Activation of double-stranded DNA by one pcPNA strand for its site-selective scission with CeIV/EDTA

Chemistry Letters

Volumn 36, Issue 6, 2007, Pages 780-781

  Aiba, Yuichiro ^a   Yamamoto, Yoji ^a   Komiyama, Makoto ^a  

^a UNIVERSITY OF TOKYO   (Japan)

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EID: 34347267230     PISSN: 03667022     EISSN: None     Source Type: Journal    
DOI: 10.1246/cl.2007.780     Document Type: Article

References (19)

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15. The sequence-dependency was also notable when 20-mer pcPNA was used (data not shown).
16. One conventional PNA (bearing A and T, in place of D and U) invaded homopurine-homopyrimidine sequences in double-stranded DNA (P. E. Nielsen, L. Christensen, J. Am. Chem. Soc. 1996, 118, 2287. Conditions: [Tris-HCl] = 10 mM at room temperature and pH 7.2). These specific sequences were absolutely necessary for the invasion. However, gel-shift assay gave no new bands. Accordingly, these authors concluded the formation of "single invasion complex" in terms of titration experiments.
17. Invasion of one conventional mixed-base PNA to supercoiled DNA was also proposed. However, the invasion never occurred to nonsupercoiled DNA (X. Zhang, T. Ishihara, D. R. Corey, Nucleic Acids Res. 2000, 28, 3332. Conditions: [Tris-HCl] = 10 mM at 37 or 50°C and pH 7.5).
18. m) of the duplexes of PNA 15-1, 15-2, 15-3, 15-4, and 20-1 with the corresponding complementary single-stranded DNA were 82.0, 87.5, 88.0, 84.5, and 92.0°C, respectively (Conditions: [pcPNA] = [DNA] = 2 μM, [HEPES] = 5 mM, and [NaCl] = 100 mM).
19. According to rough estimation, the scission efficiency obtained by using one 15-mer pcPNA is about 1/5-1/10 of the two-pcPNA-based cutters reported in Ref. 2. When 20-mer pcPNA is used, however, the one-pcPNA-based cutter is almost as active as the two-pcPNA-based cutter. Precise comparison is difficult because of high sequence-dependence for the scission by the one-pcPNA system.