1. Molecular Biology CHM6640/7640 Lecture #2 “Structure of DNA and RNA” Presented by Joanna Klapacz For Dr. Ashok S. Bhagwat Thursday January 10, 2008

2. Nucleic Acids: 2 major types: DNA and RNA Molecular repositories of genetic information in cells Variety of other roles in cellular metabolism: energy currency of metabolic transactions messengers in signaling pathways components of enzyme cofactors

3. 1.Nucleotides are the building blocks/polymers of nucleic acids. 2.Nucleotides are composed of three parts: Nitrogen containing base Pentose sugar moiety Phosphate group 3.Nucleoside is composed of base + sugar.

4. Solution Confirmations of Ribose Sugar Moiety 1’ 2’3’ 4’ 5’ 1’ 2’ 3’ 4’ 5’ Remember the numbering!

5. D-ribose Ribonucleotide Found in Ribonucleic Acids (RNA)

6. Deoxyribonucleotide Found in Deoxyribonucleic Acids (DNA) H D-deoxyribose

7. Remember the numbering! Two Parent Nitrogenous Bases

8. Bases Found in Nucleic Acids

10. Nucleotides in RNA

11. Nucleotides in DNA

12. or TTP Nucleoside can have more than one phosphate groups

13. Rotation Between Seven Bonds is Observed in Nucleic Acids GLYCOSYL BOND C1’

14. Conformation of Purines with Respect to Attached Sugar Only the anti- configuration is found in DNA

15. or 2’-H Default or 2’-H Structures of Adenosine Monophosphates Found in DNA and RNA: Found in RNA only:

16. RNA is Chemically Less Stable pH >11

17. Naturally occurring base modifications in nucleic acids

18. Practice drawing: 8-oxoguanosine 2,6-diaminopurine etc

19. Covalent backbones of nucleic acids consist of alternating phosphate and sugar residues. DNA RNA

20. Schematic Representation of DNA Sequence

21. Hydrogen –Bonding of Base Pairs

22. O HN C OH N C keto enol NH HN C NH 2 N C amino imino >10,000 : 1 Keto and Amino Groups in Bases Can Undergo Rearrangements.

23. Resonance Structure of Bases Keto- and Amino groups in bases can undergo rearrangements. Predominant Forms Could Lead to Base Mispairing

24. Chemical Properties of Nucleic Acids If pH is 10 in solution, the base pairs are disrupted because of protonation/deprotonation of keto and amino groups. Site Affected pKa Adenylate N1 3.9 Guanylate N1 10.0 Cytidylate N3 4.5 Thymidylate N3 10.5 Adenylate N7 2.4 Guanylate N7 2.4

25. B-Form DNA Defined by Watson-Crick base pairing. Most stable structure of DNA under physiological conditions.

26. Schematic Representation of DNA (b) Stick Model (c) Space-Filling Model

27. Comparison of A and B Form DNA

28. dsRNA or DNA:RNA double-stranded (ds) DNA

29. Specialized Structure in Nucleic Acids : read identically either forwards or backwards Regions of DNA with inverted repeats that are self-complementary.

30. Hairpin Structures Formed in DNA and RNA from a Single Nucleic Acid Strand

31. Cruciform Structures Formed in DNA and RNA from both Strands of Nucleic Acids

32. RNA Can Adopt Complex Structures

33. Transfer-RNA (tRNA) Tertiary (3D) Structure Secondary Structure

34. tRNA Contains Modified Bases 1-Methyladenine 1

35. DNA Damaging Agents Hoeijmakers. Nature. 2001. 411:366-74.

36. DISEASE CELL DEATH Mutation Cell cycle arrest DNA REPAIR Alkylating Agents Occur Ubiquitously and Cause DNA Damage

37. Endogenous Environmental Man-made Alkylating Agents Bi-functional/ Cross-Linking S N 1 Alkylating Agent S N 2 Agent

38. S N 1 Alkylating Agents * Alkylating Agents used clinically as chemotherapeutics Model Mono- functional Bi- functional

39. Wyatt and Pittman. 2006. Chem. Res. Toxicol. 19:1580-94 DNA Methylating Agents Induce More than a Dozen Different Lesions in DNA Other targets phosphotriesters deoxyribose Filled Arrows: S N 1 Empty Arrows: S N 1 and S N 2

40. O 6 -methylguanine is Mutagenic CytosineGuanine Thymine O 6 -methylguanine

41. 3-methyladenine is a Toxic Lesion that Inhibits DNA Polymerases 3meA also rapidly depurinates

42. 7-methyl Adduct Causes Rapid Base Loss H OH Abasic (AP) site in DNA Free Base +