Sequence‐Specific DNA Alkylation Targeting for Kras Codon 13 Mutation by Pyrrole–Imidazole Polyamide seco‐CBI Conjugates |
| |
| Authors: | Rhys Dylan Taylor Sefan Asamitsu Tomohiro Takenaka Makoto Yamamoto Kaori Hashiya Yusuke Kawamoto Dr Toshikazu Bando Prof Dr Hiroki Nagase Prof Dr Hiroshi Sugiyama |
| |
| Institution: | 1. Department of Chemistry, Kyoto University, Kitashirakawa‐Oiwaketyo, Sakyo, Kyoto, 606‐8502 (Japan), Fax: (+81)?75‐753‐3670;2. Chiba Cancer Center Research Institute, Chuo‐Ku, Chiba 260‐8717 (Japan);3. Institute for Integrated Cell‐Materials Science (iCeMS) Kyoto University, Sakyo, Kyoto, 606‐8502 (Japan);4. CREST (Japan) Science and Technology Corporation (JST), Sanbancho, Chiyoda‐ku, Tokyo 102‐0075 (Japan) |
| |
| Abstract: | Hairpin N‐methylpyrrole‐N‐methylimidazole polyamide seco‐CBI conjugates 2 – 6 were designed for synthesis by Fmoc solid‐phase synthesis, and their DNA‐alkylating activities against the Kras codon 13 mutation were compared by high‐resolution denaturing gel electrophoresis with 225 base pair (bp) DNA fragments. Conjugate 5 had high reactivity towards the Kras codon 13 mutation site, with alkylation occurring at the A of the sequence 5′‐ACGTCACC A ‐3′ (site 2), including minor 1 bp‐mismatch alkylation against wild type 5′‐ACG C CACC A ‐3′ (site 3). Conjugate 6 , which differs from conjugate 5 by exchanging one Py unit with a β unit, showed high selectivity but only weakly alkylated the A of 5′‐ACGTCACC A ‐3′ (site 2). The hairpin polyamide seco‐CBI conjugate 5 thus alkylates according to Dervan′s pairing rule with the pairing recognition which β/β pair targets T–A and A–T pairs. SPR and a computer‐minimized model suggest that 5 binds to the target sequence with high affinity in a hairpin conformation, allowing for efficient DNA alkylation. |
| |
| Keywords: | adenine alkylation Kras codon 13 mutation PAGE analysis pyrrole– imidazole polyamides sequence specificity |
|
|
