Gene2Oligo

Gene2Oligo designs contiguous, overlapping oligonucleotides representing both DNA strands to support in vitro gene synthesis by optimizing melting temperatures and sequence specificity.

Key Features:

• Dual-Strand Representation: Generates oligonucleotide sets that include segments from both strands of the input DNA to enable complementary hybridization during assembly.
• Contiguous and Overlapping Design: Arranges oligonucleotides adjacently on each strand with overlaps to complementary sequences on the opposite strand to facilitate accurate assembly.
• Dynamic Optimization of Oligonucleotide Length: Adjusts oligonucleotide lengths algorithmically to achieve uniform melting temperatures and target specificity.
• Thermodynamic Consistency: Ensures thermodynamic properties such as melting temperature are consistent across the oligonucleotide set to promote stable hybridization.
• Specificity Assurance: Designs oligonucleotides to minimize off-target interactions and reduce incorrect assemblies by focusing on sequence specificity.

Scientific Applications:

• In vitro gene synthesis (LCR and assembly PCR): Provides oligonucleotide designs suitable for ligase chain reaction (LCR) and assembly PCR workflows.
• Synthetic gene construction: Has been applied to synthesize genes such as the Saccharomyces cerevisiae cytochrome b5 gene using designed oligonucleotides.

Methodology:

The algorithm divides a long input DNA sequence into adjacent, contiguous oligonucleotides representing both strands, enforces overlaps with complementary strands, and dynamically optimizes oligonucleotide lengths to maintain uniform melting temperatures and sequence specificity.