Journal
CHEMBIOCHEM
Volume 17, Issue 18, Pages 1752-1758Publisher
WILEY-V C H VERLAG GMBH
DOI: 10.1002/cbic.201600282
Keywords
Bind-n-Seq; DNA recognition; NGS; polyamide; sequence determination; small molecule
Funding
- JSPS KAKENHI [24225005, 24310155, 15J00928]
- Basic Science and Platform Technology Program for Innovative Biological Medicine from Japan Agency for Medical Research and Development, AMED
- JSPS-NSF International Collaborations in Chemistry (ICC)
- Grants-in-Aid for Scientific Research [15J00928, 16H06356] Funding Source: KAKEN
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Many long pyrrole-imidazole polyamides (PIPs) have been synthesized in the search for higher specificity, with the aim of realizing the great potential of such compounds in biological and clinical areas. Among several types of PIPs, we designed and synthesized hairpin and cyclic PIPs targeting identical sequences. Bind-n-Seq analysis revealed that both bound to the intended sequences. However, adenines in the data analyzed by the previously reported Bind-n-Seq method appeared to be significantly higher in the motif ratio than thymines, even though the PIPs were not expected to distinguish A from T. We therefore examined the experimental protocol and analysis pipeline in detail and developed a new method based on Bind-n-Seq motif identification with a reference sequence (Bind-n-Seq-MR). High-throughput sequence analysis of the PIP-enriched DNA data by Bind-n-Seq-MR presented A and T comparably. Surface plasmon resonance assays were performed to validate the new method.
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