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Transcript of DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie...
![Page 1: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/1.jpg)
DNA: Structure, Dynamics DNA: Structure, Dynamics and Recognitionand Recognition
Les Houches 2004
Richard Lavery
Institut de Biologie Physico-Chimique, Paris
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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
![Page 3: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/3.jpg)
DNA: Structure, Dynamics DNA: Structure, Dynamics and Recognitionand Recognition
Les Houches 2004
L1: Biological context, history, basic DNA structure
![Page 4: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/4.jpg)
BIOLOGICAL CONTEXT
![Page 5: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/5.jpg)
140 Mb
3300 Mb
0.6 Mb
4.4 Mb
4.6 Mb
![Page 6: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/6.jpg)
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
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E. coli membrane region© David S. Goodsell
500 Å
![Page 8: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/8.jpg)
• 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
![Page 9: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/9.jpg)
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 m (10-6 m)
Bacterial cell 5 m (10-5 m)
Chromosome DNA 10 cm (10-1 m)
![Page 10: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/10.jpg)
Biological length scale
If 20 Å 1 cm then ...
1 m 5000 km ...
Nucleus 15 m2 room
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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
![Page 12: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/12.jpg)
Modelling the budding yeast cell cycle (Tyson & Novak)
K.C. Chen et al. Mol. Biol. Cell Cycle 11 (2000) 369
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E-cell project
580,000 bp
500 genes
![Page 14: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/14.jpg)
Molecular machines .... transcriptosome
Nanobiotechnology D.S. Goodsell
![Page 15: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/15.jpg)
Nucleosome
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A LITTLE HISTORY ...
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History of DNA
1865 Gregor Mendel publishes his work on plant breeding with the notionof "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 inthe 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
![Page 18: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/18.jpg)
History of DNA
1944 Oswald Avery (Rockefeller Institute) proves that DNA carries thegenetic message by transforming bacteria
![Page 19: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/19.jpg)
History of DNA
1950 Erwin Chargaff discovers A/G = T/C
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History of DNA
1953 Watson and Crick propose the double helix as the structure of DNAbased on the work of Erwin Chargaff, Jerry Donohue, Rosy Franklinand John Kendrew
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Maurice Wilkins – Kings College, London
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Rosalind Franklin (in Paris)
![Page 23: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/23.jpg)
X-ray fibre diffraction pattern of B-DNA
![Page 24: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/24.jpg)
Linus Pauling’s DNA
![Page 25: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/25.jpg)
Watson-Crick base pairs
Thymine -Adenine Cytosine -Guanine
![Page 26: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/26.jpg)
![Page 27: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/27.jpg)
Watson and Crick
![Page 28: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/28.jpg)
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.
![Page 29: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/29.jpg)
Double helix ?
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Dickerson Dodecamer (Oct. 1980)
![Page 31: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/31.jpg)
DNA STRUCTURE
![Page 32: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/32.jpg)
Nucleoside
Nucleotide
OH ribose
H deoxyribose
![Page 33: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/33.jpg)
.
