Finding a basis for flipping bases.
Rotation of a DNA nucleotide out of the double helix and into a protein binding pocket ('base flipping') was first observed in the structure of a DNA methyltransferase. There is now evidence that a variety of proteins use base flipping in their interactions with DNA. Though the mechanism for base flipping is still unclear, we propose a three-step pathway: recognizing the target site and increasing the interstrand phosphate-phosphate distance nearby, initiating base flipping by protein invasion of the DNA, and trapping the flipped DNA structure.
Cheng
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WM Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, NY 11724, USA.
Blumenthal
R M
RM
D000595:Amino Acid Sequence; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D015257:DNA-Cytosine Methylases / Q000737:chemistry / Q000378:metabolism; D043224:Deoxyribonuclease (Pyrimidine Dimer); D004706:Endodeoxyribonucleases / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009711:Nucleotides / Q000378:metabolism; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment
D009711:Nucleotides; D011506:Proteins; D004247:DNA; C037664:DNA modification methylase HhaI; D015257:DNA-Cytosine Methylases; C027823:Cytosine 5-methyltransferase; D004706:Endodeoxyribonucleases; D043224:Deoxyribonuclease (Pyrimidine Dimer)