DNA and RNA binding properties of an arginine-based ‘Extended Chiral Box’ Peptide Nucleic Acid Alessandro Calabretta, Tullia Tedeschi, Roberto Corradini, Rosangela Marchelli, Stefano Sforza ⇑ Department of Organic and Industrial Chemistry, University of Parma, Viale G.P. Usberti 17a, University Campus, I-43124 Parma, Italy article info Article history: Received 3 September 2010 Revised 4 November 2010 Accepted 8 November 2010 Keywords: Chiral PNA Binding selectivity DNA recognition RNA recognition Backbone modification abstract Lys-based ‘chiral box’ Peptide Nucleic Acids (PNAs with three adjacent 2D-Lys-based chiral monomers) have shown unsurpassed specificity in DNA recognition. In this Letter, the binding performances of argi- nine-based chiral PNAs were evaluated for PNAs containing in the middle part of the strand either a 2D,5L-Arg monomer or three adjacent 2D-; 2D,5L-; 5L-Arg monomers (‘Extended Chiral Box’), a combi- nation never studied before. The binding performances of the PNAs were studied by evaluating the melt- ing temperatures of fullmatch and mismatch PNA–DNA and PNA–RNA hybrids and by studying their structure by circular dichroism (CD). The data indicated that the arginine side chains inserted in the PNA structure are perfectly equivalent to lysine side chains as far as oligonucleotide recognition is con- cerned. The insertion of an ‘Extended Chiral Box’ into PNA differently influences the binding properties to DNA and RNA: the additional side chains had no observable effect on binding affinity and selectivity toward DNA, whereas, seemed to slightly disturb the binding affinity to RNA but at the same time highly enhancing the recognition selectivity. Ó 2010 Elsevier Ltd. All rights reserved. 1. Introduction The development of new molecules able to efficiently bind spe- cific nucleic acid sequences is one of the hot topics in the field of nucleic acid chemistry. Improved DNA and/or RNA recognition is actually mandatory for many diagnostic and therapeutic applica- tions. Oligonucleotide-like molecules, either modified in the back- bone 1 or in the nucleobases, 2 allowed to obtain, in some cases, promising probes able to bind complementary sequences with en- hanced affinity and specificity. Peptide Nucleic Acids (PNAs, Fig. 1A) are among the most promising oligonucleotide analogs. 3 PNAs are chemically different from natural nucleic acids, due to their backbone structure based on a pseudopeptide motif and for the carboxymethylene linker between the backbone and the nucle- obases. Anyway, they are able to bind complementary DNA or RNA sequences via Watson–Crick interactions. Due to the neutral back- bone and the different structure, PNA–DNA and PNA–RNA com- plexes show enhanced affinity and specificity, when compared to DNA–DNA or DNA–RNA counterparts. 3 Moreover, PNAs have a very high enzymatic and chemical stability. 4 Many modifications of the basic PNA structure have been studied in order to further improve their properties. The introduction of different type of modifications within the backbone, based on cyclic or acyclic structures, 5 led to significant improvements in terms of affinity for complementary sequences, selectivity, solubility, or bioavaibility. 6 In particular, chiral amino acid-based PNAs seem to be particu- larly interesting: 5,7 these molecules are characterized by the pres- ence of one or more chiral monomers substituted in position 2 or 5 0040-4039/$ - see front matter Ó 2010 Elsevier Ltd. All rights reserved. doi:10.1016/j.tetlet.2010.11.034 ⇑ Corresponding author. Fax: +39 0521 905472. E-mail address: stefano.sforza@unipr.it (S. Sforza). N H N O O Base R 1 R 2 1 2 3 4 5 6 N H N O O Base 1 2 3 4 5 6 N H N O O Base R 1 2 3 4 5 6 N H N O O Base R 1 2 3 4 5 6 N H N O O Base R N H N O O Base R N H N O O Base R A B D C E Figure 1. Structure of standard PNA (A) and of different generation of chiral PNAs: 2D (B); 5L (C); 2D,5L (D) and 2D-Chiral Box (E). Tetrahedron Letters 52 (2011) 300–304 Contents lists available at ScienceDirect Tetrahedron Letters journal homepage: www.elsevier.com/locate/tetlet