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Unformatted text preview: Lecture 9 Super coiling - it is when the regular DNA starts to have tertiary structure All naturally occurring DNA have supercoils in them Linking number- determines how many times the two strands cross over each other. It is split into twists and writhing (super turns) numbers Occurs in vivo Eliminate enzymes, such as topoisomerase, there becomes a greater amount of knotting because there is no means to relieve the super turns resulting in the DNA becoming too energetically unfavorable that the strands cannot be un- wound. Fig 19.12 Supercoiling affects the structures of DNA Supercoiling occurs only in a closed DNA within free ends A closed DNA can be a circular DNA molecule or a linear molecule where both ends are anchored in a protein structure If run DNA that is supercoiled in an agarose gel, the supercoiled DNA will travel faster than the DNA that is relaxed or linear Property of Supercoiling is only for DNA that constrained by having no free ends. The free ends will swivel around making it look relaxed DNA is constrained in higher organisms by a scaffold, which means that the DNA is anchored into this protein RNA blob, their units are 40 kb that forms double stranded loops Any closed DNA molecule has a linking number the linking number is the sum of the twisting number and the writing number L = T + W Turning can be repartitioned between the twisting number and writing number A change in the structure of the double helix can compensate for a change in its coiling in space The linking number can be changed only by breaking and making bonds in DNA Linking number - number of times the two strands cross over each other The strands cross over each other either as twists or relaxed DNA sum of the ways DNA can cross over each other Writhing - when the DNA is melted and forming super turns, the amount of super turns produced L is fixed the moment the backbone is sealed. different linking numbers implies different topoisomers The linking number changes enzymatically. L the linking number is the number of times one strand crosses over the other in space. Closed circle of identical sequences may have different linking numbers. Dependent of the distribution of T and W. T is the twisting number and it is the rotation of one strand about the other. For b form DNA it is the number of base pairs divided by base pairs per turn divided by 10 (bp/(bp/turn))/10 for all intent and purposes T is the number of base pairs divided by 10 (bp/10)...
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