Abstract
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.
Publication types
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Research Support, Non-U.S. Gov't
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Research Support, U.S. Gov't, Non-P.H.S.
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Research Support, U.S. Gov't, P.H.S.
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Review
MeSH terms
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Amino Acid Sequence
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DNA / chemistry*
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DNA / metabolism
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DNA-Cytosine Methylases / chemistry
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DNA-Cytosine Methylases / metabolism
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Deoxyribonuclease (Pyrimidine Dimer)
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Endodeoxyribonucleases / chemistry
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Endodeoxyribonucleases / metabolism
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Models, Molecular
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Molecular Sequence Data
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Nucleic Acid Conformation
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Nucleotides / metabolism
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Protein Conformation
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Proteins / chemistry*
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Sequence Alignment
Substances
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Nucleotides
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Proteins
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DNA
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DNA modification methylase HhaI
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DNA-Cytosine Methylases
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Cytosine 5-methyltransferase
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Endodeoxyribonucleases
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Deoxyribonuclease (Pyrimidine Dimer)