DNA sequence selectivity of hairpin polyamide turn units
Abstract
A class of hairpin polyamides linked by 3,4-diaminobutyric acid, resulting in a β-amine residue at the turn unit, showed improved binding affinities relative to their α-amino-γ-turn analogs for particular sequences. We incorporated β-amino-γ-turns in six-ring polyamides and determined whether there are any sequence preferences under the turn unit by quantitative footprinting titrations. Although there was an energetic penalty for G·C and C·G base pairs, we found little preference for T·A over A·T at the β-amino-γ-turn position. Fluorine and hydroxyl substituted α-amino-γ-turns were synthesized for comparison. Their binding affinities and specificities in the context of six-ring polyamides demonstrated overall diminished affinity and no additional specificity at the turn position. We anticipate that this study will be a baseline for further investigation of the turn subunit as a recognition element for the DNA minor groove.
Additional Information
© 2009 Elsevier. Received 24 February 2009; revised 13 March 2009; accepted 18 March 2009. Available online 24 March 2009. We are grateful to the National Institutes of Health for research support. We thank David M. Chenoweth for helpful discussions. Mass spectrometry analyses were performed in the Mass Spectrometry Facility of the Division of Chemistry and Chemical Engineering at the California Institute of Technology. Supplementary data associated with this article can be found, in the online version, at doi:10.1016/j.bmcl.2009.03.072.Attached Files
Accepted Version - nihms-279883.pdf
Supplemental Material - SupTable1.pdf
Supplemental Material - SupTable2.pdf
Supplemental Material - SupTable3.pdf
Supplemental Material - SupTable4.pdf
Supplemental Material - SuppData.doc
Supplemental Material - SuppFig1.jpg
Supplemental Material - SuppFig2.jpg
Supplemental Material - SuppFig3.jpg
Supplemental Material - SuppFig4.jpg
Supplemental Material - SuppFig5.jpg
Supplemental Material - SuppFig6.jpg
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Additional details
- PMCID
- PMC3062503
- Eprint ID
- 15289
- Resolver ID
- CaltechAUTHORS:20090825-081429009
- NIH
- Created
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2009-09-09Created from EPrint's datestamp field
- Updated
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2021-11-08Created from EPrint's last_modified field