DpnI

DpnI (pronounced "D-P-N one") is a Type IIM restriction endonuclease isolated from Streptococcus pneumonae (formerly Diplococcus pneumonae). It recognizes and cuts methylated DNA at the sequence Gm6A↓TC.^[1][2]

Type II Methyl-directed restriction enzyme DpnI
Identifiers
Organism	Streptococcus pneumoniae
Symbol	dpnC
PDB	4ESJ
UniProt	P0A460
Other data
EC number	3.1.21.4
Search for Structures Swiss-model Domains InterPro

Structure

The structure of DpnI comprises an N-terminal catalytic domain and a C-terminal winged helix DNA binding domain, both of which show specificity for the methylated GATC sequence. The catalytic domain is disordered in solution and becomes ordered upon binding DNA.^[3][4]

Uses in molecular biology

DpnI is commonly used to digest template DNA after site-directed mutagenesis. Most strains of E. coli used in molecular biology express Dam methylase, a protein that methylates DNA at the sequence GATC. Adding DpnI to the product of a PCR reaction digests only the template DNA, as the template DNA was isolated from E. coli and will have methylation at this sequence while the newly synthesized DNA will not.^[5] DpnI is widely available commercially, both alone and in "KLD" enzyme mixes containing kinase and ligase enzymes for treatment of site-directed mutagenesis reactions.^[6]

DpnI is also used to digest methylated GATC sequences in DamID, a technique that uses Dam methylation combined with sequencing to identify protein-DNA interactions.^[7][8]

See also

• DpnII restriction endonuclease family, also isolated from S. pneumonae
• List of restriction enzyme cutting sites
• Restriction modification system