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Binding of hairpin pyrrole and imidazole polyamides to DNA: relationship between torsion angle and association rate constants.

Han YW, Matsumoto T, Yokota H, Kashiwazaki G, Morinaga H, Hashiya K, Bando T, Harada Y, Sugiyama H - Nucleic Acids Res. (2012)

Bottom Line: It was found that association rate (k(a)) of the Py-Im polyamides with their target DNA decreased with the number of Im in the Py-Im polyamides.The structures of four-ring Py-Im polyamides derived from density functional theory revealed that the dihedral angle of the Py amide carbonyl is 14∼18°, whereas that of the Im is significantly smaller.The data explain that an increase in planarity of Py-Im polyamide induced by the incorporation of Im reduces the association rate of Py-Im polyamides.

View Article: PubMed Central - PubMed

Affiliation: Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida Honmachi, Sakyo, Kyoto 606-8501, Japan. han.yongwoon.4u@kyoto-u.ac.jp

ABSTRACT
N-methylpyrrole (Py)-N-methylimidazole (Im) polyamides are small organic molecules that bind to DNA with sequence specificity and can be used as synthetic DNA-binding ligands. In this study, five hairpin eight-ring Py-Im polyamides 1-5 with different number of Im rings were synthesized, and their binding behaviour was investigated with surface plasmon resonance assay. It was found that association rate (k(a)) of the Py-Im polyamides with their target DNA decreased with the number of Im in the Py-Im polyamides. The structures of four-ring Py-Im polyamides derived from density functional theory revealed that the dihedral angle of the Py amide carbonyl is 14∼18°, whereas that of the Im is significantly smaller. As the minor groove of DNA has a helical structure, planar Py-Im polyamides need to change their conformation to fit it upon binding to the minor groove. The data explain that an increase in planarity of Py-Im polyamide induced by the incorporation of Im reduces the association rate of Py-Im polyamides. This fundamental knowledge of the binding of Py-Im polyamides to DNA will facilitate the design of hairpin Py-Im polyamides as synthetic DNA-binding modules.

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Structures of Py–Im polyamides 1–5.
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gks897-F1: Structures of Py–Im polyamides 1–5.

Mentions: To investigate the binding properties of Py and Im in hairpin Py–Im polyamides, we designed and synthesized five hairpin eight-ring Py–Im polyamides 1–5 (Figure 1) by the Fmoc-chemistry solid-phase synthesis method. Two β-alanines were attached to the N-terminal of 1–5 (Figure 1) for the optional construction of a fluorescence Py–Im polyamide conjugate (Han et al., unpublished data). We purified 1–5 by reverse-phase HPLC, and then confirmed that the purity of 1–5 was >95% by analytical HPLC and ESI-TOFMS. The β-Dp linker at the C-terminal has ∼100-fold steric preference for A•T or T•A relative to G•C or C•G (23). Based on the recognition rule of polyamides, the target DNA sequences of 1–5 are 5′-WWWWWW-3′, 5′-WWWWCW-3′, 5′-WWWGCW-3′, 5′-WWCGCW-3′ and 5′-WGCGCW-3′, respectively, and we prepared five 5′-biotinylated hairpin DNAs (ODN1–5) (Figure 2). However, because of two β-alanines attached to the N-terminal of 1–5, steric hinderance between the tails of 1–5 and the DNA minor groove may suppress the steric preference for A•T or T•A relative to G•C or C•G. To characterize the effect of the two β-alanines, we also prepared five 5′-biotinylated hairpin DNAs (ODN6–10) (Supplementary Figure S1).Figure 1.


Binding of hairpin pyrrole and imidazole polyamides to DNA: relationship between torsion angle and association rate constants.

Han YW, Matsumoto T, Yokota H, Kashiwazaki G, Morinaga H, Hashiya K, Bando T, Harada Y, Sugiyama H - Nucleic Acids Res. (2012)

Structures of Py–Im polyamides 1–5.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC3526260&req=5

gks897-F1: Structures of Py–Im polyamides 1–5.
Mentions: To investigate the binding properties of Py and Im in hairpin Py–Im polyamides, we designed and synthesized five hairpin eight-ring Py–Im polyamides 1–5 (Figure 1) by the Fmoc-chemistry solid-phase synthesis method. Two β-alanines were attached to the N-terminal of 1–5 (Figure 1) for the optional construction of a fluorescence Py–Im polyamide conjugate (Han et al., unpublished data). We purified 1–5 by reverse-phase HPLC, and then confirmed that the purity of 1–5 was >95% by analytical HPLC and ESI-TOFMS. The β-Dp linker at the C-terminal has ∼100-fold steric preference for A•T or T•A relative to G•C or C•G (23). Based on the recognition rule of polyamides, the target DNA sequences of 1–5 are 5′-WWWWWW-3′, 5′-WWWWCW-3′, 5′-WWWGCW-3′, 5′-WWCGCW-3′ and 5′-WGCGCW-3′, respectively, and we prepared five 5′-biotinylated hairpin DNAs (ODN1–5) (Figure 2). However, because of two β-alanines attached to the N-terminal of 1–5, steric hinderance between the tails of 1–5 and the DNA minor groove may suppress the steric preference for A•T or T•A relative to G•C or C•G. To characterize the effect of the two β-alanines, we also prepared five 5′-biotinylated hairpin DNAs (ODN6–10) (Supplementary Figure S1).Figure 1.

Bottom Line: It was found that association rate (k(a)) of the Py-Im polyamides with their target DNA decreased with the number of Im in the Py-Im polyamides.The structures of four-ring Py-Im polyamides derived from density functional theory revealed that the dihedral angle of the Py amide carbonyl is 14∼18°, whereas that of the Im is significantly smaller.The data explain that an increase in planarity of Py-Im polyamide induced by the incorporation of Im reduces the association rate of Py-Im polyamides.

View Article: PubMed Central - PubMed

Affiliation: Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida Honmachi, Sakyo, Kyoto 606-8501, Japan. han.yongwoon.4u@kyoto-u.ac.jp

ABSTRACT
N-methylpyrrole (Py)-N-methylimidazole (Im) polyamides are small organic molecules that bind to DNA with sequence specificity and can be used as synthetic DNA-binding ligands. In this study, five hairpin eight-ring Py-Im polyamides 1-5 with different number of Im rings were synthesized, and their binding behaviour was investigated with surface plasmon resonance assay. It was found that association rate (k(a)) of the Py-Im polyamides with their target DNA decreased with the number of Im in the Py-Im polyamides. The structures of four-ring Py-Im polyamides derived from density functional theory revealed that the dihedral angle of the Py amide carbonyl is 14∼18°, whereas that of the Im is significantly smaller. As the minor groove of DNA has a helical structure, planar Py-Im polyamides need to change their conformation to fit it upon binding to the minor groove. The data explain that an increase in planarity of Py-Im polyamide induced by the incorporation of Im reduces the association rate of Py-Im polyamides. This fundamental knowledge of the binding of Py-Im polyamides to DNA will facilitate the design of hairpin Py-Im polyamides as synthetic DNA-binding modules.

Show MeSH
Related in: MedlinePlus