Why Do Restriction Enzymes Prefer 4 and 6 Base DNA Sequences?

Tuesday, October 09, 2012 — Poster Session I
1:00 p.m. – 3:00 p.m	Natcher Conference Center, Building 45	NCI	BIOINFO-17

Authors

• T.D. Schneider
• V. Jejjala

Abstract

Restriction enzymes are widely known for precisely cutting DNA, typically at 4 or 6 base pair long sequences. The reason for these length preferences is unknown. However, as a molecule evolves to minimize its binding energy while still binding the same pattern, its efficiency increases, and we have shown that EcoRI, which cuts at 5' G/AATTC 3', has reached the optimal efficiency of 69%. Here we used information theory to determine upper and lower bounds on the dimensionality of the nucleic acid recognition coding space. During evolution to optimality, these bounds converge to twice the information content given in bits. 4 base cutters recognize 8 bits and use 16 dimensions, which is known to have a good lattice packing. Likewise the 6 base pair cutter EcoRI recognizes 12 bits and uses a 24 dimensional coding space. This is an intriguing result since it is well known that the best packing coding lattice is the Leech lattice in 24 dimensions. So 6 base pair restriction enzymes may use the Leech lattice to distinguish their specific binding sites from non-specific DNA sequences. If restriction enzymes utilize the 24 dimensional Leech lattice for decoding, novel single molecule communication devices may be possible.

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