title: Incorporation of thio-pseudoisocytosine into triplex-forming peptide nucleic acids for enhanced recognition of RNA duplexes.
abstract: Peptide nucleic acids (PNAs) have been developed for applications in biotechnology and therapeutics. There is great potential in the development of chemically modified PNAs or other triplex-forming ligands that selectively bind to RNA duplexes, but not single-stranded regions, at near-physiological conditions. Here, we report on a convenient synthesis route to a modified PNA monomer, thio-pseudoisocytosine (L), and binding studies of PNAs incorporating the monomer L. Thermal melting and gel electrophoresis studies reveal that L-incorporated 8-mer PNAs have superior affinity and specificity in recognizing the duplex region of a model RNA hairpin to form a pyrimidine motif major-groove RNA2-PNA triplex, without appreciable binding to single-stranded regions to form an RNA-PNA duplex or, via strand invasion, forming an RNA-PNA2 triplex at near-physiological buffer condition. In addition, an L-incorporated 8-mer PNA shows essentially no binding to single-stranded or double-stranded DNA. Furthermore, an L-modified 6-mer PNA, but not pseudoisocytosine (J) modified or unmodified PNA, binds to the HIV-1 programmed -1 ribosomal frameshift stimulatory RNA hairpin at near-physiological buffer conditions. The stabilization of an RNA2-PNA triplex by L modification is facilitated by enhanced van der Waals contacts, base stacking, hydrogen bonding and reduced dehydration energy. The destabilization of RNA-PNA and DNA-PNA duplexes by L modification is due to the steric clash and loss of two hydrogen bonds in a Watson-Crick-like G-L pair. An RNA2-PNA triplex is significantly more stable than a DNA2-PNA triplex, probably because the RNA duplex major groove provides geometry compatibility and favorable backbone-backbone interactions with PNA. Thus, L-modified triplex-forming PNAs may be utilized for sequence-specifically targeting duplex regions in RNAs for biological and therapeutic applications.
authors.affiliation: Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371.
authors.forename: Gitali
authors.initials: G
authors.lastname: Devi
authors.forename: Zhen
authors.initials: Z
authors.lastname: Yuan
authors.forename: Yunpeng
authors.initials: Y
authors.lastname: Lu
authors.forename: Yanli
authors.initials: Y
authors.lastname: Zhao
authors.forename: Gang
authors.initials: G
authors.lastname: Chen
mesh_terms: D020029:Base Pairing; D003596:Cytosine / Q000031:analogs & derivatives* / Q000737:chemistry; D004247:DNA / Q000737:chemistry; D018965:Frameshifting, Ribosomal; D015497:HIV-1 / Q000235:genetics; D020135:Peptide Nucleic Acids / Q000138:chemical synthesis / Q000737:chemistry*; D012313:RNA / Q000737:chemistry; D012330:RNA, Double-Stranded / Q000737:chemistry*; D012367:RNA, Viral / Q000737:chemistry
chemical_list: D020135:Peptide Nucleic Acids; D012330:RNA, Double-Stranded; D012367:RNA, Viral; D012313:RNA; D003596:Cytosine; D004247:DNA