Limits...
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.

Show MeSH

Related in: MedlinePlus

Threading intercalation binding mode of 2,7-BisNP (purple) to TT-DNA from NMR-restrained molecular dynamics calculations, viewed (a) from the major groove and (b) from the side of the flipped-out T17. (c) Top view of the naphthalene rings of 2,7-BisNP stacking with the encapsulated thymine T16. (d) Close-up view of the binding site (view from the minor groove, only heteroatom-bound hydrogen atoms are shown) showing direct and water-mediated hydrogen bonds (cyan sticks) between 2,7-BisNP and TT-DNA.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3367172&req=5

gks067-F8: Threading intercalation binding mode of 2,7-BisNP (purple) to TT-DNA from NMR-restrained molecular dynamics calculations, viewed (a) from the major groove and (b) from the side of the flipped-out T17. (c) Top view of the naphthalene rings of 2,7-BisNP stacking with the encapsulated thymine T16. (d) Close-up view of the binding site (view from the minor groove, only heteroatom-bound hydrogen atoms are shown) showing direct and water-mediated hydrogen bonds (cyan sticks) between 2,7-BisNP and TT-DNA.

Mentions: The 23 intermolecular distance restraints determined from the NOESY spectra were used for molecular dynamics calculation in order to obtain a model of 2,7-BisNP binding to TT-DNA that would agree with NMR data. The structure obtained after 40 ps of dynamics in explicit water is displayed in Figures 7 and 8. It shows the threading of the macrocyclic ligand through TT-DNA and the specific binding around the central thymine–thymine mismatch site. One of the naphthalene rings of 2,7-BisNP faces T6 and occupies the place of T17, which is extruded toward the major groove. This naphthalene is almost perpendicular to the main axis of A7–T16 base pair, which allows a good stacking with T16, but not with A7 (Figure 8c). The T6 remains stacked with the flanking G5 residue. The sandwiched base pair A7–T16 forms a buckle of around 38° to allow the ligand to snugly fit inside the helix. The second naphthalene ring of 2,7-BisNP also stacks with T16, leading to the ‘sandwiching’ of the latter in the cavity delineated by the two naphthalene units. The side chains of 2,7-BisNP are located in the middle of each groove. Stabilization of the complex occurs, in addition to the aforementioned π–stacking interactions, due to formation of the hydrogen bonds (Figure 8d) between the protonated amino groups of the ligand and carbonyl groups of thymines T6 and T16 (C13-NH2+ and T6O4, C19-NH2+ and T16O2, C24-NH2+ and T16O2). In particular, the hydrogen bond with T6 may explain the specificity of the ligand for T-X mismatch, while the two hydrogen bonds with the ‘encapsulated’ thymine T16 largely contribute to the stabilization of the complex. In addition, four hydrogen bonds between the positively charged amino groups and water molecules were detected (66). One of the water molecules mediates the bonding between C18–NH2+ and T16O4, while the other one mediates the interaction between C19–NH2 and two phosphate groups (pT16p).Figure 8.


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)

Threading intercalation binding mode of 2,7-BisNP (purple) to TT-DNA from NMR-restrained molecular dynamics calculations, viewed (a) from the major groove and (b) from the side of the flipped-out T17. (c) Top view of the naphthalene rings of 2,7-BisNP stacking with the encapsulated thymine T16. (d) Close-up view of the binding site (view from the minor groove, only heteroatom-bound hydrogen atoms are shown) showing direct and water-mediated hydrogen bonds (cyan sticks) between 2,7-BisNP and TT-DNA.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

gks067-F8: Threading intercalation binding mode of 2,7-BisNP (purple) to TT-DNA from NMR-restrained molecular dynamics calculations, viewed (a) from the major groove and (b) from the side of the flipped-out T17. (c) Top view of the naphthalene rings of 2,7-BisNP stacking with the encapsulated thymine T16. (d) Close-up view of the binding site (view from the minor groove, only heteroatom-bound hydrogen atoms are shown) showing direct and water-mediated hydrogen bonds (cyan sticks) between 2,7-BisNP and TT-DNA.
Mentions: The 23 intermolecular distance restraints determined from the NOESY spectra were used for molecular dynamics calculation in order to obtain a model of 2,7-BisNP binding to TT-DNA that would agree with NMR data. The structure obtained after 40 ps of dynamics in explicit water is displayed in Figures 7 and 8. It shows the threading of the macrocyclic ligand through TT-DNA and the specific binding around the central thymine–thymine mismatch site. One of the naphthalene rings of 2,7-BisNP faces T6 and occupies the place of T17, which is extruded toward the major groove. This naphthalene is almost perpendicular to the main axis of A7–T16 base pair, which allows a good stacking with T16, but not with A7 (Figure 8c). The T6 remains stacked with the flanking G5 residue. The sandwiched base pair A7–T16 forms a buckle of around 38° to allow the ligand to snugly fit inside the helix. The second naphthalene ring of 2,7-BisNP also stacks with T16, leading to the ‘sandwiching’ of the latter in the cavity delineated by the two naphthalene units. The side chains of 2,7-BisNP are located in the middle of each groove. Stabilization of the complex occurs, in addition to the aforementioned π–stacking interactions, due to formation of the hydrogen bonds (Figure 8d) between the protonated amino groups of the ligand and carbonyl groups of thymines T6 and T16 (C13-NH2+ and T6O4, C19-NH2+ and T16O2, C24-NH2+ and T16O2). In particular, the hydrogen bond with T6 may explain the specificity of the ligand for T-X mismatch, while the two hydrogen bonds with the ‘encapsulated’ thymine T16 largely contribute to the stabilization of the complex. In addition, four hydrogen bonds between the positively charged amino groups and water molecules were detected (66). One of the water molecules mediates the bonding between C18–NH2+ and T16O4, while the other one mediates the interaction between C19–NH2 and two phosphate groups (pT16p).Figure 8.

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