Abstract
The murine transcription factor ALF1 belongs to the class of basic helix-loop-helix proteins specific for the NCAGNTGN-version of the E-box. Binding of homodimeric ALF1 to variants of this motif was studied by a combination of binding site selection technology and DNA modification interference analysis. The results showed that substitutions at the non-conserved positions in the E-box sequence could cause profound alterations in the patterns of specific contacts at the protein-DNA interface. Thus, both the overall extent of the binding region and the backbone phosphate contact pattern differed markedly between closely related E-boxes with similar affinities for ALF1. The identity of the base at the inner N was an important determinant of contact pattern specification. The E-box variants differed in their ability to mediate ALF1 dependent transcriptional activation in vivo. We discuss the possibility that adaptability in basic helix-loop-helix protein-DNA interactions can result in complexes with different functional properties.
Publication types
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Research Support, Non-U.S. Gov't
MeSH terms
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Amino Acid Sequence
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Animals
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Base Sequence
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Basic Helix-Loop-Helix Leucine Zipper Transcription Factors
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Basic Helix-Loop-Helix Transcription Factors
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Basic-Leucine Zipper Transcription Factors
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Binding Sites / genetics
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DNA / chemistry
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DNA / genetics
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DNA / metabolism
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DNA-Binding Proteins / genetics*
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DNA-Binding Proteins / metabolism*
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Escherichia coli / genetics
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Genetic Variation
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Helix-Loop-Helix Motifs / genetics*
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Helix-Loop-Helix Motifs / physiology*
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Mice
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Models, Molecular
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Molecular Sequence Data
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Nucleic Acid Conformation
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Polymerase Chain Reaction
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Saccharomyces cerevisiae / genetics
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Sequence Homology, Amino Acid
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TCF Transcription Factors
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Transcription Factor 7-Like 1 Protein
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Transcription Factors / genetics*
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Transcription Factors / metabolism*
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Transcriptional Activation
Substances
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Basic Helix-Loop-Helix Leucine Zipper Transcription Factors
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Basic Helix-Loop-Helix Transcription Factors
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Basic-Leucine Zipper Transcription Factors
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DNA-Binding Proteins
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Myc associated factor X
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TCF Transcription Factors
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Tcf12 protein, mouse
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Tcf7l1 protein, mouse
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Transcription Factor 7-Like 1 Protein
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Transcription Factors
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Max protein, mouse
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DNA