4 research outputs found
Incorporating a guanidine-modified cytosine base into triplex-forming PNAs for the recognition of a C-G pyrimidine–purine inversion site of an RNA duplex
RNA duplex regions are often involved in tertiary interactions and protein binding and thus there is great potential in developing ligands that sequence-specifically bind to RNA duplexes. We have developed a convenient synthesis method for a modified peptide nucleic acid (PNA) monomer with a guanidine-modified 5-methyl cytosine base. We demonstrated by gel electrophoresis, fluorescence and thermal melting experiments that short PNAs incorporating the modified residue show high binding affinity and sequence specificity in the recognition of an RNA duplex containing an internal inverted Watson-Crick C-G base pair. Remarkably, the relatively short PNAs show no appreciable binding to DNA duplexes or single-stranded RNAs. The attached guanidine group stabilizes the base triple through hydrogen bonding with the G base in a C-G pair. Selective binding towards an RNA duplex over a single-stranded RNA can be rationalized by the fact that alkylation of the amine of a 5-methyl C base blocks the Watson–Crick edge. PNAs incorporating multiple guanidine-modified cytosine residues are able to enter HeLa cells without any transfection agent.NRF (Natl Research Foundation, S’pore)MOE (Min. of Education, S’pore)Published versio
Targeting RNA Editing of Antizyme Inhibitor 1: a Potential Oligonucleotide-Based Antisense Therapy for Cancer.
10.1016/j.ymthe.2021.05.008Mol The
Selective Binding to mRNA Duplex Regions by Chemically Modified Peptide Nucleic Acids Stimulates Ribosomal Frameshifting
Minus-one
programmed ribosomal frameshifting (−1 PRF) allows
the precise maintenance of the ratio between viral proteins and is
involved in the regulation of the half-lives of cellular mRNAs. Minus-one
ribosomal frameshifting is activated by several stimulatory elements
such as a heptameric slippery sequence (X XXY YYZ) and an mRNA secondary
structure (hairpin or pseudoknot) that is positioned 2–8 nucleotides
downstream from the slippery site. Upon −1 RF, the ribosomal
reading frame is shifted from the normal zero frame to the −1
frame with the heptameric slippery sequence decoded as XXX YYY Z instead
of X XXY YYZ. Our research group has developed chemically modified
peptide nucleic acid (PNA) L and Q monomers to recognize G-C and C-G
Watson–Crick base pairs, respectively, through major-groove
parallel PNA·RNA–RNA triplex formation. L- and Q-incorporated
PNAs show selective binding to double-stranded RNAs (dsRNAs) over
single-stranded RNAs (ssRNAs). The sequence specificity and structural
selectivity of L- and Q-modified PNAs may allow the precise targeting
of desired viral and cellular RNA structures, and thus may serve as
valuable biological tools for mechanistic studies and potential therapeutics
for fighting diseases. Here, for the first time, we demonstrate by
cell-free <i>in vitro</i> translation assays using rabbit
reticulocyte lysate that the dsRNA-specific chemically modified PNAs
targeting model mRNA hairpins stimulate −1 RF (from 2% to 32%).
An unmodified control PNA, however, shows nonspecific inhibition of
translation. Our results suggest that the modified dsRNA-binding PNAs
may be advantageous for targeting structured RNAs