Organization of DNA

1. Organization of DNA Andy HowardIntroductory Biochemistry12 October 2010 Biochem: Nucleic Acid Structure II

2. Restriction Enzymes Review of A,B,Z DNA Intercalation Denaturation and renaturation of DNA DNA density DNA tertiary structure Review of supercoiling Gyrases Nucleosomes Higher levels Bacterial organization What we’ll discuss Biochem: Nucleic Acid Structure II

3. Restriction Endonucleases • Evolve in bacteria as antiviral tools • “Restriction” because they restrict the incorporation of foreign DNA into the bacterial chromosome • Recognize and bind to specific palindromic DNA sequences and cleave them • Self-cleavage avoided by methylation • Types I, II, III: II is most important • I and III have inherent methylase activity; II has methylase activity in an attendant enzyme Biochem: Nucleic Acid Structure II

4. What do we mean by palindromic? • In ordinary language, it means a phrase that reads the same forward and back: • Madam, I’m Adam. (Genesis 3:20) • Eve, man, am Eve. • Sex at noon taxes. • Able was I ere I saw Elba. (Napoleon) • A man, a plan, a canal: Panama! (T. Roosevelt) • With DNA it means the double-stranded sequence is identical on both strands Biochem: Nucleic Acid Structure II

5. Quirky math problem • Numbers can be palindromic:484, 1331, 727, 595… • Some numbers that are palindromic have squares that are palindromic…222 = 484, 1212 = 14641, . . . • Question: if a number is perfect square and a palindrome, is its square root a palindrome? (answer will be given orally) Biochem: Nucleic Acid Structure II

6. Palindromic DNA • Example: G-A-A-T-T-C • Single strand isn’t symmetric: but the combination with the complementary strand is: • G-A-A-T-T-CC-T-T-A-A-G • These kinds of sequences are the recognition sites for restriction endonucleases. This particular hexanucleotide is the recognition sequence for EcoRI. Biochem: Nucleic Acid Structure II

7. Cleavages by restriction endonucleases • Breaks can be • cohesive (if off-center within the sequence) or • non-cohesive (blunt) (if they’re at the center) • EcoRI leaves staggered 5’-termini: cleaves between initial G and A • PstI cleaves CTGCAG between A and G, so it leaves staggered 3’-termini • BalI cleaves TGGCCA in the middle: blunt! Biochem: Nucleic Acid Structure II

8. iClicker question • 1. Which of the following is a potential restriction site? • (a) ACTTCA • (b) AGCGCT • (c) TGGCCT • (d) AACCGG • (e) none of the above. Biochem: Nucleic Acid Structure II

9. Example for E.coli • 5’-N-N-N-N-G-A-A-T-T-C-N-N-N-N-3’3’-N-N-N-N-C-T-T-A-A-G-N-N-N-N-5’ • Cleaves G-A on top, A-G on bottom: • 5’-N-N-N-N-GA-A-T-T-C-N-N-N-N-3’3’-N-N-N-N-C-T-T-A-AG-N-N-N-N-5’ • Protruding 5’ ends:5’-N-N-N-N-GA-A-T-T-C-N-N-N-N-3’3’-N-N-N-N-C-T-T-A-AG-N-N-N-N-5’ Biochem: Nucleic Acid Structure II

10. How often? • 4 types of bases • So a recognition site that is 4 bases long will occur once every 44 = 256 bases on either strand, on average • 6-base site: every 46= 4096 bases, which is roughly one gene’s worth Biochem: Nucleic Acid Structure II

11. EcoRI structure • Dimeric structure enables recognition of palindromic sequence •  sandwich in each monomer EcoRI pre-recognition complex PDB 1CL8 57 kDa dimer + DNA Biochem: Nucleic Acid Structure II

12. The biology problem • How does the bacterium mark its own DNA so that it does replicate its own DNA but not the foreign DNA? • Answer: by methylating specific bases in its DNA prior to replication • Unmethylated DNA from foreign source gets cleaved by restriction endonuclease • Only the methylated DNA survives to be replicated • Most methylations are of A & G,but sometimes C gets it too Biochem: Nucleic Acid Structure II

13. How this works • When an unmethylated specific sequence appears in the DNA, the enzyme cleaves it • When the corresponding methylated sequence appears, it doesn’t get cleaved and remains available for replication • The restriction endonucleases only bind to palindromic sequences Biochem: Nucleic Acid Structure II

