3. Figure 5-11 Three- dimensional structure of B-DNA. Figure 5-12Watson- Crick base pairs.

4. http://rutchem.rutgers.edu/~xiangjun/ 3DNA/images/bp_step_hel.gif

5. Twist varies with sequence. Note: importance of sequence > importance of composition.

6. Figure 29-7The conformation of a nucleotide unit is determined by the seven indicated torsion angles. Figure 29-9bSugar ring pucker. (b) The steric strain resulting in Part a is partially relieved by ring puckering in a half-chair conformation in which C3¢ is the out-of-plane atom.

7. Table 4.T02: Comparison of Major Features in A-, B-, and Z-Forms of DNA Adapted from Ussery, D. W. Encyclopedia of Life Sciences. John Wiley & Sons, Ltd., May 2002. [doi: 10.1038/npg.els.0003122].

8. Table 29-1Structural Features of Ideal A-, B-, and Z-DNA.

9. Figure 29-10a Nucleotide sugar conformations. (a) The C3-endo conformation (on the same side of the sugar ring as C5), which occurs in A-RNA and RNA-11. Figure 29-10b Nucleotide sugar conformations. (b) The C2-endo conformation, which occurs in B- DNA. Greater flexibility of B-DNA allows it to exhibit significant variation in the configuation of its sugar pucker under in vivo conditions. But see: http://www.chem.qmul.ac.uk/iupac/misc/pnuc2.html

10. From: http://www.chem.qmul.ac.uk/iupac/misc/pnuc2.html

11. Figure 4.05a: Deoxyguanylate in B-DNA in anti conformation

12. Figure 4.05b: Deoxyguanylate in Z-DNA in syn conformation

13. Figure 29-1aStructure of B-DNA. (a) Ball and stick drawing and corresponding space- filling model viewed perpendicular to the helix axis. ~10 bp/turn- right handed Pitch of 34 Angstroms Wide major groove Narrow minor groove Structure adopted by Real DNA deviates from ideal structure in a sequence-specific manner.

14. Figure 4.04a: The C2’-endo conformation Adapted from Voet, D., and Voet, J. G. Biochemistry, Third Edition. John Wiley & Sons, Ltd., 2005.

15. Figure 4.04b: The C3’-endo conformation Adapted from Voet, D., and Voet, J. G. Biochemistry, Third Edition. John Wiley & Sons, Ltd., 2005.

16. Figure 29-1bStructure of B-DNA. (b) Ball and stick drawing and corresponding space- filling model viewed down the helix axis.

17. Figure 4.01a: A-DNA Protein Data Bank ID: 213D. Ramakrishnan, B., and Sundaralingam, M., Biophys. J. 69 (1995): 553-558 (top).

18. Figure 29-2aStructure of A-DNA. (a) Ball and stick drawing and corresponding space- filling model viewed perpendicular to the helix axis. 11.6 bp/turn- right handed Pitch of 34 Angstroms Deep major groove Very shallow minor groove Structure adopted by A-RNA (aka. RNA-11)

19. Figure 29-2bStructure of A-DNA. (b) Ball and stick drawing and corresponding space- filling model viewed down the helix axis.

20. Figure 4.01b: B-DNA Protein Data Bank ID: 1BNA. Drew, H. R., et al., Proc. Natl. Acad. Sci. USA 78 (1981): 2179-2183 (middle).

21. Figure 29-3aStructure of Z-DNA. (a) Ball and stick drawing and corresponding space-filling model viewed perpendicular to the helix axis. 12 bp/turn- left-handed helix Pitch of 44 Angstroms No major groove Deep minor groove Structure adopted by Alternating Purine- Pyrimidine pairs (e.g., repeats of 2 bases pairs) Methylation of C favors formation, as does high salt conc. Genetic switch?

22. Figure 29-3bStructure of Z-DNA. (b) Ball and stick drawing and corresponding space- filling model viewed down the helix axis.

