Limits...
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.

Show MeSH

Related in: MedlinePlus

DNA sequence 1 is the binding site for 1. DNA sequences 2–5 are the proposed bindingsite sequences for 2 and 3. Arrows indicatethe overall expected N to C amide bond directionality of the correspondingbound tetraintercalator.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3369501&req=5

fig3: DNA sequence 1 is the binding site for 1. DNA sequences 2–5 are the proposed bindingsite sequences for 2 and 3. Arrows indicatethe overall expected N to C amide bond directionality of the correspondingbound tetraintercalator.

Mentions: The DNA binding site for 2 and 3 was designed by creating a hybrid 14bp binding site from the individual bisintercalator binding sites.A combination of the minor–major–minor groove linkerbinding sites produces DNA sequence 2 (Figure 3). For reference, the palindromic binding site for 1 is also shown (DNA sequence 1). Arrows in thefigure have been added to emphasize the overall expected N to C directionalityof the corresponding bound tetraintercalator. We foresaw a potentialproblem with the CA intercalation step (highlighted in bold) in thehybrid DNA sequence 2. This position is expected to bethe site of intercalation for NDI unit B, but NDI inthe context of our previously reported molecules is known to preferpurine-purine intercalation steps, GG especially.30,32 For this reason, three other potential binding sites for 2 were designed in an attempt to evaluate this potential problem,listed as DNA sequences 3–5. For example, in DNA sequence 3, the major groove linker binding site is modifiedby switching a CG base pair to a GC base pair to allow for a GA intercalationstep. In DNA sequences 4 and 5, the secondminor groove linker binding site is modified. The AT base pair isswitched to a TA base pair in DNA sequence 4 and is exchangedfor a CG base pair in DNA sequence 5. All modificationsproduce a purine-purine intercalation site, with only DNA sequence5 allowing for a GG intercalation site.


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

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

DNA sequence 1 is the binding site for 1. DNA sequences 2–5 are the proposed bindingsite sequences for 2 and 3. Arrows indicatethe overall expected N to C amide bond directionality of the correspondingbound tetraintercalator.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig3: DNA sequence 1 is the binding site for 1. DNA sequences 2–5 are the proposed bindingsite sequences for 2 and 3. Arrows indicatethe overall expected N to C amide bond directionality of the correspondingbound tetraintercalator.
Mentions: The DNA binding site for 2 and 3 was designed by creating a hybrid 14bp binding site from the individual bisintercalator binding sites.A combination of the minor–major–minor groove linkerbinding sites produces DNA sequence 2 (Figure 3). For reference, the palindromic binding site for 1 is also shown (DNA sequence 1). Arrows in thefigure have been added to emphasize the overall expected N to C directionalityof the corresponding bound tetraintercalator. We foresaw a potentialproblem with the CA intercalation step (highlighted in bold) in thehybrid DNA sequence 2. This position is expected to bethe site of intercalation for NDI unit B, but NDI inthe context of our previously reported molecules is known to preferpurine-purine intercalation steps, GG especially.30,32 For this reason, three other potential binding sites for 2 were designed in an attempt to evaluate this potential problem,listed as DNA sequences 3–5. For example, in DNA sequence 3, the major groove linker binding site is modifiedby switching a CG base pair to a GC base pair to allow for a GA intercalationstep. In DNA sequences 4 and 5, the secondminor groove linker binding site is modified. The AT base pair isswitched to a TA base pair in DNA sequence 4 and is exchangedfor a CG base pair in DNA sequence 5. All modificationsproduce a purine-purine intercalation site, with only DNA sequence5 allowing for a GG intercalation site.

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