Next to its well–known helix structure, double stranded DNA can form alternative structures that might have biological importance. For example, in guanine–rich DNA sites of the c–MYC promotor a...Show moreNext to its well–known helix structure, double stranded DNA can form alternative structures that might have biological importance. For example, in guanine–rich DNA sites of the c–MYC promotor a second order structure called a G–Quadruplex has been found. In the G–Quadruplex, one strand of the DNA forms a stack of 4 interacting guanines. In this thesis we study the formation of G–Quadruplexes in double–stranded DNA using a combination of F¨oster Resonance Energy Transfer (FRET) and multiplex Magnetic Tweezers (MT). Moreover, a two–state model was developed which describes the probability to form a G–Quadruplex in double–stranded DNA. Using this model we calculated how the extension and the FRET efficiency depends on force, twist and the sequence of the DNA. Because the synthesis of double–stranded DNA containing a G–Quadruplex site proved challenging, the experimental data could not be compared to the outcomes of the two–state model. Based on simulations we conclude that adding a 3–bp mismatch to the DNA tether next to the G4 site is required for the formation of a G–Quadruplex in dsDNA. Our findings may be relevant for understanding a link with transcription and/or replication.Show less
