Photon induced charge and structural dynamics in gas-phase DNA

Abstract

2 1.1. DNA 3 wound around each other in an antiparallel direction. Each DNA strand consists of a long chain of nucleotides -the basic building blocks of DNA primary structure. As it is shown in fig. 1.1, a nucleotide is made up of a phosphate group, a deoxyribose sugar molecule, and one of four nitrogenous bases: adenine (A), guanine (G), cytosine (C) and thymine (T), of which A and G are purines, while C and T are pyrimidines. The nucleotides are combined together forming a long chain through the covalent bonds between the phosphate of one nucleotide and the sugar molecule of the neighboring nucleotide. This phosphate-sugar backbone is located on the outside of the DNA helix. DNA double strands are held together by hydrogen bonds between the nucleobases which are placed perpendicular to the axis of the helix [4], and located on the inside of the helix. The base pairing is specific and the rule is that the hydrogen bonds only form between A and T, or between G and C, leading to the fact that double strands are complementary to each other. The base pairing rule also plays an important role in DNA duplication. The DNA can reproduce by opening up the two paired strands. Each strand can act as a template to reconstruct a new partner strand by following the base pairing rule. In the end, one double-strand can replicate into two identically new DNA molecules.In addition to the canonical helical structure of DNA, which is also called B-form DNA (B-DNA), it has been found that DNA can form various secondary structures, such as A-DNA and Z-DNA, which also belong to the DNA helix families [8], as well as triplexes [9] and Gquadruplexes (G4) [10]. It was demonstrated that DNA capable of forming those structures was conserved throughout evolution. These conformations are known to have critical functional roles in vivo. In this thesis, structural dynamics of G4 unfolding are investigated on the molecular level by near-infrared (NIR) and vacuum ultraviolet (VUV) photoabsorption experiments. G4 self-assemble in solution from G-rich DNA monomers and fascinate with their beautiful topology. More details of G4 are given in the following. 4 1.2. DNA biochemical properties 5 6 8 1.4. X-rays interactions with DNA 9 10 12 1.5. Thesis outline 13 14 1. Introduction