Restriction Site Sequence Mapper

DNA Sequence Maps in Molecular Biology

Annotated sequence maps are essential for communicating construct design in molecular biology publications. A well-designed map shows:

• Restriction sites: Where key enzymes cut, critical for cloning strategy • ORFs / CDS: Protein-coding regions with reading frame information • Regulatory elements: Promoters, terminators, origins of replication • Primer binding sites: For PCR verification and sequencing

Circular maps (plasmid maps) are the standard representation for vector constructs. Linear maps are used for PCR products, chromosomal regions, and linearized constructs.

NEBcutter and Restriction Mapping

NEBcutter, developed by New England Biolabs, has been the standard online tool for restriction enzyme analysis since 2003. It generates annotated sequence maps showing where restriction enzymes cut a given DNA sequence.

Key features of restriction mapping: • Single-cutter identification: Enzymes that cut exactly once are ideal for linearizing circular DNA • Unique site analysis: Important for inserting DNA at a specific location • Multi-enzyme maps: Show the relative positions of multiple enzyme sites • ORF overlay: Identify potential coding regions in the sequence

Creating Publication-Quality Figures

For journal submissions, vector maps should be:

• Vector format (SVG/EPS): Journals require 300+ DPI; vector formats scale infinitely • Clearly labeled: Gene names, restriction sites, and key features should be legible • Color-coded: Use distinct colors for different feature types • Properly oriented: Convention places the origin of replication at 12 o’clock • Size-annotated: Include the total construct size in bp/kb

Export the SVG from this tool and refine labels in a vector editor (Illustrator, Inkscape) for final publication.