Enhanced Triplex Hybridization of DNA and RNA via Syndiotactic Side Chain Presentation in Minimal bPNAs

Area of Science:

• Chemical Biology
• Nucleic Acid Chemistry
• Supramolecular Chemistry

Background:

• General design principles for recognition at noncanonical DNA and RNA interfaces are not well understood.
• Bifacial peptide nucleic acids (bPNAs) offer a robust platform for studying synthetic triplex formation and structure-function relationships.

Purpose of the Study:

• To investigate the impact of amino acid secondary structural propensity, stereochemistry, and backbone cyclization on bPNA hybridization with DNA and RNA.
• To identify design principles for enhancing bPNA targeting of both DNA and RNA substrates.

Main Methods:

• Synthesis of minimal (mw < 1 kD) bPNA variants.
• Optical melting analyses to determine thermodynamic parameters of bPNA-DNA/RNA hybrids.
• Thymine-uracil substitutions in DNA substrates to probe binding preferences.

Main Results:

• Alternating (d, l) configuration and homochiral dipeptide cyclization to diketopiperazine significantly improve bPNA hybridization.
• All bPNA variants show a preference for binding DNA over RNA.
• Diketopiperazine bPNAs exhibit greater sensitivity to RNA conformation and optimized base stacking compared to open-chain bPNAs.

Conclusions:

• Key factors for tuning triplex hybridization include chiral centers, backbone conformation, base stacking, and the nucleic acid substrate.
• A structural blueprint for enhanced bPNA targeting involves syndiotactic base presentation, expanded base stacking, and backbone preorganization.