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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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1D imino spectra of (a) free TT-DNA at 10°C and (b) 2,7-BisNP–TT-DNA complex at 5°C. T16 and G5, which undergo most significant shifts, are highlighted in bold.
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gks067-F3: 1D imino spectra of (a) free TT-DNA at 10°C and (b) 2,7-BisNP–TT-DNA complex at 5°C. T16 and G5, which undergo most significant shifts, are highlighted in bold.

Mentions: The exchangeable imino protons were assigned with the 1D and 2D NOESY spectrum recorded in 90% H2O at 10 or 5°C. The 1D spectrum shows three main sets of imino proton: thymine imino protons in the range 13.5–14.0 ppm, guanine imino proton in the range 12.8–13.1 ppm and two resonances at 10.56 ppm and 10.61 ppm, corresponding to the mismatched thymines (Figure 3a). It is known that non-hydrogen-bound imino protons, such as those of bulged bases (56), bases facing abasic sites (57), or non-Watson–Crick base pairs like base mismatches (58–62) or wobble base pairs (63,64) resonate in this range. These resonances were assigned to the imino protons of T6 and T17, respectively, based on the cross-peaks observed in the 2D spectra. However, it was not possible to deduce the hydrogen bonding pattern between T6 and T17, as the imino protons of these bases were almost coincident. Nevertheless, we can conclude that the T–T mismatch does not introduce dramatic distortions to the duplex structure, as chemical shifts of the DNA protons are in the common range observed for regular DNA.Figure 3.


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)

1D imino spectra of (a) free TT-DNA at 10°C and (b) 2,7-BisNP–TT-DNA complex at 5°C. T16 and G5, which undergo most significant shifts, are highlighted in bold.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

gks067-F3: 1D imino spectra of (a) free TT-DNA at 10°C and (b) 2,7-BisNP–TT-DNA complex at 5°C. T16 and G5, which undergo most significant shifts, are highlighted in bold.
Mentions: The exchangeable imino protons were assigned with the 1D and 2D NOESY spectrum recorded in 90% H2O at 10 or 5°C. The 1D spectrum shows three main sets of imino proton: thymine imino protons in the range 13.5–14.0 ppm, guanine imino proton in the range 12.8–13.1 ppm and two resonances at 10.56 ppm and 10.61 ppm, corresponding to the mismatched thymines (Figure 3a). It is known that non-hydrogen-bound imino protons, such as those of bulged bases (56), bases facing abasic sites (57), or non-Watson–Crick base pairs like base mismatches (58–62) or wobble base pairs (63,64) resonate in this range. These resonances were assigned to the imino protons of T6 and T17, respectively, based on the cross-peaks observed in the 2D spectra. However, it was not possible to deduce the hydrogen bonding pattern between T6 and T17, as the imino protons of these bases were almost coincident. Nevertheless, we can conclude that the T–T mismatch does not introduce dramatic distortions to the duplex structure, as chemical shifts of the DNA protons are in the common range observed for regular DNA.Figure 3.

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