TReSR: A PCR-compatible DNA sequence design method for engineering proteins containing tandem repeats.

Area of Science:

• Molecular Biology
• Protein Engineering
• Synthetic Biology
• Bioinformatics

Background:

• Protein tandem repeats (TRs) are common motifs involved in protein interactions.
• TRs are valuable for designing protein constructs due to their diverse biological functions.
• Synthesizing DNA encoding TRs is challenging for traditional molecular biology methods.

Purpose of the Study:

• To develop a computational method for redesigning DNA sequences encoding TRs.
• To facilitate the synthesis and manipulation of TR-containing proteins.
• To enable broader applications of TRs in protein engineering and synthetic biology.

Main Methods:

• Developed TReSR (Tandem Repeat DNA Sequence Redesign), a computational protocol.
• Utilized TReSR to reduce DNA sequence complementarity for TRs.
• Demonstrated utility by constructing a novel single-chain TR repressor using assembly PCR.

Main Results:

• Successfully designed a DNA sequence encoding a TR using TReSR.
• Constructed a novel constitutive repressor with a tandem repeat of the LacI DNA binding domain.
• Validated repressor function within a genetic circuit using a fluorescent reporter.

Conclusions:

• TReSR effectively redesigns DNA sequences for tandem repeats, overcoming synthesis challenges.
• The developed method enables the creation of novel TR-containing proteins.
• This facilitates the incorporation of diverse TR domains in protein engineering and synthetic biology.