The first crystal structures of RNA–PNA duplexes and a PNA-PNA duplex containing mismatches—toward anti-sense therapy against TREDs

Abstract

PNA is a promising molecule for antisense therapy of trinucleotide repeat disorders. We present the first crystal structures of RNA–PNA duplexes. They contain CUG repeats, relevant to myotonic dystrophy type I, and CAG repeats associated with poly-glutamine diseases. We also report the first PNA–PNA duplex containing mismatches. A comparison of the PNA homoduplex and the PNA–RNA heteroduplexes reveals PNA's intrinsic structural properties, shedding light on its reported sequence selectivity or intolerance of mismatches when it interacts with nucleic acids. PNA has a much lower helical twist than RNA and the resulting duplex has an intermediate conformation. PNA retains its overall conformation while locally there is much disorder, especially peptide bond flipping. In addition to the Watson–Crick pairing, the structures contain interesting interactions between the RNA's phosphate groups and the Π electrons of the peptide bonds in PNA.

Experimental DNA- or RNA-Directed Therapies for Trinucleotide Repeat Disease

“…Kiliszek et al [51] demonstrated the high sequence-specificity of PNAs in studies of the crystal structures of RNA-PNA duplexes and a PNA-PNA duplex containing mismatches. Using this technique, only fully complementary RNA-PNA duplexes could be obtained, while co-crystallization trials of mismatching RNA with PNA resulted only in crystals of mismatched PNA-PNA [51]. This sequence selectivity is a desirable property for antisense therapeutic strategies against trinucleotide repeat expansion diseases since it will allow inhibition of mutant gene expression without interfering with the wild-type gene.…”

Structures of RNA repeats associated with neurological diseases

“…Red sphere is a water molecule. The presented base pairs and helices were derived from the following PDB entries: (a) code 4PCJ , (b) code 5EMG , (c) code 3GLP , 5EME , 5EMG .…”

“…The next example are crystal structures of CUG and CAG repeats in complex with their antisense PNA oligomers as well as the structure of PNA‐PNA duplex having CTG repeats (PDB code: 5EME, 5EMF, 5EMG) . PNA (peptide nucleic acid) is a homolog of a nucleic acid having the sugar‐phosphate backbone replaced by a peptide backbone .…”

Evaluation of the Amber Force Fields for Molecular Dynamics Simulation of a PNA–DNA Duplex

“…Solution structures have been determined for an octameric PNA–DNA and a hexameric PNA–RNA by NMR. Crystal structures are also available for a few PNA–DNA duplexes . All these structures show in common that a PNA–DNA duplex is a right‐handed helix with the N‐terminus of the PNA strand hybridized with the 3′‐end of the DNA strand.…”