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DNA: Structure, Dynamics DNA: Structure, Dynamics and Recognitionand Recognition
Les Houches 2004
L4: DNA deformation
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BASE PAIR OPENING
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Biological time scale
Bond vibrations 1 fs (10-15 s)
Sugar repuckering 1 ps (10-12 s)
DNA bending 1 ns (10-9 s)
Domain movement 1 s (10-6 s)
Base pair opening 1 ms (10-3 s)
Transcription 2.5 ms / nucleotide
Protein synthesis 6.5 ms / amino acid
Protein folding ~ 10 s
RNA lifetime ~ 300 s
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Enzymatic base chemistry
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Adenine-Thymine base pair
HN3 imino proton
S S
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Guanine-Cytosine base pair
HN1 imino proton
S
S
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Base opening lifetimes
GC 15-25 ms
AT 5-10 ms
C G C A A G A A G C G
* * 4 1 1 23 4 5 4 * *
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A4T4 versus T4A4
T T T T A A A A
1 17 19 4 4 19 17 1
A A A A T T T T
60 100 100 65 65 100 100 60
Leroy et al. Biochemistry 27, 1988, 8894
Base pair lifetimes (ms) 15°C
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B-DNA - 2ns dynamic trajectory
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Free energy calculations using restrained opening
Guidice et al. ChemPhysChem 2, 2001, 673
Varnai & Lavery J. Am. Chem. Soc. 124, 2002, 7272
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WHAM
FREE ENERGY PROFILE
BIASED PROBABILITY HISTOGRAM N
(q)
W(q
)
Reaction coordinate (q)
Nw
P*i(q) exp [Vi(q)] i =1
Pi(q)
Nw
ni exp [Fi(q)Vi(q)] i =1
Nw
Fi(q) kT ln Pi(q)
i =1
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B-DNA oligonucleotide studied
CTCTCTCTCTCTC
GAGAGAGAGAGAG
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Extraction d’une base de l’ADN
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Closed AT pair
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Adenine –50° (minor)
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Adenine –100° (minor)
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Adenine +50° (major)
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Adenine +100° (major)
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Free energy curves for base opening
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Imino proton accessibility (Å2)
T
G
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Base movements are coupled
Adenine (°)
T
hym
ine
(°)
Thymine (°)
A
deni
ne (
°)
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Sequence effects on opening: A-tracts
T A-tract T Ref
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Bending amplitude (°)
< -50°
-50° < < +50°
> +50°
G
T
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A word of warning!
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BASE FLIPPING
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Hha1 methyltransferaseKlimašauskas et al. Cell 76 (1994) 357
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Minor groove Major groove
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-200° opening
+160° opening
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Backbone rearrangements
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Backbone rearrangements
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SUPERCOILING
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DNA supercoiling (circular plasmid)
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DNA supercoiling
L = linking number = number of strand crossings
T = twist = number of turns of double helix
W = writhe = number of helix crossovers
L = T + W
= supercoiling density = (L – L0) / L0 = L / L0
typically ~ -0.06 (1 crossing less per 17 turns)
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Linking number (L or Lk) – a topological constant
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Twist (T) versus Writhe (W)
Low force High force
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L = T + W
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Interwound and toroidal forms of a negatively supercoiled plasmid
L.H.
R.H.
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Ethidium bromide intercalates into DNA and reduces its twist by ~26°
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Effect of an intercalator on a negatively supercoiled plasmid
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Topoisomerases
Topoisomerase I - single strand cuts- releases negative supercoiling
Topoisomerase II - double strand cuts(eukaryotes) - releases negative supercoiling
Topo II (gyrase) - generates negative supercoiling(prokaryotes) - consumes ATP
Reverse gyrase - generates positive supercoiling(thermophiles)
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Topoisomerase I – single strand cuts
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Topoisomerase II – double strand cuts
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Topo II (gyrase)DNA wrapping
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DNA packed on nucleosomes
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Nucleosome – schematic view
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EXTREME DEFORMATIONS
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DNA stretching
Cluzel et al. Science 271, 1996, 792
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70 pN phase transition
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S-DNA: fibre and ribbon forms
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Fibre diffraction of stretched DNA
Greenall et al.
J. Mol. Biol. 2001, 305, 669
Rise ~ 5.6 Å
Helix spacing ~ 13 Å
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TBP-DNA complex
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DNA: local stretching
3'
3'
5'
5'
5' 3'
3' 5'
Major
Minor
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DNA: global and local 3'3' stretching
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TBP induced deformation
X-ray Model
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Magnetic twisting control
DIG : AntiDIG
Biotin : Streptavidin
N S
Strick et al. Biophys. J. 74, 1998, 2016
Allemand et al. Proc. Natl. Acad. Sci. (USA) 95, 1998, 14152
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Twisted DNA forms plectonemes
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DNA twisting under tension
> 3 pN
< 0.3 pN
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Simulation of DNA twisting
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Simulating twisting