1. DNA: Structure, Dynamics and Recognition
Richard Lavery
Institut de Biologie Physico-Chimique, Paris
Les Houches 2004

2. L1: Biological context, history, basic DNA structure
L2: Introductory DNA biophysics and biology
L3: DNA dynamics
L4: DNA deformation
L5: Recognizing DNA
Les Houches 2004

3. DNA: Structure, Dynamics and Recognition
L1: Biological context, history, basic DNA structure
Les Houches 2004

4. BIOLOGICAL CONTEXT

5. 140 Mb
3300 Mb
4.4 Mb
0.6 Mb
4.6 Mb

6. 50 mm Escherichia Coli, ≈4.6 Mb
VEVRLREDPETFLVQLYQHCPPLARIDSVEREPFIWSQLPTEFTIRQSTGGTMNTQIVP FT DAATCPACLAEMNTPGERRYRYPFINCTHCGPRFTIIRAMPYDRPFTVMAAFPLCPACD FT KEYRDPLDRRFHAQPVACPECGPHLEWVSHGEHAEQEAALQAAIAQLKMGKIVAIKGIG FT GFHLACDARNSNAVATLRARKHRPAKPLAVMLPVADGLPDAARQLLTTPAAPIVLVDKK FT YVPELCDDIAPDLNEVGVMLPANPLQHLLLQELQCPLVMTSGNLSGKPPAISNEQALAD FT LQGIADGFLIHNRDIVQRMDDSVVRESGEMLRRSRGYVPDALALPPGFKNVPPVLCLGA FT DLKNTFCLVRGEQAVLSQHLGDLSDDGIQMQWREALRLMQNIYDFTPQYVVHDAHPGYV FT SSQWAREMNLPTQTVLHHHAHAAACLAEHQWPLDGGDVIALTLDGIGMGENGALWGGEC FT LRVNYRECEHLGGLPAVALPGGDLAAKQPWRNLLAQCLRFVPEWQNYSETASVQQQNWS FT VLARAIERGINAPLASSCGRFFDAVAAALGCAPATLSYEGEAACALEALAASCHGVTHP FT VTMPRVDNQLDLATFWQQWLNWQAPVNQRAWAFHDALAQGFAALMREQATMRGITTLVF
Escherichia Coli, ≈4.6 Mb

7. 500 Å
E. coli membrane region
© David S. Goodsell

8. DNA
Double helix
Stores genetic code as a linear sequence of bases
≈ 20 Å in diameter
Human genome ≈ 3.3 x 109 bp
≈ 25,000 genes

9. Biological length scale
Chemical bond 1 Å (10-10 m)
Amino acid 10 Å (10-9 m)
Globular protein 100 Å (10-8 m)
Virus 1000 Å (10-7 m)
Cell nucleus 1 mm (10-6 m)
Bacterial cell 5 mm (10-5 m)
Chromosome DNA 10 cm (10-1 m)
Biological length scale

10. Biological length scale
If 20 Å  1 cm then ...
1 m  5000 km ...
Nucleus  15 m2 room
Biological length scale

11. A "minimal" organism Hutchinson et al. Science 286, 1999, 2165
"We are wondering if we can come up with a molecular definition of life"
"The goal is to fundamentally understand the components of the most basic living cell"
Craig Venter, founder of Celera Genomics, IBEA and several other gene tech companies
Hutchinson et al. Science 286, 1999, 2165

12. Modelling the budding yeast cell cycle (Tyson & Novak)
K.C. Chen et al. Mol. Biol. Cell Cycle 11 (2000) 369
Modelling the budding yeast cell cycle (Tyson & Novak)

13. 580,000 bp
500 genes
E-cell project

14. Molecular machines .... transcriptosome
Nanobiotechnology D.S. Goodsell

15. Nucleosome

16. A LITTLE HISTORY ...

17. 1865 Gregor Mendel publishes his work on plant breeding with the notion
of "genes" carrying transmissible characteristics
1869 "Nuclein" is isolated by Johann Friedrich Miescher à Tübingen
in the laboratory of Hoppe-Seyler
1892 Meischer writes to his uncle "large biological molecules composed
of small repeated chemical pieces could express a rich language in
the same way as the letters of our alphabet"
1920 Recognition of the chemical difference between DNA and RNA
Phoebus Levene proposes the "tetranucleotide hypothesis"
1938 William Astbury obtains the first diffraction patters of DNA fibres
History of DNA

18. 1944 Oswald Avery (Rockefeller Institute) proves that DNA carries the
genetic message by transforming bacteria
History of DNA

19. 1950 Erwin Chargaff discovers A/G = T/C
History of DNA

20. 1953 Watson and Crick propose the double helix as the structure of DNA
based on the work of Erwin Chargaff, Jerry Donohue, Rosy Franklin
and John Kendrew
History of DNA

