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OpenBio provides molecular biology tools for primer design, PCR, cloning, and DNA assembly.

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Primer Design

Purpose: Design optimal primers for PCR, sequencing, and mutagenesis Available tools:
  • PCR primer design (18-25 bp, Tm 55-65°C, GC 40-60%)
  • Sequencing primer design
  • Site-directed mutagenesis primers
  • Primer analysis (Tm, secondary structures, dimers)
Example: “Design primers to amplify the BRCA1 gene”

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PCR Tools

Purpose: Plan and optimize PCR reactions Available tools:
  • Generate complete PCR protocols
  • Calculate optimal annealing temperatures
  • Troubleshoot PCR issues
Example: “Generate PCR protocol for 2kb product”

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DNA Assembly

Gibson Assembly: Seamless multi-fragment DNA assembly
  • 15-40 bp overlaps between fragments
  • Design assembly strategies
  • Optimize overlap sequences
  • Best for: Multiple fragment assembly
Golden Gate Assembly: Ordered assembly using Type IIS enzymes
  • 4 bp overhangs, directional assembly
  • Plan modular cloning strategies
  • Best for: Modular constructs, scarless assembly
General Cloning: Traditional restriction enzyme cloning
  • Find restriction sites and plan digests
  • Design ligation reactions
  • Best for: Simple insertions

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DNA/RNA Analysis

Sequence Manipulation:
  • Reverse complement, transcription, translation
  • ORF finding in all 6 frames
  • Codon optimization for expression
Restriction Analysis:
  • Find restriction sites in sequences
  • Virtual digests to predict fragment sizes
  • Find compatible enzyme pairs
Gel Electrophoresis:
  • Design appropriate gel conditions
  • Estimate DNA sizes from gels

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Quick Examples

  • “Design primers to amplify the insulin gene”
  • “Plan Gibson assembly of these three fragments”
  • “Generate PCR protocol for 2kb product”
  • “Find all EcoRI sites in this sequence”
  • “Get the reverse complement of this sequence”