O
H
H
OH
H
H
H
O N
N
NH2
CH2P O
O
O -
P O
O
O -
P O- O
O
O - 1'
2'3'
4'
5'
2'-deoxycytidine 5' triphosphate
O
H
H
H
H
CH2P O
O
O -
P O
O
O -
P O- O
O
O - 1'
2'3'
4'
5'
N
N
NH2
N
N
2'-deoxyadenosine 5' triphosphate
OH H
O
H
H
OH
H
H
H
CH2P O
O
O -
P O
O
O -
P O- O
O
O - 1'
2'3'
4'
5'
N
NHN
N
O
H2N
2'-deoxyguanosine 5' triphosphate
O
H
H
OH
H
H
H
CH2P O
O
O -
P O
O
O -
P O- O
O
O - 1'
2'3'
4'
5'
O N
H N
O
CH3
thymidine 5' triphosphate
Nucleotide triphosphates
![Page 34: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/34.jpg)
Nucleotides are linked by phosphodiester bonds
Strand has a direction (5'3')
![Page 35: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/35.jpg)
DNA/RNA chemical structure
DNA : A ,T,G,C + deoxyriboseRNA : A,U,G,C + ribose
![Page 36: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/36.jpg)
Base families
Purine (Pur / R) Pyrimidine (Pyr / Y)
C2
N1
C5C6N7
C4
C8
N9
N3
N1
C4
N3
C2
C5
C6
![Page 37: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/37.jpg)
Watson-Crick base pairs
Thymine -Adenine Cytosine -Guanine
![Page 38: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/38.jpg)
Base pair dimensions
![Page 39: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/39.jpg)
34 Å
3.4 Å
20 Å
MinorGroove
MajorGroove
GC
CG
AT
TA
CG
GCAT
TA
TA
AT
GCCG
GC
Strands areantiparallel
CGCGTTGACAACTGCAGAATC
![Page 40: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/40.jpg)
A and B DNA allomorphs
B A
Hydration
Antiparallel strands
5’5’3’
3’
![Page 41: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/41.jpg)
DNA grooves
MINOR
MAJOR
![Page 42: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/42.jpg)
B-DNA (longitudinal view)
![Page 43: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/43.jpg)
B-DNA (lateral view)
R.H. helix
![Page 44: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/44.jpg)
A-DNA (longitudinal view)
![Page 45: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/45.jpg)
A-DNA (lateral view)
R.H. helix
![Page 46: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/46.jpg)
Z-DNA (longitudinal view)
![Page 47: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/47.jpg)
Z-DNA (lateral view)
L.H. helix
![Page 48: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/48.jpg)
Base pairs are rotated in Z-DNA
![Page 49: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/49.jpg)
Backbone dihedrals - I
0
![Page 50: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/50.jpg)
+60°+10°
Dihedral angle definition
Staggered Eclipsed
![Page 51: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/51.jpg)
Favoured conformations
gauche +
trans
gauche -
![Page 52: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/52.jpg)
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’ – P t
: C3’ – O3’ – P – O5’ g-(Y) : O4’ – C1’ – N1 – C2 g-
(R) : O4’ – C1’ – N9 – C4
![Page 53: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/53.jpg)
syn-anti glycosidic conformations
![Page 54: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/54.jpg)
Baird & Tatlock 1901
![Page 55: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/55.jpg)
Medicine SetsManufactures by Messrs Burroughs, Wellcome & Co.
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Sugar ring puckering
C5’
ENDO
EXO
Base
![Page 57: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/57.jpg)
Sugar pucker described as
pseudorotation
North : C3’-endo
East : O4’-endo
South : C3’-endo
"2 B or not 2 B ...." W. Shakespeare 1601
![Page 58: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/58.jpg)
Pseudorotation Equations
Altona et al. J. Am. Chem. Soc. 94, 1972, 8205
0
2
13
4
Basetan P = (4 - 1) - (3 - 0)
22 (Sin 36° + Sin72°)
Amp = 2 / Cos P
![Page 59: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/59.jpg)
Preferred sugar puckers
![Page 60: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/60.jpg)
Sugar pucker and P-P distance
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UNUSUAL DNA STRUCTURES
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Alternative base pairs
Watson-Crick
Reversed Watson-Crick
Hoogsteen Reversed Hoogsteen
![Page 63: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/63.jpg)
Watson-Crick + Hoogsteen = Base triplet
- note C(N3) protonation
![Page 64: DNA: Structure, Dynamics and Recognition Les Houches 2004 Richard Lavery Institut de Biologie Physico-Chimique, Paris.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649c795503460f9492e3a0/html5/thumbnails/64.jpg)
Triple helix DNA
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Guanine Hoogsteen pairing Base tetraplex
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Quadruplex DNA
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Inverted repeat can lead to loop formation
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DNA cruciform
Holliday junction
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PNA versus DNA
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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
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Parallel-stranded DNA
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I-DNA: intercalated parallel-stranded duplexes
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and nucleotide anomers
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H OH is not the only change in passing from DNA to RNA ....
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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