Comparative Analysis of DNA-Binding Selectivity of Hairpin and Cyclic Pyrrole-Imidazole Polyamides Based on Next-Generation Sequencing

• Published in: Chembiochem : a European journal of chemical biology Vol. 17; no. 18; pp. 1752 - 1758
• Main Authors: Kashiwazaki, Gengo, Chandran, Anandhakumar, Asamitsu, Sefan, Kawase, Takashi, Kawamoto, Yusuke, Sawatani, Yoshito, Hashiya, Kaori, Bando, Toshikazu, Sugiyama, Hiroshi
• Format: Journal Article
• Language: English
• Published: WEINHEIM Blackwell Publishing Ltd 15.09.2016; Wiley; Wiley Subscription Services, Inc
• Subjects: Bind-n-Seq; Binding Sites; Biochemistry & Molecular Biology; Chemistry, Medicinal; Deoxyribonucleic acid; DNA; DNA - chemistry; DNA - genetics; DNA recognition; Imidazoles - chemistry; Life Sciences & Biomedicine; Molecular Conformation; NGS; Nylons - chemistry; Pharmacology & Pharmacy; polyamide; Pyrroles - chemistry; Science & Technology; sequence determination; small molecule; Substrate Specificity; Surface Plasmon Resonance; small molecule; DESIGN; RECOGNITION; TELOMERE REPEAT SEQUENCES; SMALL-MOLECULE; sequence determination; ALKYLATION; SECO-CBI; polyamide; PAIR SEQUENCES; Bind-n-Seq; RESPONSE ELEMENT; GENE-EXPRESSION; DNA recognition; NGS; MINOR-GROOVE
• ISSN: 1439-4227; 1439-7633
• DOI: 10.1002/cbic.201600282

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. Hairpin and cyclic N‐methylpyrrole‐N‐methylimidazole polyamides (PIPs) with biotin were synthesized, and their binding specificities against randomized DNA sequences were evaluated with next‐generation sequencing. Both PIP types recognized DNA sequences by base‐pairing rules. We propose a Bind‐n‐Seq method that is particularly relevant for analyzing PIP binding.