DNA Structure and
Analysis
Activity 4.1: Restriction Site
Prediction Using NEBcutter
Activity 4.1: Restriction Site Prediction Using
NEBcutter
 Research Questions:
– How many times does a given restriction enzyme cut lambda
DNA?
– When cutting lambda DNA with a given restriction enzyme,
what pattern will the resulting DNA fragments make on a gel?
 Objectives:
– Use NEBcutter to predict where restriction enzymes will cut the
bacteriophage lambda DNA sequence
– Produce a virtual gel image of lambda DNA cut with a specific
restriction enzyme
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Skills to Master
 Use NEBcutter software to predict restriction enzyme
sites
 Record detailed software instructions into a laboratory
notebook
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Student Workstation Materials
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Protocol Highlights/Tips
 Go to the NEB website
– tools.neb.com/NEBcutter2/
 Select Lambda under
Standard sequences
 Ensure that the radio button
for Linear sequence is
selected
 Write detailed steps into
notebook
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Summary
 Make sure to:
– Record all steps in your notebook
– Lambda sequence is selected under standard
sequences
– Sequence is selected as linear
– Print the fragments list and gel image to paste
into your notebook
– Adjust the gel type to 1% agarose and adjust the
marker to Lambda-HindIII Digest
– DNA type should be unmethylated
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