Dr. Parvin Pasalar Tehran University of Medical Sciences

1. Nucleic Acid Structure دانشگاه علوم پزشكي وخدمات بهداشتي درماني تهران Dr. Parvin Pasalar Tehran University of Medical Sciences

2. Objectives: To know and identify the structure, roles and classifications of bases sugars nucleosides nucleotides DNAs RNAs

3. Bases

4. Nucleic Acids / Bases/Definition Nucleobases are: Aromatic (planner) Heterocyclic, Nitrogen containing Classified into: Purine Pyrimidine Hetero atoms are referred to atoms other than C and H. In biology they are N, O and S (planner character facilitates their close association or stacking which stabilizes double stranded DNA)

5. Nucleic Acids / Bases/Structure Imidazole Pyrimidine By the attachment of different groups to the rings, different types of Py and Pu are generated.

6. NA / Bases/ Classification • Purine Bases (pu): • Major : (A)&(G) • Minor: Inosine(I) & methyl guanine(7mG) • Unnatural : Mercaptopurine, Allopurinol & 8-Azaguanine

7. NA / Bases/ Classification/ Py Hot spot • Pyrimidines (py): • Major : (T), (C) & (U) • Minor: DHU , 5mC & 5hmC • Unnatural: Fluorouracil (5FU) & 6-aza cytosine( AZC)

8. Sugars

9. Nucleic Acids / Sugars D-family Aldo pentose Furanose β-Anomer Ribose or deoxy Ribose Numbered by Prime Isomerism ( 2’ endo in DNA , 3’ endo in RNA)

10. Nucleosides

11. Nucleic Acids / Nucleosides β-N-glycosidic linkage of a base and a pentose (1‘ to 9 in PU and 1‘ to 1 in PY). Major:Cytidine & deoxy cytidine. • There are 8 major nucleosides. Minor: ribothymidine (rT) & psudouracil (ΨU). Unnatural: Cytarabin. Structure: Isomerism: Nomenclature: Roles: Classification: They are major part of nucleosides. Synthetic forms are used as drugs (Cytarabin) Name of the base + suffix sine for Pus(adenosine & guanosine) dine for PYs (uridine & thymidine) syn or anti conformation

12. Nucleotides

13. NA / Nucleosides Biomedical importance • Synthetic pu & py analogs that contain Halogens,thiols or additional nitrogen are employed in: Gout or Hyperuricemia(Allopurinol) Chemotherapy of cancer ( cytarabine) AIDS treatment ( azathioprine) Immunosuppression responses during organ transplantation ( azathioprine) • Building block • Coenzymes (NAD, FAD & Co-A) • Group transfer • Energy carrier ( ATP & GTP) • Regulatory roles: • Drugs • in lipid ( CDP-acylglycerol) • in sugar( UDP-glucose) • in protein (tRNA) synthesis • methyl donor as SAM (S-adenosylmethionine) • Second messenger for hormones(cAMP or GMP) • Allosteric regulator of many enzymes(ATP & AMP in metabolic pathways)

14. 1-Name of the nucleoside + the number of phosphate group. 2-Name of their corresponding acid such as thymidylic or guanylic acid. Nucleic Acids / Nucleotides 1-Nucleoside+ Phosphate group(s =phospho ester of nucleosides 2-In most cases the phosphate group is linked to the 5’ carbon. 3- They may have 1, 2,0r 3 phosphate groups. Structure: Isomerism: Nomenclature: Roles: Classification: They may have syn or anti conformation with predominate anti conformer. Building block Coenzymes (NAD, FAD & Co-A) Group transfer Energy carrier ( ATP & GTP) Regulatory roles: Drugs Major:CMP, dCMP, CDP, CTP There are 24 major nucleotides Minor :cAMP, cGMP Unnatural :Cytarabin

15. Nucleic Acid:1-DNA2-RNA

16. Objectives To know and identify different levels of DNA organization 1- Primary structure 2-Secondary structure Different geometry of base pairs & base steps 3-Higher order of DNA structure in prokaryotes in Eukaryotes Nucleic Acids /DNA/ Structure

17. DNA / General facts • Its structure was discovered in 1953 • It is a polyester compound • Has acidic character It is a polymer in which the monomers (nucleotides) are joined by PDE bonds between 5’ and 3’ carbon atoms of two successive nucleotides. Because of the phosphate moiety, they have acidic character (negatively charged).

18. DNA / General facts • Has polarity • It is double helix • The two strand are: • 1- in opposite polarities • 2- stabled by different bonds: Hydrophobic bond H bond DNA has end-to-end chemical Orientation (3’ and 5’ ends) and by convention it is written in the 5’ ---- 3’ direction

19. Different bonds and interactions in • Covalent: PDE bonds in the backbone • Hydrogen: between complementary bases Primary or Natural (Watson-Crick) Secondary or Hoogsteen pairing (non-Watson-Crick) • Hyrophobic (van der Waals) between the stacked adjacent base pairs.

