Specificity of hydroxylmethyluracil-containing DNA for transcription factor 1: structural insights

Enhancement of the in vitro transcription by T7 RNA polymerase of short DNA templates containing oxidative thymine lesions

5-(Hydroxymethyl)uracil, 5-formyluracil or 5-carboxyuracil can be formed in DNA upon exposure to ionizing radiations. We report the effect of the latter oxidative lesions on the in vitro transcription by T7 RNA polymerase using a single-stranded short model template. Kinetic experiments showed that the transcription yield was increased with the modified template. Due to the unforeseen presence of a hairpin structure within the transcribed RNA, we postulated that we are in the presence of a T7 RNA polymerase pausing signal and that the lesions within this critical DNA structure could interfere with normal regulation of RNA transcription.

Solution structure of a mutant of transcription factor 1: implications for enhanced DNA binding

An NMR solution structure of a mutant of the homodimer protein transcription factor 1, TF1-G15/I32 (22 kDa), has been solved to atomic resolution, with 23 final structures that converge to an r.m. s.d. of 0.78 A. The overall shape of TF1-G15/I32 remains similar to that of the wild-type protein and other type II DNA-binding proteins. Each monomer has two N-terminal alpha-helices separated by a short loop, followed by a three-stranded beta-sheet, whose extension between the second and third beta-strands forms an antiparallel beta-ribbon arm, leading to a C-terminal third alpha-helix that is severely kinked in the middle. Close examination of the structure of TF1-G15/I32 reveals why it is more stable and binds DNA more tightly than does its wild-type counterpart. The dimeric core, consisting of the N-terminal helices and the beta-sheets, is more tightly packed, and this might be responsible for its increased thermal stability. The DNA-binding domain, composed of the top face of the beta-sheet, the beta-ribbon arms and the C-terminal helices, is little changed from wild-type TF1. Rather, the enhancement in DNA affinity must be due almost exclusively to the creation of an additional DNA-binding site at the side of the dimer by changes affecting helices 1 and 2: helix 2 of TF1-G15/I32 is one residue longer than helix 2 of the wild-type protein, bends inward, and is both translationally and rotationally displaced relative to helix 1. This rearrangement creates a longer, narrower fissure between the V-shaped N-terminal helices and exposes additional positively charged surface at each side of the dimer.