Aromatic stacking and bending of the DNA helix by the individual repeat units of the carboxy-terminal domain of RNA polymerase II.
The carboxy-terminal domain (CTD) of RNA polymerase II consists of multiple repeats of the unique heptad sequence -(Ser-Pro-Thr-Ser-Pro-Ser-Tyr)- which may interact with DNA through the intercalation of adjacent tyrosine aromatic rings. We have examined details of the interaction of this motif with calf thymus DNA through analysis of peptide analogues that contain (1) an amino-terminal tyrosine which mimics the presence of an adjacent heptad repeat and (2) positively-charged lysine residues which facilitate the initial contact between peptide and DNA. Results of fluorescence experiments, NMR titrations, and viscometric analyses indicate that these peptides bind to the DNA helix through a non-classical intercalation mode involving partial aromatic stacking of the tyrosine rings with the Watson-Crick base pairs.
Huang
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Department of Chemistry, Indiana University-Purdue University at Indianapolis 46202-3274.
Shullenberger
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Long
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D000595:Amino Acid Sequence; D004247:DNA / Q000737:chemistry / Q000187:drug effects*; D004996:Ethidium / Q000494:pharmacology; D009682:Magnetic Resonance Spectroscopy; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation / Q000187:drug effects*; D010455:Peptides / Q000737:chemistry / Q000494:pharmacology*; D011485:Protein Binding; D012319:RNA Polymerase II / Q000737:chemistry / Q000494:pharmacology*; D012091:Repetitive Sequences, Nucleic Acid; D014443:Tyrosine / Q000737:chemistry; D014783:Viscosity
D010455:Peptides; D014443:Tyrosine; D004247:DNA; D012319:RNA Polymerase II; D004996:Ethidium