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Analyzing and Building Nucleic Acid Structures with 3DNA

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Published on: April 26, 2013

Probing DNA bulges with designed helical spirocyclic molecules.

Lizzy S Kappen¹, Yiqing Lin, Graham B Jones

¹Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.

|January 11, 2007

Summary

Researchers designed novel spirocyclic molecules to probe DNA bulge function. These compounds effectively inhibit DNA cleavage and polymerase activity at bulge sites, demonstrating potential for modifying DNA structure and function.

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Area of Science:

Molecular Biology
Medicinal Chemistry
Biochemistry

Background:

Bulged structures (unpaired bases) in nucleic acids are biologically significant.
Designing specific molecular probes for bulge function is of interest.
Previous work involved the DNA bulge-binding metabolite from neocarzinostatin chromophore (NCS-chrom).

Purpose of the Study:

To design and synthesize small helical spirocyclic molecules mimicking NCS-chrom.
To investigate the ability of these analogues to interfere with bulge-specific DNA cleavage and DNA polymerase activity.
To evaluate the binding affinities of these molecules for DNA containing bulges.

Main Methods:

Synthesis of three small helical spirocyclic molecules, including analogues with aminoglucose and N-methylfucosamine sugars.
Assay of analogue interference with NCS-chrom-mediated bulge-specific DNA cleavage.
Assessment of analogue effects on DNA polymerase I activity using bulged DNA as a template.

Main Results:

All three synthesized analogues interfered with bulge-specific cleavage by NCS-chrom and DNA polymerase activity.
Inhibition potency correlated with binding affinities for DNA containing two-base bulges.
Analogues with the natural sugar (N-methylfucosamine) in alpha-glycosidic linkage showed the highest potency as inhibitors.

Conclusions:

The designed bulge-binding compounds show potential for modifying DNA structure and function.
These molecules effectively impede nucleotide extension at DNA bulge sites.
Further development could lead to reactive species for covalently modifying bulged DNA.