LCR Oligo Design Software: Key Tools, Recommendations, and Design Considerations

LCR Oligo Design Software: Tools and Best Practices

Designing oligos for Ligase Cycling Reaction (LCR) requires software that can tile oligos of 40 to 60 bases effectively, ensuring coverage and functionality for circular DNA constructs. Multiple programs can perform this task, but choosing the right software and strategy is critical for successful oligo design and ligation.

Programs Suitable for Oligo Tiling

Software that tiles oligos within the 40-60 base range provides a solid foundation for LCR design. These lengths balance specificity and efficient ligation during cycling reactions. The user should prioritize programs optimized for this oligo size range.

Recommended Software Options

• Ninth Bio: Offers functional tiling and LCR-compatible design (ninthbio.com).
• Gene2oligo: Was a reliable option but is currently offline.
• LCR Software: Works but produces oligos that may not always be full length. These oligos often require purification to enable effective ligation.

Design Considerations for Circular DNA

When working with circular DNA, including a bridging oligo that spans the origin of replication is essential. This bridging oligo ensures continuity during the ligation steps and helps maintain the circular topology throughout the reaction.

Limitations and Alternative Strategies

LCR design can be limited by incomplete oligo lengths and purity, which affect ligation efficiency. Purifying oligos mitigates this problem but adds an extra step. An alternative approach involves PCR amplification followed by Gibson assembly, which can streamline the construction process and improve assembly fidelity.

Oligo Source Recommendations

Quality oligos impact LCR success. Commercial oligo pools such as those from Integrated DNA Technologies (IDT) provide reliable, high-quality oligos optimized for such applications.

Key Takeaways

• LCR oligo design requires tiling of 40-60 bp oligos for effective assembly.
• Ninth Bio is a current, functional platform; Gene2oligo is offline.
• Bridging oligos spanning the origin are vital for circular DNA constructs.
• LCR oligos may need purification or alternative assembly methods like Gibson for best results.
• IDT oligo pools are a preferred oligo source for quality and consistency.