Enzymes sensitive to methylation
Prokaryotic Methylation
Most laboratory strains of E. coli contain Dam and Dcm methylases
Dam methylase methylates at the N6 position of the adenine in the sequence GATC
Dcm methylase methylates at the C5 position of cytosine in the sequences CCAGG and CCTGG
Some restriction enzymes cannot cleave their recognition sites when certain bases within the site are methylated
To cleave such sites you need to clone your DNA into a dam-, dcm- strain of E.coli
Methylation sensitivity can be complicated, in that for some enzymes, cleavage is 'impaired' by methylation, rather than completely blocked.
In addition, some enzymes may only be block/impaired by certain combinations of overlapping methylation
The dam/dcm function in DNADynamo does not accommodate 'impaired cleavage' or enzymes where only 'certain combinations of overlapping methylation' block cleave.
In DNADynamo, the following set of enzymes are the default for 'blocked by dam methylation'
AlwI, BcgI, BclI, BsaBI, BspDI, BspEI, BspHI, ClaI, DpnII, HphI, Hpy188III, MboI, MboII, NruI, TaqI, XbaI
while, the following set of enzymes are the default for 'blocked by dcm methylation'
AlwNI, ApaI, AvaII, BsaI, BsmFI, BssKI, EaeI, EcoO109I, MscI, NlaIV, PflMI, PpuMI, Sau96I, ScrFI, SexAI, StuI, StyD4I
DpnI is a special case - where cleave requires dam methylation
You can edit whether or not DNADynamo will block enzymes with sites that contain or overlap dam or dcm methylation sites by double clicking enzyme names to bring
up the 'Enzyme Information' window, and checking or not the 'Dam/Dcm sensitive' check boxes. CheckBoxes are only selectable if the recognition sites has the potential to be blocked
Eukaryotic Methylation
CpG methylases found in higher eukaryotes transfer a methyl group to the C5 position of cytosine residues
Some restriction enzymes cannot cleave their recognition sites when they are methylated by CpG methylases
The CpG function in DNADynamo does not accommodate 'impaired cleavage' or enzymes where only 'certain combinations of overlapping methylation' block cleave.
In DNADynamo, the following set of enzymes are the default for 'blocked by CpG methylation'
AccI, AciI, AclI, AfeI, AgeI, ApaI, ApaLI, AscI, AsiSI, AvaI, AvaII, BceAI, BfuCI, BmgBI, BsaAI, BsaHI, BseYI, BsiEI
, BsiWI, BsmBI, BsmFI,"BspDI, BsrFI, BssHII, BssKI, BstBI, BstUI, ClaI, DpnI, EaeI, EagI, FauI, Fnu4HI, FseI"
, FspI, HaeII, HgaI, HhaI, HinP1I, HpaII, Hpy166II, Hpy188III, Hpy99I, HpyCH4IV, KasI, MluI, MmeI, MspA1I, NaeI, NarI
, NgoMIV, NotI, NruI, PaeR7I, PluTI, PmlI, PvuI, SacII, SalI, Sau3AI, Sau96I, ScrFI, SfoI, SgrAI, SmaI, SnaBI, TspMI, ZraI
DNADynamo does not accomodate methylation dependent cleavage by enzymes such as FspEI, LpnPI, McrBC or MspJI
ou can edit whether or not DNADynamo will block enzymes with sites that contain or overlap CpG methylation sites by double clicking enzyme names to bring
up the 'Enzyme Information' window, and checking or not the 'CpG sensitive' check boxes. CheckBoxes are only selectable if the recognition sites has the potential to be blocked