23. Figure 4.01c: Z-DNA Protein Data Bank ID: 2ZNA. Wang, A. H. J., et al. (bottom).

24. Figure 4.02a: Z-DNA with zig-zag sugar phosphate backbone shown in white Protein Data Bank ID: 2ZNA. Wang, A. H. J., et al.

25. Figure 4.02b: The same Z-DNA with the zigzag sugar phosphate backbone shown in space filling display Protein Data Bank ID: 2ZNA. Wang, A. H. J., et al.

26. Figure 29-4Conversion of B-DNA to Z- DNA. Base pairs flipped by 180 degrees Repeat is d(pXpY) Polyd(GC)-polyd(GC) Polyd(AC)-polyd(GT) Anti-C or T Syn-G or A May form transiently behind actively transcribing RNA polymerase

27. Figure 29-5X-Ray structure of two ADAR1 Z  domains in complex with Z-DNA. Thought to targeted to Z-DNA upstream of actively transcribing genes

28. Figure 4.03: Drosophila (fruit fly) chromosomes with bound antibody to Z-DNA. Reproduced from Nordheim, A., et al., Nature 294 (1981): 417-422. Photo courtesy of Alexander Rich, Massachusetts Institute of Technology.

29. Forces stabilizing nucleic acid structure BASE PAIRING 1)Geometric complementarity 2)Electronic complementarity Book: contribute -2 to -8 kJ/mol of base pair Other sources: A=U/A=T -5 to -9 kJ/mol of bp G=C -13 to -21 kJ/ mol of bp Base pairs replaced by H-bonds to water of nearly equivalent strength when DNA is denatured. Non Watson-Crick H-bonding have little stability in dsDNA However, they do stabilize tertiary structure of tRNAs and have other roles (e.g., wobble base pairing in codon/anti-codon recognition.

30. Forces stabilizing nucleic acid structure BASE STACKING 1)Van der Waals radii of aromatic ring ~1.7 angstroms 2)Adjacent bases 3.4 angstroms apart in helix 3)Contribute -4 kJ/mol 4)Base stacking is responsible for the hyperchromic effect observed when dsDNA is denatured

31. Forces stabilizing nucleic acid structure HYDROPHOBIC FORCES 1)Sugar-phosphates on outside interacting with water. 2)Hydrophobic bases in interior 3)Base stacking is enthalpically driven and entropically opposed 4)Hydrophobic forces poorly understood 5)Increases in ionic strength stabilizes dsDNA and dsRNA.

32. Table 4.T01: Sizes of Various DNA Molecules

34. Figure 4.08: DNA melting curve.

35. Figure 4.09: Effect of G-C content on DNA melting temperature.

36. Figure 4.10: Several effects of cooperativity of base-stacking.

38. Figure 4.11: The effect of lowering the temperature to 25°C after strand separation has taken place.

39. Figure 4.06a: Inverted repeats Adapted from Bacolla, A., and Wells, R. D., J. Biol. Chem. 279 (2004): 47411-47414.

40. Figure 4.06b: Cruciform structure Adapted from Bacolla, A., and Wells, R. D., J. Biol. Chem. 279 (2004): 47411-47414.

41. Figure 4.07: Hairpin RNA. Adapted from Horton, R. H., et al. Principles of Physical Biochemistry, Second Edition. Prentice Hall, 2006.

42. Hyperchromic effect- increase of 1.4xA 260 upon denaturation of double-stranded nucleic Acids (dsDNA or dsRNA

43. Forces stabilizing nucleic acid structure IONIC INTERACTIONS 1.Electrostatic repulsion of phosphates destabilize dsDNA structure 2.Effect counteracted or stabilized by cations -Metal ions: Na +, K +, Mg 2+ -polyamines -basic proteins -Mg 2+ effect 100-1000X of Na + ions. ENTROPICALLY UNFAVORABLE 1)Highly ordered 2)Increase temperature= decrease stability T m =41.1X G+C + 16.6log[Na + ] +81.5