TBP-DNA interactions in the minor groove discriminate between A:T and T:A base pairs

• Published in: Nucleic acids research Vol. 22; no. 10; pp. 1890 - 1896
• Main Authors: Wong, Jie Min, Bateman, Erik
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 25.05.1994
• Subjects: Base Composition; Base Sequence; Binding Sites; Biological and medical sciences; Consensus Sequence; DNA - analysis; DNA - chemistry; DNA - metabolism; DNA Probes; DNA-Binding Proteins - metabolism; Fundamental and applied biological sciences. Psychology; Kinetics; Molecular and cellular biology; Molecular genetics; Molecular Sequence Data; Nucleic Acid Conformation; Osmolar Concentration; Polydeoxyribonucleotides - chemical synthesis; Protein Binding; TATA Box - genetics; TATA-Box Binding Protein; Transcription Factors - metabolism; Transcription. Transcription factor. Splicing. Rna processing; Protozoa; Sequence specificity; Stability; Ionic strength; Acanthamoeba; DNA; DNA binding protein; TATA box; Rhizoflagellata; Environmental factor; Molecular interaction; In vitro
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/22.10.1890

In this report, we test the hypothesis that TBP binds DNA promiscuously due to its manner of recognition of the DNA minor groove. The experiment performed was to select TBP-binding sequences from a pool of random double stranded oligonucleotides. Sixty two clones from this pool were sequenced. Surprisingly, the results show that TBP has a marked preference for stably binding one sequence (TATATAA) over all others, yet only four classes of TATA box were selected. The features of the selected sequences allow definition of a binding consensus for TBP. The DNA binding properties of TBP to the four TATA variants was examined, the results being in accord with the observed selection frequencies. However, the nature of TBP-DNA binding is strongly affected by ionic strength. We infer that recognition of DNA via the minor groove can be highly selective even where A:T and T:A discrimination is required. Models for how this might be accomplished are discussed.