Detection of CAG repeat DNA sequences by pyrene-functionalized pyrrole-imidazole polyamides

• Published in: Bioorganic & medicinal chemistry Vol. 15; no. 22; pp. 6937 - 6942
• Main Authors: Bando, Toshikazu, Fujimoto, Jun, Minoshima, Masafumi, Shinohara, Ken-ichi, Sasaki, Shunta, Kashiwazaki, Gengo, Mizumura, Masatoshi, Sugiyama, Hiroshi
• Format: Journal Article
• Language: English
• Published: Oxford Elsevier Ltd 15.11.2007; Elsevier Science
• Subjects: Analytical, structural and metabolic biochemistry; Base Sequence; Biological and medical sciences; CAG repeat; DNA - analysis; Dna, deoxyribonucleoproteins; Excimer; Fluorescence; Fundamental and applied biological sciences. Psychology; Imidazoles - chemistry; Nucleic acids; Nylons - chemical synthesis; Nylons - chemistry; Oligodeoxyribonucleotides - chemistry; Pyrene; Pyrenes - chemistry; Pyrroles - chemistry; Py–Im polyamide; Sequence Analysis, DNA - methods; Spectrometry, Fluorescence - methods; Trinucleotide Repeats; Pyrene; Py–Im polyamide; CAG repeat; Excimer; Sequence specificity; Nylon; Minor groove; Repeated sequence; Py-Im polyamide; Pyrene derivatives; Fluorescence spectrometry; Biological fixation; DNA; Solid phase; Fluorescent compound; Detection; Chemical synthesis
• ISSN: 0968-0896; 1464-3391
• DOI: 10.1016/j.bmc.2007.07.055

Five N-methylpyrrole- N-methylimidazole (Py–Im) polyamides possessing a fluorescent pyrene were synthesized by Fmoc solid-phase synthesis using Py/Im monomers and pyrenylbutyl-pyrrole monomer compound 9. The steady state fluorescence of conjugates 1– 5 was examined in the presence and absence of (CAG) 12-containing oligodeoxynucleotides (ODNs) 1 and 2. Of the conjugates, conjugate 1 showed no background emission around 470 nm in the absence of ODNs, and a clear increase of emission at 475 nm was observed upon addition of ODNs 1 and 2. The emission of conjugate 1 at 475 nm increased linearly with the concentration of ODN and the number of CAG repeats. The results indicate that conjugate 1 efficiently forms a pyrene excimer upon binding in the minor groove of DNA.