20. DNA / General facts Has specific groove (s) It is flexible about its long axis It It may be linear or circular Particular region bound to protein clearly depart from the standard conformation MOVIE

21. DNA / Different ways to show primary structure Primary structureis a huge linearpolymer of dNTPs that are joined toeach other by 5’-3’ PDE bonds. 5’3’

22. Secondary structure of DNA / Different ways to show it Secondary structureis formed bybase pairing between two complementary strands. It may be B, A, Z or C-form. 5’ 3’ 3’ 5’

23. What about DNA grooves • They are generated because of the angle of base pairs • They are important for the interaction with proteins

24. Why DNA is Helical? Mother Nature loves a helix!

25. DNA / Different secondary structures • B (duplex) • A (duplex) • Z (duplex)

26. 2nd structure of DNA/ B- DNA • Is the abundant form • Has 2 groooves • Has 10 (10.5)m bp/ turn • Is right handed • The stacked bases are perpendicular to the backbone • Has a pitch per turn of helix 33.2 Ao The helix tilted 32˚ from the viewer to show minor (m) and major (M) grooves. Side and top view of B-DNA in ball-and-stick and space filling representation

27. Supercoiling Topoisomerism

28. Supercoiling/ general facts 1. DNA molecule is very long and has to be contained within cells that are so small. 2. In free form the repulsion of negatively charged DNA is responsible for the large volume occupied by DNA. 3. Chromosomes are compacted DNAs. 4. Double helices can be compacted and form higher order structures that are referred to super helices which are shorter and thicker. 5. In cells there are some positively chargedproteins that responsible for the compaction ( supercoiling) of DNA. 6. Histons in eukaryotes and histon like proteins in prokaryotes .

29. Higher order of DNA structure Supercoiling/ Topoisomerism • Definition: • Where it can be find: • When it can be formed: • Different names: • Different types: • Where the two ends of a DNA molecule are fixed , the molecule exhibit a superstructure under certain conditions. When the base pairing is interrupted and a local region unwind such as during replication, transcription and binding of many binding protein to DNA. The special type of isomerism that is find in supercoiled DNA Relax: There is no superhelix turn Positive: The handness of double and super helix are the same Negative: The handness of double and super helix are opposite • superhelix • supertwist • supercoil.

30. Topoisomerses Class 1 class 2 Mechanism of their function:

31. .

32. Supercoiling In Eukaryotes

33. DNA Compaction( higher order of DNA structure) Human beings have roughly 3 billion base pairs of DNA in 23 chromosomes (haploid). Yeast has 13 million base pairs in 17 chromosomes Distance between bases is 3.4 Angstrom For human this would be 3.4×3×109 Angstroms. This equals 1.02 meters per haploid genome, 2.04 meters per cell The size of the nucleus is roughly 10 micrometers in diameter

34. Double helix (Nucleosomes) 10 nm fibril30 nm fiberloops on scaffoldheterochromatinchromosome Hierarchy

36. Different level of Eukaryotic DNA compaction (Chromosome Structure) • Nucleosome formation. • 10 nm fibril • 30 nm fiber • 300 nm loops (Rosette) • 700 nm helix

37. Operational Classification Euchromatin [Transcriptionally active] Structural genes, rRNA genes, regulatory regions, etc. Chromatin Heterochromatin [Transcriptionally inactive] Centromeric chromatin Attachment sites to nuclear matrix

38. Histones/Classification & structure • Classification: • H1 • H2a • H2b • H3 • H4 & • Numbers of their variants

39. Histone Structure and nucleosome assembly

40. + + + - + - - - - - - - - - - - - - - + + Nucleosome with & without H1

41. Nucleosome/ top & side view

42. centromere telomere

43. Objectives: After studying this session you have to know : Primary structure, secondary and Tertiary structure of RNA. Structure and function of tRNA. Structure and function of rRNA. Structure and function of mRNA. RNA Structure

44. RNA Structure • It has ribose instead of deoxyribose so, it is more labile and more reactive than DNA. • As a result of more liability, RNA is cleaved into mononucleotides by alkaline solution. • It has thymine instead of uracil. • Like DNA it can be double/single stranded, linear / circular. • Unlike DNA, RNA may have different tridimentional structure.

45. Different level of RNA Structure • Its primary structure is a relatively short linear polymer of ribonucleotides. Such as linear form of tRNA. • Secondary structure may be stem-loop, hairpin or other types. Such as clover leaf form of tRNA. • RNA-RNA and RNA-DNA helices exist in A-form. • Tertiary structure is formed between the flexible loops, such as pesudoknot. Such as L-shaped tRNA.

46. Secondary structure of RNAs

47. The importance of tridimentional structure of RNAs A typical right -handed single -stranded RNA A hammerhead ribozyme Phe tRNA (yeast)

48. RNA functions • Structural functionsuch as ribosome • Catalytic function (ribozyme)for example in splicing and self-splicing, rRNA play a catalytic role in peptide bond formation. • Regulatory functionsuch as 5’ an 3’ UTRs of mRNA in the rate of protein synthesis.