14. Methylases HhaI methyltransferasePDB 1SVU2.66Å; 72 kDa dimer • A typical bacterium protects its own DNA against cleavage by its restriction endonucleases by methylating a base in the restriction site • Methylating agent is generally S-adenosylmethionine Biochem: Nucleic Acid Structure II

15. Use of restriction enzymes • Nature made these to protect bacteria; we use them to cleave DNA in analyzable ways • Similar to proteolytic digestion of proteins • Having a variety of nucleases means we can get fragments in multiple ways • We can amplify our DNA first • Can also be used in synthesis of inserts that we can incorporate into plasmids that enable us to make appropriate DNA molecules in bacteria Biochem: Nucleic Acid Structure II

16. Summaries of A, B, Z DNA Biochem: Nucleic Acid Structure II

17. DNA is dynamic • Don’t think of these diagrams as static • The H-bonds stretch and the torsions allow some rotations, so the ropes can form roughly spherical shapes when not constrained by histones • Shape is sequence-dependent, which influences protein-DNA interactions Biochem: Nucleic Acid Structure II

18. Intercalating agents • Generally: aromatic compounds that can form -stack interactions with bases • Bases must be forced apart to fit them in • Results in an almost ladderlike structure for the sugar-phosphate backbone locally • Conclusion: it must be easy to do local unwinding to get those in! Biochem: Nucleic Acid Structure II

19. Instances of inter-calators Biochem: Nucleic Acid Structure II

20. Denaturing and Renaturing DNA See Figure 11.17 • When DNA is heated to 80+ degrees Celsius, its UV absorbance increases by 30-40% • This hyperchromic shift reflects the unwinding of the DNA double helix • Stacked base pairs in native DNA absorb less light • When T is lowered, the absorbance drops, reflecting the re-establishment of stacking Biochem: Nucleic Acid Structure II

21. Heat denaturation • Figure 11.14Heat denaturation of DNA from various sources, so-called melting curves. The midpoint of the melting curve is defined as the melting temperature, Tm.(From Marmur, J., 1959. Nature183:1427–1429.) Biochem: Nucleic Acid Structure II

22. GC content vs. melting temp • High salt and no chelators raises the melting temperature Biochem: Nucleic Acid Structure II

23. How else can we melt DNA? • High pH deprotonates the bases so the H-bonds disappear • Low pH hyper-protonates the bases so the H-bonds disappear • Alkalai is better: it doesn’t break the glycosidic linkages • Urea, formamide make better H-bonds than the DNA itself so they denature DNA Biochem: Nucleic Acid Structure II

24. What happens if we separate the strands? • We can renature the DNA into a double helix • Requires re-association of 2 strands: reannealing • The realignment can go wrong • Association is 2nd-order, zippering is first order and therefore faster Biochem: Nucleic Acid Structure II

25. Steps in denaturation and renaturation Biochem: Nucleic Acid Structure II

26. Rate depends on complexity • The more complex DNA is, the longer it takes for nucleation of renaturation to occur • “Complex” can mean “large”, but complexity is influenced by sequence randomness: poly(AT) is faster than a random sequence Biochem: Nucleic Acid Structure II

27. Second-order kinetics • Rate of association: -dc/dt = k2c2 • Boundary condition is fully denatured concentration c0 at time t=0: • c / c0 = (1+k2c0t)-1 • Half time is t1/2 = (k2c0)-1 • Routine depiction: plot c0t vs. fraction reassociated (c /c0) and find the halfway point. Biochem: Nucleic Acid Structure II

28. Typical c0t curves Biochem: Nucleic Acid Structure II

29. Hybrid duplexes • We can associate DNA from 2 species • Closer relatives hybridize better • Can be probed one gene at a time • DNA-RNA hybrids can be used to fish out appropriate RNA molecules Biochem: Nucleic Acid Structure II

30. GC-rich DNA is denser • DNA is denser than RNA or protein, period, because it can coil up so compactly • Therefore density-gradient centrifugation separates DNA from other cellular macromolecules • GC-rich DNA is 3% denser than AT-rich • Can be used as a quick measure of GC content Biochem: Nucleic Acid Structure II

