Synergistic DNA‐ and Protein‐Based Recognition Promote an RNA‐Templated Bio‐orthogonal Reaction

Abstract

Biomolecular assemblies composed of proteins and oligonucleotides play a central role in biological processes. While in nature, oligonucleotides and proteins usually assemble via non-covalent interactions, synthetic conjugates have been developed which covalently link both modalities. The resulting peptide-oligonucleotide conjugates have facilitated novel biological applications as well as the design of functional supramolecular systems and materials. However, despite the importance of concerted protein/oligonucleotide recognition in nature, conjugation approaches have barely utilized the synergistic recognition abilities of such com-plexes. Herein, the structure-based design of peptide-DNA conjugates that bind RNA through Watson-Crick base pairing combined with peptide-mediated major groove recognition is reported. Two distinct conjugate families with tunable binding characteristics have been designed to adjacently bind a particular RNA sequence. In the resulting ternary complex, their peptide elements are located in proximity, a feature that was used to enable an RNA-templated click reaction. The introduced structure-based design approach opens the door to novel functional biomolecular assemblies.

From Protein Structures to Functional Biomimetics

“…To facilitate sequence-specific binding of RNA, we designed peptide-DNA hybrids using a truncated version of wt33 and 10-to 12-mer DNA sequences that were complementary to a single-stranded RNA target (Figure 5d). 37 Notably, we observed 100-fold increased binding affinity to miR-21 when comparing the DNA-peptide conjugate 1-A12 (Kd = 4 nM) with the non-conjugated system (apparent Kd ca. 0.4 µM).…”

“…For these hybrids, we confirmed sequence-specific binding allowing the execution of selective RNA-templated ligations using a strain-promoted click reaction. 37 Compared with the untemplated reaction, a rate acceleration in the range of two orders of magnitude was achieved.…”

Synthetic Peptides: Promising Modalities for the Targeting of Disease‐Related Nucleic Acids

“…Additionally, the peptide was able to inhibit Dicer cleavage of pre‐miR‐21. In another study the Grossmann group coupled the unstapled TAV2B peptidomimetics to complementary DNA to generate peptide‐oligonucleotide conjugates that were able to form DNA/RNA/peptide complexes with single stranded RNA and make them more sequence specific [147] …”

Environment‐Responsive Peptide Dimers Bind and Stabilize Double‐Stranded RNA

“…[14] The tomato aspermy virus 2b (TAV2b) protein, a gene silencing suppressor that counteracts host defense during infection, and the human La protein have also served as starting points for the design of RNA ligands. [13,15,16] In the realm of natural products, antimicrobial peptides such as viomycin [17] and capreomycin, [18] derived from bacteria, stand out as potent RNA binders. [19] These peptides specifically target ribosomal RNA, effectively inhibiting protein biosynthesis.…”