DNA: Structure, Dynamics and
Recognition
Richard Lavery
Institut de Biologie Physico-Chimique, Paris
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
Les Houches 2004
DNA: Structure, Dynamics and
Recognition
L1: Biological context, history, basic DNA structure
Les Houches 2004
BIOLOGICAL CONTEXT
140 Mb
3300 Mb
4.4 Mb
0.6 Mb
4.6 Mb
50 mm
VEVRLREDPETFLVQLYQHCPPLARIDSVEREPFIWSQLPTEFTIRQSTGGTMNTQIVP FT
DAATCPACLAEMNTPGERRYRYPFINCTHCGPRFTIIRAMPYDRPFTVMAAFPLCPACD FT
KEYRDPLDRRFHAQPVACPECGPHLEWVSHGEHAEQEAALQAAIAQLKMGKIVAIKGIG F
GFHLACDARNSNAVATLRARKHRPAKPLAVMLPVADGLPDAARQLLTTPAAPIVLVDKK FT
YVPELCDDIAPDLNEVGVMLPANPLQHLLLQELQCPLVMTSGNLSGKPPAISNEQALAD FT
LQGIADGFLIHNRDIVQRMDDSVVRESGEMLRRSRGYVPDALALPPGFKNVPPVLCLGA F
DLKNTFCLVRGEQAVLSQHLGDLSDDGIQMQWREALRLMQNIYDFTPQYVVHDAHPGYV
SSQWAREMNLPTQTVLHHHAHAAACLAEHQWPLDGGDVIALTLDGIGMGENGALWGGEC
LRVNYRECEHLGGLPAVALPGGDLAAKQPWRNLLAQCLRFVPEWQNYSETASVQQQNWS
VLARAIERGINAPLASSCGRFFDAVAAALGCAPATLSYEGEAACALEALAASCHGVTHP FT
VTMPRVDNQLDLATFWQQWLNWQAPVNQRAWAFHDALAQGFAALMREQATMRGITTLV
Escherichia Coli, ≈4.6 Mb
500 Å
E. coli membrane region
© David S. Goodsell
• 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
Chemical bond
1Å
(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
If 20 Å  1 cm then ...
1 m  5000 km ...
Nucleus  15 m2 room
Biological length scale
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
K.C. Chen et al. Mol. Biol. Cell Cycle 11 (2000) 369
Modelling the budding yeast cell cycle (Tyson & Novak)
580,000 bp
500 genes
E-cell project
Molecular machines ....
transcriptosome
Nanobiotechnology D.S. Goodsell
Nucleosome
A LITTLE HISTORY ...
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
1944
Oswald Avery (Rockefeller Institute) proves that DNA carries the
genetic message by transforming bacteria
History of DNA
1950
Erwin Chargaff discovers A/G = T/C
History of DNA
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
Maurice Wilkins – Kings College, London
Rosalind Franklin (in Paris)
X-ray fibre diffraction pattern of B-DNA
Linus Pauling’s DNA
Thymine -Adenine
Cytosine -Guanine
Watson-Crick base pairs
Watson and Crick
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 …
Double helix ?
Dickerson Dodecamer (Oct. 1980)
DNA STRUCTURE
OH ribose
H deoxyribose
Nucleoside
Nucleotide
Nucleotide triphosphates
 Nucleotides are linked by
phosphodiester bonds
 Strand has a direction
(5'3')
RNA : A,U,G,C + ribose
DNA : A ,T,G,C + deoxyribose
DNA/RNA chemical structure
N7
C5
C4
C6
C8
N1
N9
C6
N3
C2
C4
C5
N1
C2
N3
Purine (Pur / R)
Pyrimidine (Pyr / Y)
Base families
Thymine -Adenine
Cytosine -Guanine
Watson-Crick base pairs
Base pair dimensions
20 Å
GC
AT
CG
CGCGTTGACAACTGCAGAATC
34 Å
TA
TA
GC
AT
Major
Groove
TA
3.4 Å
Strands are
antiparallel
Minor
Groove
CG
CG
GC
AT
GC
Hydration
5’
3’
3’
5’
Antiparallel
strands
B
A
A and B DNA allomorphs
DNA grooves
B-DNA (longitudinal view)
R.H. helix
B-DNA (lateral view)
A-DNA (longitudinal view)
R.H. helix
A-DNA (lateral view)
Z-DNA (longitudinal view)
L.H. helix
Z-DNA (lateral view)
Base pairs are rotated in Z-DNA
n0
Backbone dihedrals - I
+10°
+60°
Staggered
Eclipsed
Dihedral angle definition
gauche +
gauche -
trans
Favoured conformations
:
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
(R) :
O4’ – C1’ – N9 – C4
Backbone dihedrals - II
g-
syn-anti glycosidic conformations
Baird & Tatlock 1901
Medicine Sets
Manufactures by Messrs Burroughs, Wellcome & Co.
C5’
Base
ENDO
EXO
Sugar ring puckering
Sugar pucker
described as
pseudorotation
North : C3’-endo
East : O4’-endo
South : C3’-endo
"2 B or not 2 B ...."
W. Shakespeare 1601
tan P = (n4 - n1) - (n3 - n0)
n4
n0
2n2 (Sin 36° + Sin72°)
n1
n3
Amp = n2 / Cos P
n2
Pseudorotation Equations
Altona et al. J. Am. Chem. Soc. 94, 1972, 8205
Base
Preferred sugar puckers
Sugar pucker and P-P distance
UNUSUAL DNA STRUCTURES
Reversed Watson-Crick
Watson-Crick
Hoogsteen
Reversed Hoogsteen
Alternative base pairs
- note C(N3) protonation
Watson-Crick + Hoogsteen = Base triplet
Triple helix DNA
Guanine Hoogsteen pairing  Base tetraplex
Quadruplex DNA
Inverted repeat can lead to loop formation
Holliday junction
DNA cruciform
PNA versus DNA
 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)
Parallel-stranded DNA
I-DNA: intercalated parallel-stranded duplexes
 and  nucleotide anomers
H  OH is not the only change in passing from DNA to RNA ....
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