TATA binding protein binds to single stranded DNA: A new model for eukaryotic transcription

Abstract

Although the players mediating the initiation of eukaryotic transcription appear to be known, the mechanism is not. In this paper we report findings on the interaction between the TATA box binding protein (TBP) and DNA, using a novel optical technology, that point to a potential plausible physical mechanism, and at the same time tie together a number of otherwise disparate observations. TBP plays a central and ubiquitous role in initiating eukaryotic transcription, binding to promoters with and without the canonical 5’ TATA(A/T)A(A/T)(G/A) 3’ motif1. It also tends to bind to double-stranded DNA promiscuously, and though affinity is lower, the number of binding opportunities is greater. TBP-DNA complexes have been characterized structurally2,3 and thermodynamically4,5, the standard model representing the TBP double-helix complex as the biologically significant entity. Here we show, using a label-free detection method termed Spectral Reflectance Imaging Biosensor6 (SRIB) that TBP binds to single stranded (ss), as well as double stranded (ds), oligonucleotides with the TATA motif, and binds the single-stranded form preferentially. Moreover, TBP binds preferentially to single stranded pyrimidine-rich sequences over purine-rich sequences, which is similar to the Single-Stranded DNA-binding protein (SSB) binding pattern. These observations suggest a new model for eukaryotic transcription in which TBP destabilizes the double helix, thereby initiating the open complex bubble necessary for transcription. Furthermore, the role of TBP as a multifunctional protein is discussed.