טכניון מכון טכנולוגי לישראל
הטכניון מכון טכנולוגי לישראל - בית הספר ללימודי מוסמכים  
M.Sc Thesis
M.Sc StudentEnav Hagay
SubjectThe Spatial Properties of Different TATA Boxes and Their
Influence on TATA-TBP Interaction
DepartmentDepartment of Biology
Supervisor Professor Tali Haran
Full Thesis textFull thesis text - English Version


Abstract

DNA-protein interactions are at the heart of many important cellular processes. These interactions often operate through a mechanism called “indirect readout”, which is based upon recognition of the DNA structure, or the ability of the double helix to go through conformational changes at low energetic cost.

The aim of this study was to further our understanding of the relationship between the structural properties of DNA and the manner in which it interacts with proteins. In order to do so, I chose to study the TATA box-TATA binding protein (TBP) system, which utilizes exclusively the indirect readout mechanism.

Ten variants of TATA boxes were prepared and their global structural properties were studied. These structural properties (intrinsic bending, bend flexibility, twist and twist flexibility) were obtained using a novel experimental method, employing cyclization kinetics of DNA mini-circles. In addition, structural profiles were calculated for the TATA box variants, using previously published dinucleotide values. To better understand the relationship between structure and function, the experimental structural properties were compared to the calculated profiles, as well as to experimental data regarding the stability of different TBP-TATA box complexes.

The results of this study show that TATA-boxes can be divided into two groups, differing in their fourth dinucleotide step identity. The two groups also differ in their average intrinsic bending and twist flexibility. Correlation between intrinsic bending, sequence composition and calculated rigidity in the TATA-box group that contains two adenines in the fourth and fifth position of the consensus sequence was observed.