Small Molecule Recognition Triggers Secondary and Tertiary Interactions in DNA Folding and Hammerhead Ribozyme Catalysis

Abstract

We have identified tris(2-aminoethyl)amine (tren)-derived scaffolds with two (t2M) or four (t4M) melamine rings that can target oligo T/U domains in DNA/RNA. Unstructured T-rich DNAs cooperatively fold with the tren derivatives to form hairpin-like structures. Both t2M and t4M act as functional switches in a family of hammerhead ribozymes deactivated by stem or loop replacement with a U-rich sequence. Catalysis of bond scission in these hammerhead ribozymes could be restored by putative t2M/t4M refolding of stem secondary structure or tertiary bridging interactions between loop and stem. The simplicity of the t2M/t4M binding site enables programming of allostery in RNAs, recoding oligo-U domains as potential sites for secondary structure or tertiary contact. In combination with a facile and general method for installation of the t2M motif on primary amines, the method described herein streamlines design of synthetic allosteric riboswitches and small molecule−nucleic acid complexes.

Melamine driven supramolecular self‐assembly of nucleobase derivatives in water

“…28 Kitamura et al developed a well-defined columnar structure based on CAfunctionalized perylene bisimide and substituted M. 29 Among the natural nucleobases, thymine (T) contains complementary NHÁÁÁO and NHÁÁÁN hydrogen bonds with M. 30 Intrigued by this recognition unit, Liu et al synthesized amphiphilic polystyreneco-poly(N-acryloylthymine), which could be used for detecting M. 31 Besides, Bong et al reported that M-displaying a-peptides were able to mediate discrete assembly of T-rich DNA/ RNA. [32][33][34] However, this molecular recognition has rarely been applied to supramolecular polymer in aqueous environment owing to poor water-solubility of T and M.…”

“…Intrigued by this recognition unit, Liu et al synthesized amphiphilic polystyrene‐ co ‐poly( N ‐acryloylthymine), which could be used for detecting M . Besides, Bong et al reported that M‐displaying α‐peptides were able to mediate discrete assembly of T‐rich DNA/RNA . However, this molecular recognition has rarely been applied to supramolecular polymer in aqueous environment owing to poor water‐solubility of T and M.…”

Restoration of Ribozyme Tertiary Contact and Function by Using a Molecular Glue for RNA

“…Ligand binding to the aptamer domain stabilized the secondary structure that often accompanies the indirect stabilization of the tertiary contact . Recently, another type of conditional ribozymes was developed based on the direct stabilization of the tertiary contact by synthetic ligands . In the latter strategy, rational design of ligand and/or RNA sequences is essential, but there are few guidelines available for the chemical trigger design.…”

Branched Sidechain bPNA + Reports on RNA-Loop Tertiary Interactions via Triplex Hybridization Stem Replacement at Internal Domains

“…Studies on triazine assembly [1][2][3][4][5] with native bases [5][6][7] and as artificial base pairs [8][9][10] in PNA 11 revealed that monosubstituted melamine (M) is "bifacial" 12 with regard to base recognition; melamine can dock two equivalents of thymine (T) or uracil (U) via the Watson-Crick face to form a UMU base triple 13 when displayed on small-molecule, 13,14 peptide, [15][16][17][18][19][20] peptoid 21 and polymer 17,22 scaffolds, reminiscent of a TAT or UAU base triple. [23][24][25] An unstructured oligo T/U loop may be folded into a triplex hybrid stem with a class of peptides that sidechain-display melamine, called bifacial peptide nucleic acid (bPNA).…”