DNA Structure and Supercoiling (Lecture 2) PDF

Watson and Crick model James Watson and Francis Crick Features: -DNA is composed of two helical strands (double stranded helix) - sugar-phosphate form the backbone - the nitrogenous bases are stacked in a helical array in the central core - The bases of one strand are hydrogen bo...

Watson and Crick model James Watson and Francis Crick Features: -DNA is composed of two helical strands (double stranded helix) - sugar-phosphate form the backbone - the nitrogenous bases are stacked in a helical array in the central core - The bases of one strand are hydrogen bonded with those on the other strand (A-T) and (G-C) -Major groove and minor groove allowing proteins to come in contact with the bases - antiparallel strands I In a sequence like: ATCGGCTAGGT Where is the 5‘ and where is the 3‘  G+C content ([G]+[C])X100/all bases G+C content is near 50% for most complex organisms: For most plants and animals, the extremes are 48% and 52% The percentage G+C varies widely from one genus to another in single-cell organisms For example: 27% for the genus Clostridium and 76% for the genus Sarcina, E- coli is 50%  Alternate DNA structures 1) B- helix 2)A-helix 3) Z-helix (Right handed helix) (left-handed helix) The origin of these different forms are related to 1) The conformation of the sugar 2) Orientation of the base relative to the sugar 3) Hydration/salt-content  Alternate DNA structures 1) A- helix Features: 1) Predominant form of double stranded RNA 2) Has 11 bases per turn rather than 10 3) Has plane of the bases tilted 30°C with respect to the helical axis 4) This helix is favored under conditions of dehydration 5) It is wider and shorter than the B helix and the distinction between the major and minor grooves is reduced  Alternate DNA structures 2) Z- helix Features: 1) The backbone has a zigzag shape 2) Double stranded but left-handed 3) Has 12 base per turn 4) The length of the turn is 4.5 nm rather than 3.4 nm 5) Appears longer and slimmer than the B-helix 6) Regions of the Z conformation can be found interspersed among regions of the B conformation 7) Z-helix result due to a primary structure or sequence of G alternating with C 8) The presence of regions of Z DNA near genes on the same molecule can influence their expression  3) Single-stranded DNA 1) Occur in some viruses 2) The structure is irregular 3) It folds back on itself 4) Short double stranded helical regions are formed between complementary regions 5) SSDNA is more dense than DSDNA 6) Helix-loop structures are also a feature 4) Triple and four-stranded DNA 1) Found in DNA that has repeating streches of purines alternating with stretches of pyrimidines complementary to the purine stretches 2) Found at the end of chromosomes in the telomers and may be important in the process of meiosis  DNA Structure: Supercoiling The chromosome of E.coli, if linearized would be more than 1mm in length i.e. about 400 times longer than the E.coli cell itself The very long DNA molecule can be packaged into the cell because it is supercoiled Supercoiling is defined as the process in which the double stranded DNA is further twisted  Supercoiling Negative supercoiling Positive supercoiling When the DNA is twisted When the DNA is twisted about its axis in the opposite about its axis in the same direction from that of the right direction from that of the right handed double helix handed double helix Number of times the strands Number of times the strands cross is less cross is more Loosening Tightening Negatively supercoiled DNA is predominantely found in nature  DNA gyrase is a key enzyme in prokaryotes, introducing negative supercoils to the DNA. Reverse gyrase introduces positive supercoiling.  In prokaryotes, this supercoiling is produced by enzymes called topoisomerases. Topoisomerase II (DNA Gyrase) enhances supercoiling and Topoisomerase I releases supercoiling In eukaryotic chromosomes, DNA is wound around proteins called histones, forming structures called nucleosomes Little proteins are associated with the chromosomes of prokaryotes Positive charge Negative charge