Sequence-specific recognition of cytosine C5 and adenine N6 DNA methyltransferases requires different deformations of DNA.
DNA methyltransferases modify specific cytosines and adenines within 2-6 bp recognition sequences. We used scanning force microscopy and gel shift analysis to show that M.HhaI, a cytosine C-5 DNA methyltransferase, causes only a 2 degree bend upon binding its recognition site. Our results are consistent with prior crystallographic analysis showing that the enzyme stabilizes an extrahelical base while leaving the DNA duplex otherwise unperturbed. In contrast, similar analysis of M.EcoRI, an adenine N6 DNA methyltransferase, shows an average bend angle of approximately 52 degrees. This distortion of DNA conformation by M.EcoRI is shown to be important for sequence-specific binding.
Garcia
R A
RA
Department of Chemistry, University of California, Santa Barbara 93106, USA.
Bustamante
C J
CJ
Reich
N O
NO
D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000737:chemistry / Q000378:metabolism*; D015245:Deoxyribonuclease BamHI / Q000737:chemistry / Q000378:metabolism; D015246:Deoxyribonuclease EcoRI / Q000737:chemistry / Q000378:metabolism*; D015252:Deoxyribonucleases, Type II Site-Specific / Q000737:chemistry / Q000378:metabolism; D004926:Escherichia coli / Q000201:enzymology; D018625:Microscopy, Atomic Force; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D016133:Polymerase Chain Reaction; D011487:Protein Conformation; D015265:Site-Specific DNA-Methyltransferase (Adenine-Specific) / Q000737:chemistry / Q000378:metabolism*; D013379:Substrate Specificity
D004247:DNA; C020098:DNA modification methylase EcoRI; D004248:DNA (Cytosine-5-)-Methyltransferases; D015265:Site-Specific DNA-Methyltransferase (Adenine-Specific); D015245:Deoxyribonuclease BamHI; D015246:Deoxyribonuclease EcoRI; C067043:endodeoxyribonuclease NheI; D015252:Deoxyribonucleases, Type II Site-Specific; C027440:GATATC-specific type II deoxyribonucleases