Type II restriction endonucleases — How do they recognize and bind their DNA sites?

Introduction:
Type II restriction endonucleases are essential tools for DNA manipulation. Their high specificity arises from precise DNA recognition and binding strategies. This question reviews the key features of that recognition.

Given Data / Assumptions:

• Type II enzymes cut within or near their recognition sites.
• Recognition often involves symmetric sequences.
• Binding includes both base-specific and backbone contacts.

Concept / Approach:
Most type II enzymes recognize short palindromic sequences and achieve specificity through networks of hydrogen bonds with base edges in the major or minor groove. At the same time, non-sequence-specific interactions with the sugar–phosphate backbone stabilize the complex and aid docking and catalysis.

Step-by-Step Solution:

Verification / Alternative check:
Crystal structures (e.g., EcoRI–DNA) show direct H-bonding to bases plus contacts to the phosphate backbone, and palindromic recognition consistent with dimer binding.

Why Other Options Are Wrong:

• Picking any single feature alone is incomplete; enzymes typically use all listed strategies.
• Nonpalindromic, AT-only tracts: not a general rule for type II enzymes.

Common Pitfalls:
Assuming specificity derives only from base contacts; backbone interactions and DNA bending also contribute significantly to catalysis.

Final Answer:
All of the above.