21. Maurice Wilkins – Kings College, London

22. Rosalind Franklin (in Paris)

23. X-ray fibre diffraction pattern of B-DNA

24. Linus Pauling’s DNA

25. Watson-Crick base pairs
Thymine -Adenine
Cytosine -Guanine
Watson-Crick base pairs

27. Watson and Crick

28. It has not escaped our notice …
It has not escaped our notice that the specific pairing we have postulated suggests a possible copying mechanism for the genetic material.
It has not escaped our notice …

29. Double helix ?

30. Dickerson Dodecamer (Oct. 1980)

31. DNA STRUCTURE

32. OH ribose
H deoxyribose
Nucleoside
Nucleotide

33. Nucleotide triphosphates

34. Nucleotides are linked by
phosphodiester bonds
Strand has a direction
(5'3')

35. DNA/RNA chemical structure
RNA : A,U,G,C + ribose
DNA : A ,T,G,C + deoxyribose
DNA/RNA chemical structure

36. Base families Purine (Pur / R) Pyrimidine (Pyr / Y) C5 C4 N7 C6 C5 C6

37. Watson-Crick base pairs
Thymine -Adenine
Cytosine -Guanine
Watson-Crick base pairs

38. Base pair dimensions

39. CGCGTTGACAACTGCAGAATC

40. Hydration 3’ 5’ 5’ 3’
Antiparallel strands B A
A and B DNA allomorphs

41. MAJOR
MINOR
DNA grooves

42. B-DNA (longitudinal view)

43. R.H. helix
B-DNA (lateral view)

44. A-DNA (longitudinal view)

45. R.H. helix
A-DNA (lateral view)

46. Z-DNA (longitudinal view)

47. L.H. helix
Z-DNA (lateral view)

48. Base pairs are rotated in Z-DNA

49. n0
Backbone dihedrals - I

50. Dihedral angle definition
+60°
+10°
Staggered
Eclipsed
Dihedral angle definition

51. Favoured conformations
gauche +
gauche -
trans
Favoured conformations

52. Backbone dihedrals - II
: O3’ – P – O5’ – C5’ g-
: P – O5’ – C5’ – C4’ t
g : O5’ – C5’ – C4’ – C3’ g+
: C5’ – C4’ – C3’ – O3’ g+
e : C4’ – C3’ – O3’ – P t
z : C3’ – O3’ – P – O5’ g-
(Y) : O4’ – C1’ – N1 – C2 g-
c(R) : O4’ – C1’ – N9 – C4
Backbone dihedrals - II

53. syn-anti glycosidic conformations

54. Baird & Tatlock 1901

55. Medicine Sets Manufactures by Messrs Burroughs, Wellcome & Co.

56. C5’
ENDO
EXO
Base
Sugar ring puckering

57. Sugar pucker described as pseudorotation
North : C3’-endo
East : O4’-endo
South : C3’-endo
"2 B or not 2 B ...." W. Shakespeare 1601

58. Pseudorotation Equations
Base
tan P = (n4 - n1) - (n3 - n0)
2n2 (Sin 36° + Sin72°)
Amp = n2 / Cos P
Pseudorotation Equations
Altona et al. J. Am. Chem. Soc. 94, 1972, 8205

59. Preferred sugar puckers

60. Sugar pucker and P-P distance

61. UNUSUAL DNA STRUCTURES

62. Alternative base pairs
Reversed Watson-Crick
Watson-Crick
Hoogsteen
Reversed Hoogsteen
Alternative base pairs

63. Watson-Crick + Hoogsteen = Base triplet
- note C(N3) protonation
Watson-Crick + Hoogsteen = Base triplet

64. Triple helix DNA

65. Guanine Hoogsteen pairing  Base tetraplex

66. Quadruplex DNA

67. Inverted repeat can lead to loop formation

68. Holliday junction
DNA cruciform

69. PNA versus DNA

70. Peptide Nucleic acid(PNA)
Achiral, peptide-like backbone
Backbone is uncharged  High thermal stability
High-specificity hybridization with DNA
Resistant to enzymatic degradation
Can displace DNA strand of duplex
Pyrimidine PNA strands can form 2:1 triplexes with ssDNA
Biotechnological applications
Peptide Nucleic acid(PNA)

71. Parallel-stranded DNA

72. I-DNA: intercalated parallel-stranded duplexes

73. a and b nucleotide anomers

74. H  OH is not the only change in passing from DNA to RNA ....

75. Principles of Nucleic Acid Structure, W. Saenger, 1984 Springer-Verlag
Nucleic Acid Structure, Ed. S. Neidle, 1999 Oxford University Press
DNA Structure and Function, R.R. Sinden, 1994 Academic Press
Biochemistry, D. Voet and J.G. Voet, 1998 DeBoeck
The Eighth Day of Creation, H.F. Judson, 1996 Cold Spring Harbour Press
Books on DNA