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Double threading through DNA: NMR structural study of a bis-naphthalene macrocycle bound to a thymine-thymine mismatch.

Jourdan M, Granzhan A, Guillot R, Dumy P, Teulade-Fichou MP - Nucleic Acids Res. (2012)

Bottom Line: The ligand forms a single type of complex with the DNA, in which one of the naphthalene rings of the ligand occupies the place of one of the mismatched thymines, which is flipped out of the duplex.The second naphthalene unit of the ligand intercalates at the A-T base pair flanking the mismatch site, leading to encapsulation of its thymine residue via double stacking.The study highlights the uniqueness of this cyclobisintercalation binding mode and its importance for recognition of DNA lesion sites by small molecules.

View Article: PubMed Central - PubMed

Affiliation: CNRS UMR5250, ICMG FR2607, Département de Chimie Moléculaire, Université Joseph Fourier, 570 rue de la Chimie, 38041 Grenoble Cedex 9, France. muriel.jourdan@ujf-grenoble.fr

ABSTRACT
The macrocyclic bis-naphthalene macrocycle (2,7-BisNP), belonging to the cyclobisintercalator family of DNA ligands, recognizes T-T mismatch sites in duplex DNA with high affinity and selectivity, as evidenced by thermal denaturation experiments and NMR titrations. The binding of this macrocycle to an 11-mer DNA oligonucleotide containing a T-T mismatch was studied using NMR spectroscopy and NMR-restrained molecular modeling. The ligand forms a single type of complex with the DNA, in which one of the naphthalene rings of the ligand occupies the place of one of the mismatched thymines, which is flipped out of the duplex. The second naphthalene unit of the ligand intercalates at the A-T base pair flanking the mismatch site, leading to encapsulation of its thymine residue via double stacking. The polyammonium linking chains of the macrocycle are located in the minor and the major grooves of the oligonucleotide and participate in the stabilization of the complex by formation of hydrogen bonds with the encapsulated thymine base and the mismatched thymine remaining inside the helix. The study highlights the uniqueness of this cyclobisintercalation binding mode and its importance for recognition of DNA lesion sites by small molecules.

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Related in: MedlinePlus

Melting temperatures of TT-DNA (filled circles) and TA-DNA (empty cirlces) in the absence and in the presence of 2,7-BisNP (0–4 equivalents). Conditions: cDNA = 2 µM in cacodylate buffer, pH 6.0, [Na+] = 60 mM.
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gks067-F2: Melting temperatures of TT-DNA (filled circles) and TA-DNA (empty cirlces) in the absence and in the presence of 2,7-BisNP (0–4 equivalents). Conditions: cDNA = 2 µM in cacodylate buffer, pH 6.0, [Na+] = 60 mM.

Mentions: To confirm the selective binding of 2,7-BisNP to the 11-mer TT-DNA and get a rough idea of the binding stoichiometry and affinity, thermal denaturation experiments were performed at variable ligand-to-duplex ratios. In conditions comparable to those of the NMR experiments ([Na+] = 60 mM, pH 6), the duplex TT-DNA alone denatured at Tm = 33.0°C. The addition of 2,7-BisNP led to significant stabilization of TT-DNA, as demonstrated by large increase of the melting temperature (Figure 2). The maximal effect was observed at a 1:1 ligand-to-DNA ratio (ΔTm = 13.3°C), whereas at higher ligand loadings, the stabilization effect leveled off and slightly decreased to 12.3°C. This minor decrease is attributable to weak binding of the excess ligand to the single-stranded form, which may slightly counterbalance the strong stabilizing effect induced by duplex binding. At a ligand-to-DNA of 0.5:1, a broad melting curve was observed, indicative of incomplete saturation of the binding site (52).Figure 2.


Double threading through DNA: NMR structural study of a bis-naphthalene macrocycle bound to a thymine-thymine mismatch.

Jourdan M, Granzhan A, Guillot R, Dumy P, Teulade-Fichou MP - Nucleic Acids Res. (2012)

Melting temperatures of TT-DNA (filled circles) and TA-DNA (empty cirlces) in the absence and in the presence of 2,7-BisNP (0–4 equivalents). Conditions: cDNA = 2 µM in cacodylate buffer, pH 6.0, [Na+] = 60 mM.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3367172&req=5

gks067-F2: Melting temperatures of TT-DNA (filled circles) and TA-DNA (empty cirlces) in the absence and in the presence of 2,7-BisNP (0–4 equivalents). Conditions: cDNA = 2 µM in cacodylate buffer, pH 6.0, [Na+] = 60 mM.
Mentions: To confirm the selective binding of 2,7-BisNP to the 11-mer TT-DNA and get a rough idea of the binding stoichiometry and affinity, thermal denaturation experiments were performed at variable ligand-to-duplex ratios. In conditions comparable to those of the NMR experiments ([Na+] = 60 mM, pH 6), the duplex TT-DNA alone denatured at Tm = 33.0°C. The addition of 2,7-BisNP led to significant stabilization of TT-DNA, as demonstrated by large increase of the melting temperature (Figure 2). The maximal effect was observed at a 1:1 ligand-to-DNA ratio (ΔTm = 13.3°C), whereas at higher ligand loadings, the stabilization effect leveled off and slightly decreased to 12.3°C. This minor decrease is attributable to weak binding of the excess ligand to the single-stranded form, which may slightly counterbalance the strong stabilizing effect induced by duplex binding. At a ligand-to-DNA of 0.5:1, a broad melting curve was observed, indicative of incomplete saturation of the binding site (52).Figure 2.

Bottom Line: The ligand forms a single type of complex with the DNA, in which one of the naphthalene rings of the ligand occupies the place of one of the mismatched thymines, which is flipped out of the duplex.The second naphthalene unit of the ligand intercalates at the A-T base pair flanking the mismatch site, leading to encapsulation of its thymine residue via double stacking.The study highlights the uniqueness of this cyclobisintercalation binding mode and its importance for recognition of DNA lesion sites by small molecules.

View Article: PubMed Central - PubMed

Affiliation: CNRS UMR5250, ICMG FR2607, Département de Chimie Moléculaire, Université Joseph Fourier, 570 rue de la Chimie, 38041 Grenoble Cedex 9, France. muriel.jourdan@ujf-grenoble.fr

ABSTRACT
The macrocyclic bis-naphthalene macrocycle (2,7-BisNP), belonging to the cyclobisintercalator family of DNA ligands, recognizes T-T mismatch sites in duplex DNA with high affinity and selectivity, as evidenced by thermal denaturation experiments and NMR titrations. The binding of this macrocycle to an 11-mer DNA oligonucleotide containing a T-T mismatch was studied using NMR spectroscopy and NMR-restrained molecular modeling. The ligand forms a single type of complex with the DNA, in which one of the naphthalene rings of the ligand occupies the place of one of the mismatched thymines, which is flipped out of the duplex. The second naphthalene unit of the ligand intercalates at the A-T base pair flanking the mismatch site, leading to encapsulation of its thymine residue via double stacking. The polyammonium linking chains of the macrocycle are located in the minor and the major grooves of the oligonucleotide and participate in the stabilization of the complex by formation of hydrogen bonds with the encapsulated thymine base and the mismatched thymine remaining inside the helix. The study highlights the uniqueness of this cyclobisintercalation binding mode and its importance for recognition of DNA lesion sites by small molecules.

Show MeSH
Related in: MedlinePlus