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Subtle recognition of 14-base pair DNA sequences via threading polyintercalation.

Smith AR, Ikkanda BA, Holman GG, Iverson BL - Biochemistry (2012)

Bottom Line: Chem. 3, 875-881].Herein are described new NDI-based tetraintercalators with a different major groove-binding module and a reversed N to C directionality of one of the minor groove-binding modules.DNase I footprinting and kinetic analyses revealed that these new tetraintercalators are able to discriminate, by as much as 30-fold, 14 bp DNA binding sites that differ by 1 or 2 bp.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712, United States.

ABSTRACT
Small molecules that bind DNA in a sequence-specific manner could act as antibiotic, antiviral, or anticancer agents because of their potential ability to manipulate gene expression. Our laboratory has developed threading polyintercalators based on 1,4,5,8-naphthalene diimide (NDI) units connected in a head-to-tail fashion by flexible peptide linkers. Previously, a threading tetraintercalator composed of alternating minor-major-minor groove-binding modules was shown to bind specifically to a 14 bp DNA sequence with a dissociation half-life of 16 days [Holman, G. G., et al. (2011) Nat. Chem. 3, 875-881]. Herein are described new NDI-based tetraintercalators with a different major groove-binding module and a reversed N to C directionality of one of the minor groove-binding modules. DNase I footprinting and kinetic analyses revealed that these new tetraintercalators are able to discriminate, by as much as 30-fold, 14 bp DNA binding sites that differ by 1 or 2 bp. Relative affinities were found to correlate strongly with dissociation rates, while overall C(2) symmetry in the DNA-binding molecule appeared to contribute to enhanced association rates.

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Cartoon depicting threading tetraintercalation.
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fig1: Cartoon depicting threading tetraintercalation.

Mentions: With these novelspecificities and peptide linkers in mind, tetraintercalator 1 was designed, synthesized, and shown to bind specificallyto a 14 bp palindromic sequence, 5′-G/ATAA/GTAC/TTAT/C-3′.The NMR-determined structure of the 1–DNA complexverified that the molecule bound in a sequence-specific fashion withthe linkers residing in the minor–major–minor groovesas predicted33 (Figure 1). The minor groove-binding portions of 1 werethe aforementioned β-Ala3Lys linkers, but the majorgroove linker was derived from adipic acid, rather than Gly3Lys, to add overall C2 symmetry to themolecule to provide for a palindromic DNA binding site, simplifyingthe NMR structural analysis. This tetraintercalator was shown to bindto its 14 bp hybrid site with a dissociation half-life of 16 days,the longest reported half-life, to date, for any DNA-binding molecule.34


Subtle recognition of 14-base pair DNA sequences via threading polyintercalation.

Smith AR, Ikkanda BA, Holman GG, Iverson BL - Biochemistry (2012)

Cartoon depicting threading tetraintercalation.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3369501&req=5

fig1: Cartoon depicting threading tetraintercalation.
Mentions: With these novelspecificities and peptide linkers in mind, tetraintercalator 1 was designed, synthesized, and shown to bind specificallyto a 14 bp palindromic sequence, 5′-G/ATAA/GTAC/TTAT/C-3′.The NMR-determined structure of the 1–DNA complexverified that the molecule bound in a sequence-specific fashion withthe linkers residing in the minor–major–minor groovesas predicted33 (Figure 1). The minor groove-binding portions of 1 werethe aforementioned β-Ala3Lys linkers, but the majorgroove linker was derived from adipic acid, rather than Gly3Lys, to add overall C2 symmetry to themolecule to provide for a palindromic DNA binding site, simplifyingthe NMR structural analysis. This tetraintercalator was shown to bindto its 14 bp hybrid site with a dissociation half-life of 16 days,the longest reported half-life, to date, for any DNA-binding molecule.34

Bottom Line: Chem. 3, 875-881].Herein are described new NDI-based tetraintercalators with a different major groove-binding module and a reversed N to C directionality of one of the minor groove-binding modules.DNase I footprinting and kinetic analyses revealed that these new tetraintercalators are able to discriminate, by as much as 30-fold, 14 bp DNA binding sites that differ by 1 or 2 bp.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712, United States.

ABSTRACT
Small molecules that bind DNA in a sequence-specific manner could act as antibiotic, antiviral, or anticancer agents because of their potential ability to manipulate gene expression. Our laboratory has developed threading polyintercalators based on 1,4,5,8-naphthalene diimide (NDI) units connected in a head-to-tail fashion by flexible peptide linkers. Previously, a threading tetraintercalator composed of alternating minor-major-minor groove-binding modules was shown to bind specifically to a 14 bp DNA sequence with a dissociation half-life of 16 days [Holman, G. G., et al. (2011) Nat. Chem. 3, 875-881]. Herein are described new NDI-based tetraintercalators with a different major groove-binding module and a reversed N to C directionality of one of the minor groove-binding modules. DNase I footprinting and kinetic analyses revealed that these new tetraintercalators are able to discriminate, by as much as 30-fold, 14 bp DNA binding sites that differ by 1 or 2 bp. Relative affinities were found to correlate strongly with dissociation rates, while overall C(2) symmetry in the DNA-binding molecule appeared to contribute to enhanced association rates.

Show MeSH
Related in: MedlinePlus