Bifacial peptide nucleic acid as an allosteric switch for aptamer and ribozyme function

Area of Science:

• Biochemistry
• Molecular Biology
• Synthetic Biology

Background:

• Non-coding nucleic acids play crucial roles in cellular processes.
• Disrupting duplex stems in nucleic acids can lead to loss of function.
• Peptide nucleic acids (PNAs) offer unique binding properties.

Purpose of the Study:

• To investigate the functional substitution of DNA/RNA duplexes with bifacial PNA (bPNA) hybrid triplexes.
• To explore the use of bPNA as an allosteric trigger for modulating nucleic acid functions.
• To demonstrate the restoration of lost functions in non-coding nucleic acids using bPNA.

Main Methods:

• Replacing duplex stems in non-coding nucleic acids with unstructured oligo-T/U strands.
• Introducing bPNA binding sites to refold these strands into bPNA triplex hybrid stems.
• Assessing functional rescue in DNA/RNA aptamers and a hammerhead ribozyme.

Main Results:

• bPNA hybrid triplexes successfully substituted for duplex DNA/RNA, rescuing lost structure-function.
• bPNA binding allosterically activated protein and small-molecule binding in aptamers.
• Restoration of catalytic activity and RNA splicing function in a ribozyme model system was achieved.

Conclusions:

• Bifacial PNA (bPNA) hybrid triplexes can functionally replace DNA/RNA duplexes.
• bPNA serves as an effective allosteric trigger for modulating nucleic acid functions.
• bPNA demonstrates significant potential for diverse applications in non-coding nucleic acid engineering.