DNA And Eukaryotic Analysis

1.0 INTRODUCTION

Deoxyribonucleic acid (DNA) is the biomolecule that carries genetic information. Eukaryotic DNA is localized in the nucleus of cells on linear chromosomes. Genes are transcribed from DNA into ribonucleic acid (RNA), which is transported out of the nucleus to be translated into proteins that carry out most of the biological functions inside and outside of cells. The bases of DNA make up codons for specific amino acids, the building blocks of proteins. The knowledge that DNA may contain the blueprint for all biological processes led to a lot of interest in its structure. It was first solved through cleaver model building by James Watson and Francis Crick (1). The canonical structure of DNA is the Watson-Crick base paired B-form

However, since all cells of an organism contain the same genetic information in its DNA (with few exceptions), diversity is created by what genes are being expressed. How this is controlled is one of the main questions in biology today. Another important aspect of DNA is how it can be copied without errors and without accumulating devastating damage that may for instance lead to cancer. One of the most devastating types of damage is double-strand breaks. How can the ends of a linear chromosome be distinguished from such breaks? DNA is known to form several different non-canonical structures, of which the biological function is not as well known, but that may help control gene expression and maintain the integrity of the DNA. These include the alternative A- and Z-form double helices as well as three and four-stranded structures. The most well studied four-stranded structure, and the one that is likely to have the greatest physiological relevance, is the G-quadruplex. It has enticed structural biologists for over a century, but finding its possible biological functions has remained elusive. Only recently have G-quadruplexes been firmly proven to even exist in mammalian cells, and now evidence is building up showing they have fundamental

Walter Gilbert and Dipankar Sen proposed G-quadruplexes could aid the alignment and recombination of chromosomes during meiosis and that they may also form at telomeres, which were known to be G-rich in most species studied and to exist as single-stranded DNA in 3’ overhangs (9). In a study from Elizabeth Blackburn’s lab, a double G-G base paired hairpin was proposed to be formed by Tetrahymena telomeric DNA (10), but the year after Sen’s and Gilbert’s suggestion was published, studies from the labs of Thomas Cech and Aaron Klug showed that the telomeric sequence from the ciliates Oxytricha and Tetrahymena do indeed form G-quadruplexes (11,12). Subsequently a G- quadruplex was found to form also in a control region of the proto-oncogene c-Myc (13), suggesting a function in transcriptional regulation. Further indication of a role for G-quadruplexes in transcription came when bioinformatics were applied to look for putative quadruplex forming sequences (PQSs) in different genomes. It was found that their distribution is not random. They are largely absent in exons, but are frequently found upstream of transcription start sites (TSSs) (14,15). From then on the G-quadruplex field