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Nucleic Acids Research Advance Access originally published online on January 18, 2008
Nucleic Acids Research 2008 36(5):1464-1471; doi:10.1093/nar/gkm1154
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Nucleic Acids Research, 2008, Vol. 36, No. 5 1464-1471
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Chemistry

Chiral introduction of positive charges to PNA for double-duplex invasion to versatile sequences

Takumi Ishizuka1, Junya Yoshida1, Yoji Yamamoto1, Jun Sumaoka1, Tullia Tedeschi2, Roberto Corradini2, Stefano Sforza2 and Makoto Komiyama1,*

1Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904 Japan and 2Department of Organic and Industrial Chemistry, University of Parma, Viale G.P. Usberti 17/a, University Campus, Parma, I-43100 Italy

*To whom correspondence should be addressed. Tel: +81 3 5452 5200; Fax: +81 3 5452 5209; Email: komiyama{at}mkomi.rcast.u-tokyo.ac.jp

Received November 12, 2007. Revised December 12, 2007. Accepted December 12, 2007.

Invasion of two PNA strands to double-stranded DNA is one of the most promising methods to recognize a predetermined site in double-stranded DNA (PNA = peptide nucleic acid). In order to facilitate this ‘double-duplex invasion’, a new type of PNA was prepared by using chiral PNA monomers in which a nucleobase was bound to the {alpha}-nitrogen of N-(2-aminoethyl)-D-lysine. These positively charged monomer units, introduced to defined positions in Nielsen's PNAs (poly[N-(2-aminoethyl)glycine] derivatives), promoted the invasion without impairing mismatch-recognizing activity. When pseudo-complementary nucleobases 2,6-diaminopurine and 2-thiouracil were bound to N-(2-aminoethyl)-D-lysine, the invasion successfully occurred even at highly G–C-rich regions [e.g. (G/C)7(A/T)3 and (G/C)8(A/T)2] which were otherwise hardly targeted. Thus, the scope of sequences available as the target site has been greatly expanded. In contrast with the promotion by the chiral PNA monomers derived from N-(2-aminoethyl)-D-lysine, their L-isomers hardly invaded, showing crucial importance of the D-chirality. The promotion of double-duplex invasion by the chiral (D) PNA monomer units was ascribed to both destabilization of PNA/PNA duplex and stabilization of PNA/DNA duplexes.


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