Biochemistry of Medicinals I – Nucleic Acids

1. Biochemistry of Medicinals I – Nucleic Acids Instructor: Natalia Tretyakova, Ph.D. 760E CCRB (Cancer Center) Tel. 6-3432 e-mail trety001@umn.edu Lecture: MWF 2:30-3:20 7-135 WDH Web page: see “Web enhanced courses”

3. Chapter 1. DNA Structure. Required reading: Stryer 5th Edition p. 117-125, 144-146, 152, 745-750, 754-762, 875-877) (or Stryer’s Biochemistry 4th edition p. 75-77,80-88, 119-122, 126-128, 787-799, 975-980)

4. DNA Structure: Chapter outline • Biological roles of DNA. Flow of genetic information. • Primary and secondary structure of DNA. • Types of DNA double helix. Sequence-specific DNA recognition by proteins. • Biophysical properties of DNA. • DNA topology. Topoisomerases. • Restriction Endonucleases. Molecular Cloning

5. (ribonucleic acids) (deoxyribonucleic acids) replication transcription translation DNA

6. Why ? • Questions? • How is genetic information transmitted to progeny cells? • How is DNA synthesis initiated? • What causes DNA defects and what are their biological an physiological consequences? • What causes the differences between cells containing the same genetic information? • Relevance: • •Cancer: ex. Xeroderma pigmentosum • •Genetic diseases: ex., cystic fibrosis, sickle cell anemia, inborn errors of metabolism • •Genetic typing: ex., drug metabolism • •Rational drug design: ex., antitumor and antimicrobial drugs • •Biotechnology: ex., growth hormones

7. The Building Blocks of DNA -N-glycosidic bond

8. DNA and RNA nucleobases (DNA only) (RNA only)

9. Purine Nucleotides

10. Pyrimidine Nucleotides

11. nucleobase (Deoxy) nucleoside 5’-mononucleotide Adenine (A) Guanine (G) Thymine (T) Cytosine (C) Uracil (U) 2’-Deoxyadenosine (dA) 2’- Deoxyguanosine (dG) 2’- Deoxythymidine (dT) 2’- Deoxycytidine (dC) Uridine (U) Deoxyadenosine 5’-monophosphate (5’-dAMP) Deoxyguanosine 5’-monophosphate (5’-dGMP) Deoxythymidine 5’-monophosphate (5’-dTMP) Deoxycytidine 5’-monophosphate (5’-dCMP) Uridine 5’-monophosphate (5’-UMP) Nomenclature of nucleobases, nucleosides, and mononucleotides

12. Structural differences between DNA and RNA DNA RNA

13. Preferred conformations of nucleobases and sugars in DNA and RNA Sugar puckers: 5.9 A 7.0 A

14. Nucleosides Must Be Converted to5’-Triphosphates to be Part of DNA and RNA

15. DNA isArranged5’ to 3’Connected byPhosphates Linking inDNA biopolymer: DNA primary structure

16. DNA secondary structure – double helix • James Watson and Francis Crick, 1953- proposed a model for DNA structure • DNA is the molecule of heredity (O.Avery, 1944) • X-ray diffraction (R.Franklin and M. Wilkins) • E. Chargaff (1940s) G = C and A = T in DNA Francis Crick Jim Watson

17. Watson-Crick model of DNA was based on X-ray diffraction picture of DNA fibres (Rosalind Franklin and Maurice Wilkins) Rosalind Franklin

18. Watson-Crick model of DNA was consistent with Chargaff’s base composition rules Erwin Chargaff (Columbia University) G = C and A = T in DNA

19. DNA is Composed of Complementary Strands

20. Base Pairing is Determined by Hydrogen Bonding same size

21. Base stacking: an axial view of B-DNA

22. Forces stabilizing DNA double helix • Hydrogen bonding (2-3 kcal/mol per base pair) • Stacking (hydrophobic) interactions • (4-15 kcal/mol per base pair) • 3. Electrostatic forces.

23. B-DNA • •Sugars are in the 2’ endo conformation. • •Bases are the anti conformation. • •Bases have a helical twist of 36º • (10.4 bases per helix turn) • Helical pitch = 34 A 23.7 A right handed helix • helical axis passes through • base pairs 7.0 A • planes of bases are nearly • perpendicular to the helix axis. • 3.4 A rise between base pairs Wide and deep Narrow and deep

24. DNA can deviate from the ideal Watson-Crick structure • Helical twist ranges from 28 to 42° • Propeller twisting 10 to 20° • Base pair roll

25. Major groove and Minor groove of DNA N NH O 2 N H N O 2 N NH N N N HN C-1’ N N N N C-1’ NH O O 2 C-1’ Hypothetical situation: the two grooves would have similar size if dR residues were attached at 180° to each other To deoxyribose-C1’ C1’ -To deoxyribose C-1’

26. N NH 2 H N O 2 N N HN C-1’ N N NH O 2 C-1’ Major and minor groove of the double helix O N NH N N N N C-1’ O C-1’ Wide and deep Narrow and deep

27. B-type duplex is not possible for RNA steric “clash”

28. A-form helix:dehydrated DNA; RNA-DNA hybrids • •Sugars are in the 3’ endo conformation. • •Bases are the anti conformation. • •11 bases per helix turn • Helical pitch = 25.3 A Right handed helix • planes of bases are tilted • 20 ° relative the helix axis. • 2.3 A rise between base pairs 25.5 A Top View

29. The sugar puckering in A-DNA is 3’-endo 5.9 A 7.0 A

30. A-DNA has a shallow minor groove and a deep major groove • • Helix axis A-DNA B-DNA

31. Z-form double helix:polynucleotides of alternating purines and pyrimidines (GCGCGCGC) at high salt • • Backbone zig-zags because sugar puckers alternate between 2’ endo pyrimidines and 3’ endo (purines) • • Bases alternate between anti (pyrimidines) and syn conformation (purines). • •12 bases per helix turn • Helical pitch = 45.6 A Left handed helix • planes of the bases are • tilted 9° relative the helix • axis. • 3.8 A rise between base pairs 18.4 A • Flat major groove • Narrow and deep minor groove

32. Sugar and base conformations in Z-DNA alternate: 5’-GCGCGCGCGCGCG 3’-CGCGCGCGCGCGC C:sugar is 2’-endo, base is anti G: sugar is 3’-endo, base is syn

34. Biological relevance of the minor types of DNA secondary structure • Although the majority of chromosomal DNA is in B-form, • some regions assume A- or Z-like structure • Runs of multiple Gs are A-like • The upstream sequences of some genes contain • 5-methylcytosine = Z-like duplex • Structural variations play a role in DNA-protein interactions • RNA-DNA hybrids and ds RNA have an A-type structure