31. Density as function of GC content Biochem: Nucleic Acid Structure II

32. Tertiary Structure of DNA • In duplex DNA, ten bp per turn of helix • Circular DNA sometimes has more or less than 10 bp per turn - a supercoiled state • Enzymes called topoisomerases or gyrases can introduce or remove supercoils • Cruciforms occur in palindromic regions of DNA • Negative supercoiling may promote cruciforms Biochem: Nucleic Acid Structure II

33. DNA is wound • Standard is one winding per helical turn, i.e. 1 winding per 10 bp • Fewer coils or more coils can happen: • This introduces stresses that favors unwinding • Both underwound and overwound DNA compact the DNA so it sediments faster than relaxed DNA Biochem: Nucleic Acid Structure II

34. Linking, twists, and writhe • T=Twist=number of helical turns • W=Writhe=number of supercoils • L=T+W = Linking number is constant unless you break covalent bonds Biochem: Nucleic Acid Structure II

35. Examples with a tube Biochem: Nucleic Acid Structure II

36. How this works with real DNA Biochem: Nucleic Acid Structure II

37. How gyrases work • Enzyme cuts the DNA and lets the DNA pass through itself • Then the enzyme religates the DNA • Can introduce new supercoils or take away old ones Biochem: Nucleic Acid Structure II

38. Typical gyrase action • Takes W=0 circular DNA and supercoils it to W=-4 • This then relaxes a little by disrupting some base-pairs to make ssDNA bubbles Biochem: Nucleic Acid Structure II

39. Superhelix density • Compare L for real DNA to what it would be if it were relaxed (W=0): • That’s L = L - L0 • Sometimes we want = superhelix density= specific linking difference = L / L0 • Natural circular DNA always has  < 0 Biochem: Nucleic Acid Structure II

40.  < 0 and spools • The strain in  < 0 DNA can be alleviated by wrapping the DNA around protein spool • That’s part of what stabilizes nucleosomes Biochem: Nucleic Acid Structure II

41. Cruciform DNA • Cross-shaped structures arise from palindromic structures, including interrupted palindromes like this example • These are less stable than regular duplexes but they are common, and they do create recognition sites for DNA-binding proteins, including restriction enzymes Biochem: Nucleic Acid Structure II

42. Cruciform DNA example Biochem: Nucleic Acid Structure II

43. Eukaryotic chromosome structure • Human DNA’s total length is ~2 meters! • This must be packaged into a nucleus that is about 5 micrometers in diameter • This represents a compression of more than 100,000! • It is made possible by wrapping the DNA around protein spools called nucleosomes and then packing these in helical filaments Biochem: Nucleic Acid Structure II

44. Chromatin • Discovered long before we understood molecular biology • Seen to be banded objects in nuclei of stained eukaryotic cells • In resting cell it exists as long slender threads, 30 nm diameter From answers.com Biochem: Nucleic Acid Structure II

45. Squishing the DNA • If the double helix were fully extended, the largest human chromosome (2.4*108bp) would be 2.4*108 *0.33nm ~ 0.8*108nm=80 mm; • much bigger than the cell! • So we have to coil it up a lot to make it fit. • Longest chromosome is 10µm long • So the packing ratio is 80mm/10µm = 8000 Biochem: Nucleic Acid Structure II

46. Chromosome structure: levels • Each of the first 4 levels compacts DNA by a factor of 6-20; those multiply up to > 104 Biochem: Nucleic Acid Structure II

47. Nucleosome Structure • Chromatin, the nucleoprotein complex, consists of histones and nonhistone chromosomal proteins • Histone octamer structure has been solved • without DNA: Moudrianakis, 1991 • with DNA by Richmond • Nonhistone proteins are regulators of gene expression Biochem: Nucleic Acid Structure II

48. Histone types • H2a, H2b, H3, H4 make up core particle: two copies of each, so: octamer • All histones are KR-rich, small proteins • H1 associates with the regions between the nucleosomes Biochem: Nucleic Acid Structure II

49. Histones: table 11.2, plus… Biochem: Nucleic Acid Structure II

50. Unfolded chromatin • Treat chromatin with low ionic strength; that disrupts higher level interactions so the individual nucleosomes are strung out relative to one another like beads on a string Image courtesy U. Maine Biochem: Nucleic Acid Structure II