Design of Bivalent Nucleic Acid Ligands for Recognition of RNA-Repeated Expansion Associated with Huntington’s Disease

Abstract

We report the development of a new class of nucleic acid ligands that is comprised of Janus bases and the MPγPNA backbone and is capable of binding rCAG repeats in a sequence-specific and selective manner via, inference, bivalent H-bonding interactions. Individually, the interactions between ligands and RNA are weak and transient. However, upon the installation of a C-terminal thioester and an N-terminal cystine and the reduction of disulfide bond, they undergo template-directed native chemical ligation to form concatenated oligomeric products that bind tightly to the RNA template. In the absence of an RNA target, they self-deactivate by undergoing an intramolecular reaction to form cyclic products, rendering them inactive for further binding. The work has implications for the design of ultrashort nucleic acid ligands for targeting rCAG-repeat expansion associated with Huntington’s disease and a number of other related neuromuscular and neurodegenerative disorders.

Unnatural bases for recognition of noncoding nucleic acid interfaces

“…Ly and coworkers have recently reported on the synthesis of a set of 3 synthetic heterocycles (E, F, I) [ 153,154 ] that are also designed to disrupt existing GC, reverse‐orientation CG and intercept AA pairs to form Janus‐Wedge triples when used as bases on γ‐PNA (Figure 7). These sites in tandem are densely represented in cytosine‐adenosine‐guanosine repeat sequences, which are core to Huntington's disease progression.…”

“…McLaughlin and coworkers sought to expand the Janus-Wedge catalog of bases with W 2 , [152] a triazine (ammeline) derivative designed to insert between GC, disrupting the base pair to form a G-W 2 -C triple ( Ly and coworkers have recently reported on the synthesis of a set of 3 synthetic heterocycles (E, F, I) [153,154] that are also designed to disrupt existing GC, reverse-orientation CG and intercept AA pairs to form Janus-Wedge triples when used as bases on γ-PNA ( Figure 7).…”

Peptide nucleic acid (PNA) and its applications in chemical biology, diagnostics, and therapeutics

“…17 More recently, several nucleobases have also been developed to favor triplex formation with dsRNA, notably, 2-aminopyridine (M), 2-pyrimidinone (P) and 3-oxo-2,3-dihydropyridazine (E) that extend the design of triplexes to any dsRNA sequence (Figure 1e). 18,19 Another recent advance in nucleobase design is the design of Janus bases capable of bifacial hybridization for targeting dsDNA or dsRNA under physiological conditions (Figure 1f), 20,21 thereby providing an inroad for the design of PNAs that target the secondary and tertiary structures of nucleic acid biopolymers.…”

“…This strategy hasbeen used to target the rCAG-repeat expansion associated with Huntington's disease and a number of other related neuromuscular and neurodegenerative disorders (Figure 4d). 21,104 A supramolecular approach has also been reported to target repeat sequences. In this case, slightly longer PNA probes (6-mer) functionalized with pyrene moieties that can stabilize adjacent probe hybridization through stacking interactions were shown to be sufficient to disrupt a pathogenic interaction between the rCUGexpansion sequence and MBL1 complex.…”

Shape selective bifacial recognition of double helical DNA

“…Chemical synthesis and probe design. Encouraged by the results of MD simulations, we synthesized nucleobases E and F 44 , along with the corresponding γPNA monomers ( Supplementary Fig. 6) and oligomer, for the initial testing ( Fig.…”