> ## Documentation Index
> Fetch the complete documentation index at: https://docs.openbio.tech/llms.txt
> Use this file to discover all available pages before exploring further.

# DNA & Molecular Biology Tools

> Primer design, cloning, and molecular biology tools

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

## 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"

## 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"

## 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

## 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

## 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"