Chapter 4. Structure of DNA Chapter 4 Opener

Helical Structure of DNA: composed of two polynucleotide chains

Formation of nucleotide (Sugar, Base, Phosphate) by removal of water Formation of nuclotide by removal of water

Table 4-1 Nucleoside Nucleotide Nucleoside Nucleotide

Detailed structure of polynucleotide polymer Figure 4-3 Detailed structure of polynucleotide polymer Detailed structure of polynucleotide polymer 5

Purines and Pyrimidines Figure 4-4 Purines and Pyrimidines Purines and Pyrimidine 6

Base tautomers (상호변환이성질체) Figure 4-5 Base tautomers (상호변환이성질체) rarely forms Base tautomers rarely forms 7

A:C incompatibility A:T and G:C base pair Figure 4-7 A:T and G:C base pair, A:C incompatibility 8

Figure 4-8 Base flipping: To methylate bases or remove damaged bases, enabling base to sit in the catalytic activity center. Base flipping 9

DNA is usually a right handed double helix. Figure 4-9 DNA is usually a right handed double helix. Figure 4-9 DNA is usually a right handed double helix. 10

The major groove is rich in chemical information. Figure 4-10 The major groove is rich in chemical information. A: acceptor D: donor M: methyl group H: nonpolar hydrogen Figure 4-10 The major groove is rich in chemical information. A: acceptor D: donor M: methyl group H: nonpolar hydrogen 11

Double helix DNA Exists in multiple conformations. Figure 4-11 Double helix DNA Exists in multiple conformations. B form is usual. A form is in low humid condition and DNA-protein in certain complexes and, RNA-DNA and RNA-RNA helices (left-handed) (right-handed) Certain conditions can promote Z DNA; such as alternating purine-pyrimidine sequence (especially poly(dGC)2), negative DNA supercoiling or high salt and some cations  Figure 4-11 Double helix DNA Exists in multiple conformations. B form is usual. A form is in low humid condition and DNA-protein in certain complexes and, RNA-DNA and RNA-RNA helices 12

Syn and Anti positions of guanine in B and Z DNA Figure 4-13 Syn and Anti positions of guanine in B and Z DNA alternating purine-pyrimidine sequence (especially poly(dGC)2) Figure 4-13 13

Table 4-2 Table 4-2 14

Reannealing and hybridization Figure 4-14 Reannealing and hybridization Figure 4-14 Reannealing and hybridization 15

Figure 4-15 Figure 4-15 16

Figure 4-16 Dependence of DNA denaturation and on G+C content and salt concentration (red in low salt and green in high salt) Figure 4-16 Dependence of DNA denaturation and on G+C content and salt concentraion 17

Topological states of covalently closed, circular (ccc) DNA Figure 4-17 Topological states of covalently closed, circular (ccc) DNA (most bacterial chromosome and plasmid) Supercoiled DNA (left wound) Figure 4-17 Topological states of covalently closed, circular (ccc) DNA Linking number(Lk) = twisting number(Tw) + writhing number(Wr) Supercoiled DNA Linking number(Lk) = twisting number(Tw) + writhing number(Wr) = Number of interwound 18

Two forms of writhe of supercoiled DNA Figure 4-18 Two forms of writhe of supercoiled DNA Lko is the Linking number of fully relaxed cccDNA under physiological condition. Figure 4-18 Two forms of writhe of supercoiled DNA Lko is the Linking number of fully relaxed cccDNA under physiological condition. 19

Relaxing DNA (from supercoing) with Dnase I Figure 4-19 Relaxing DNA (from supercoing) with Dnase I Figure 4-19 Relaxing DNA with Dnase I 20

DNA in cells is negatively supercoiled. If Δ Lk = Lk –Lko is negative, that is said to be negatively supercoiled. Nucleosomes introduce negative supercoiling in eukaryotes. DNA in cells is negatively supercoiled. If Δ Lk = Lk –Lko is negative, that is said to be negatively supercoiled. Nucleosomes introduce negative supercoiling in eukaryotes. Topoisomerases can relax supercoiled DNA. Topoisomerases can relax supercoiled DNA.

Electron micrograph of supercoiled (on the right) bacteriophage PM2 Figure 4-20 Electron micrograph of supercoiled (on the right) bacteriophage PM2 Figure 4-20 Electron micrograph of supercoiled bacteriophage PM2 22

Figure 4-21 Prokaryotes have a special topoisomerase that induces supercoiles into DNA Schematic for changing the linking number in DNA with topoisomerase II (breaking double –strand break) Figure 4-21 Prokaryotes have a special topoisomerase that induces supercoiles into DNA Schematic for changing the linking number in DNA with topoisomerase II 23

Schematic mechanism of action for topoisomerase I Figure 4-22 Schematic mechanism of action for topoisomerase I Figure 4-22 Schematic mechanism of action for topoisomerase 24

Topoisomerases decatenate, disentagle, and unknot DNA. Figure 4-23 Topoisomerases decatenate, disentagle, and unknot DNA. Figure 4-23 Topoisomerases decatenate, disentagle, and unknot DNA. 25

Topoisomerases cleave DNA using a covalent tyrosine-DNA intermediate. Figure 4-24 Topoisomerases cleave DNA using a covalent tyrosine-DNA intermediate. Figure 4-24 Topoisomerases cleave DNA using a covalent tyrosine-DNA intermediate. 26

Figure 4-25 Model for the reaction cycle catalyzed by a type I topoisomerase (composed of four domains) Figure 4-25 Model for the reaction cycle catalyzed by a type I topoisomerase 27

Separation of DNA topoisomers Figure 4-26 Separation of DNA topoisomers Figure 4-26 Separation of DNA topoisomers 28

Figure 4-27 Figure 4-27 29

Inercalation of EtBr into DNA Figure 4-28 Inercalation of EtBr into DNA Figure 4-28 Inercalation of EtBr into DNA 30