 10-12, E-08028 Barcelona and Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Department of Biochemistry, University of Barcelona, Diagonal 647, 08028 Barcelona, Instituto de Química Física Rocasolano. CSIC, C/Serrano, 119, 28006 Madrid, Spain
| | - Modesto Orozco
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA, DISMA, Universita’ degli Studi di Milano. Via Celoria 2, I-20133 Milano, Italy, Institute for Research in Biomedicine, IQAC-CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Baldiri Reixac 15, E-08028 Barcelona, Joint IRB-BSC program on Computational Biology. Institute for Research in Biomedicine, Baldiri Reixac 10-12, E-08028 Barcelona and Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Department of Biochemistry, University of Barcelona, Diagonal 647, 08028 Barcelona, Instituto de Química Física Rocasolano. CSIC, C/Serrano, 119, 28006 Madrid, Spain
| | - Víctor E. Marquez
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA, DISMA, Universita’ degli Studi di Milano. Via Celoria 2, I-20133 Milano, Italy, Institute for Research in Biomedicine, IQAC-CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Baldiri Reixac 15, E-08028 Barcelona, Joint IRB-BSC program on Computational Biology. Institute for Research in Biomedicine, Baldiri Reixac 10-12, E-08028 Barcelona and Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Department of Biochemistry, University of Barcelona, Diagonal 647, 08028 Barcelona, Instituto de Química Física Rocasolano. CSIC, C/Serrano, 119, 28006 Madrid, Spain
- *To whom correspondence should be addressed. Tel: +34 93 4039942; Fax: +34 93 2045904;
| | - Ramon Eritja
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA, DISMA, Universita’ degli Studi di Milano. Via Celoria 2, I-20133 Milano, Italy, Institute for Research in Biomedicine, IQAC-CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Baldiri Reixac 15, E-08028 Barcelona, Joint IRB-BSC program on Computational Biology. Institute for Research in Biomedicine, Baldiri Reixac 10-12, E-08028 Barcelona and Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Department of Biochemistry, University of Barcelona, Diagonal 647, 08028 Barcelona, Instituto de Química Física Rocasolano. CSIC, C/Serrano, 119, 28006 Madrid, Spain
- *To whom correspondence should be addressed. Tel: +34 93 4039942; Fax: +34 93 2045904;
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Maderia M, Shenoy S, Van QN, Marquez VE, Barchi JJ. Biophysical studies of DNA modified with conformationally constrained nucleotides: comparison of 2'-exo (north) and 3'-exo (south) 'locked' templates. Nucleic Acids Res 2007; 35:1978-91. [PMID: 17341464 PMCID: PMC1895885 DOI: 10.1093/nar/gkm025] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The biophysical properties of oligodeoxyribonucleotides (ODNs) selectively modified with conformationally ‘locked’ bicyclo[3.1.0]hexane pseudosugars (Maier,M.A., Choi,Y., Gaus,H., Barchi,J.J. Jr, Marquez,V.E., Manoharan,M. (2004) Synthesis and characterization of oligonucleotides containing conformationally constrained bicyclo[3.1.0]hexane pseudosugar analogs Nucleic Acids Res., 32, 3642–3650) have been studied by various techniques. Six separate synthetic ODNs based on the Dickerson Drew dodecamer sequence (CGCGAAT*T*CGCG) were examined where each one (or both) of the thymidines (T*) were substituted with a bicyclic pseudosugar locked in either a North (2′-exo) or South (3′-exo) ring pucker. Circular dichroism spectroscopy, differential scanning calorimetry and 1H NMR spectroscopy were used to examine the duplex stability and conformational properties of the ODNs. Replacement of one or both thymidines with North-locked sugars (RNA-like) into the dodecamer did not greatly affect duplex formation or melt temperatures but distinct differences in thermodynamic parameters were observed. In contrast, incorporation of South-locked sugar derivatives that were predicted to stabilize this standard B-DNA, had the unexpected effect of causing a conformational equilibrium between different duplex forms at specific strand and salt concentrations. Our data and those of others suggest that although DNA can tolerate modifications with RNA-like (North) nucleotides, a more complicated spectrum of changes emerges with modifications restricted to South (DNA-like) puckers.
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Affiliation(s)
- Melissa Maderia
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702 USA, Molecular Targets Development Program and Laboratory of Proteomics and Analytical Technologies, SAIC-Frederick, Inc., Frederick, MD 21702 USA
| | - Shilpa Shenoy
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702 USA, Molecular Targets Development Program and Laboratory of Proteomics and Analytical Technologies, SAIC-Frederick, Inc., Frederick, MD 21702 USA
| | - Que N. Van
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702 USA, Molecular Targets Development Program and Laboratory of Proteomics and Analytical Technologies, SAIC-Frederick, Inc., Frederick, MD 21702 USA
| | - Victor E. Marquez
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702 USA, Molecular Targets Development Program and Laboratory of Proteomics and Analytical Technologies, SAIC-Frederick, Inc., Frederick, MD 21702 USA
| | - Joseph J. Barchi
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702 USA, Molecular Targets Development Program and Laboratory of Proteomics and Analytical Technologies, SAIC-Frederick, Inc., Frederick, MD 21702 USA
- *To whom correspondence should be addressed. +1 301 846 5905+1 301 846 6033
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