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

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Presentation on theme: "DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris."— Presentation transcript:

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

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

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

4 BIOLOGICAL CONTEXT

5 140 Mb 3300 Mb 0.6 Mb 4.4 Mb 4.6 Mb

6 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 50  m

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

8 DNA Double helix Stores genetic code as a linear sequence of bases ≈ 20 Å in diameter Human genome ≈ 3.3 x 10 9 bp ≈ 25,000 genes

9 Biological length scale Chemical bond1 Å( m) Amino acid10 Å(10 -9 m) Globular protein100 Å(10 -8 m) Virus1000 Å(10 -7 m) Cell nucleus1  m(10 -6 m) Bacterial cell5  m(10 -5 m) Chromosome DNA10 cm(10 -1 m)

10 Biological length scale If 20 Å  1 cm then... 1 m  5000 km... Nucleus  15 m 2 room

11 A "minimal" organism "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

13 E-cell project 580,000 bp 500 genes

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

15 Nucleosome

16 A LITTLE HISTORY...

17 History of DNA 1865Gregor 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 1892Meischer 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" 1920Recognition of the chemical difference between DNA and RNA Phoebus Levene proposes the "tetranucleotide hypothesis" 1938William Astbury obtains the first diffraction patters of DNA fibres

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

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

20 History of DNA 1953Watson 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

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 -AdenineCytosine -Guanine

26

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.

29 Double helix ?

30 Dickerson Dodecamer (Oct. 1980)

31 DNA STRUCTURE

32 Nucleoside Nucleotide OH ribose H deoxyribose

33 Nucleotide triphosphates

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

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

36 Base families Purine (Pur / R)Pyrimidine (Pyr / Y) C2 N1 C5 C6 N7 C4 C8 N9 N3 N1 C4 N3 C2 C5 C6

37 Watson-Crick base pairs Thymine -AdenineCytosine -Guanine

38 Base pair dimensions

39 CGCGTTGACAACTGCAGAATC

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

41 DNA grooves MINOR MAJOR

42 B-DNA (longitudinal view)

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

44 A-DNA (longitudinal view)

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

46 Z-DNA (longitudinal view)

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

48 Base pairs are rotated in Z-DNA

49 Backbone dihedrals - I 0

50 +60° +10° Dihedral angle definition StaggeredEclipsed

51 Favoured conformations gauche + trans gauche -

52 Backbone dihedrals - II  :O3’ – P – O5’ – C5’g -  :P – O5’ – C5’ – C4’t  :O5’ – C5’ – C4’ – C3’g +  :C5’ – C4’ – C3’ – O3’g +  :C4’ – C3’ – O3’ – Pt  :C3’ – O3’ – P – O5’g -  (Y) : O4’ – C1’ – N1 – C2g -  (R) : O4’ – C1’ – N9 – C4

53 syn-anti glycosidic conformations

54 Baird & Tatlock 1901

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

56 Sugar ring puckering C5’ ENDO EXO Base

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 Altona et al. J. Am. Chem. Soc. 94, 1972, Base tan P = ( ) - ( ) 2 2 (Sin 36° + Sin72°) Amp = 2 / Cos P

59 Preferred sugar puckers

60 Sugar pucker and P-P distance

61 UNUSUAL DNA STRUCTURES

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

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

64 Triple helix DNA

65 Guanine Hoogsteen pairing  Base tetraplex

66 Quadruplex DNA

67 Inverted repeat can lead to loop formation

68 DNA cruciform Holliday junction

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

71 Parallel-stranded DNA

72 I-DNA: intercalated parallel-stranded duplexes

73  and  nucleotide anomers

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

75 Books on DNA 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


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