mechanics of dna sticky end joints
DESCRIPTION
Mechanics of DNA Sticky End Joints. Ehsan Ban & Catalin Picu. Rensselaer Polytechnic Institute. APS March 2012. Self Assembled DNA Structures. 3D crystals Similar structures include: 2D crystals DNA origami structures & DNA guided crystallized colloidal nanoparticles. - PowerPoint PPT PresentationTRANSCRIPT
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Mechanics of DNA Sticky End JointsEhsan Ban & Catalin Picu
APS March 2012
Rensselaer Polytechnic Institute
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Self Assembled DNA Structures• 3D crystalsSimilar structures include:
– 2D crystals – DNA origami structures &– DNA guided crystallized
colloidal nanoparticles
J Zheng et al. Nature 2009PWK Rothemund Nature 2006
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• Unit Cell• Triangles• Holliday Junctions• Sticky Ends
Mechanics of 3D DNA Crystals
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Outline
• Molecular Dynamics simulation of DNA
mechanics
• Simulating stretch of dsDNA and sticky ends
• A comparison of stretching different sticky
ends
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Molecular Dynamics Simulation
• Potential functions:
– CHARMM27 Force Field
– LJ potential for non bonded interactions
– Coulomb forces for Electrostatics
• TIP3 explicit water model
• Langevin Thermostat (300K temperature)
and Barostat (1 atm pressure)• Time integration
– Newton’s second law
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Test Model
Costum DNA pdb genherated by 3D DART server; DNA Chemical Structure Image from Wikipedia
5’
5’
3’
3’
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Stretch of dsDNA
6 10 14 18 22-200
800
1800
Deformed Length (nm)
Forc
e (p
N)
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Bases’ Configuration and Stretch
6 10 14 18 22-200
800
1800
Deformed Length (nm)
Forc
e (p
N)
6 10 14 18 220
5
10
15
20
25
30
35
40
45
50
Not Paired
Facing Outward
Deformed Length (nm)
Num
ber o
f Bas
es
Total Bases
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Comparison with Existing Literature
6 8 10 12 14 16 18 200
1000
2000
3000
Deformed Length (nm)
Forc
e (p
N)
Bottom fig. from PMD Severin et. al. Nucleic Acid Research 2011
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6 7 8 9 10 11 12
-50
0
50
100
150
200
250
Length (nm)
Forc
e (p
N)
Stretch of a Sticky End Link
External work:105 * 10-20
(J)
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6 7 8 9 10 11 12 13 14 15
-100
-50
0
50
100
150
200
250
Deformed Length (nm)
Forc
e (p
N)
Sticky Ends with Different Sequences
2bp GC Replica 2
2bp AT Replica 22bp GC
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6 8 10 12 14 16 18
-200
-100
0
100
200
300
400
500
600
700
Deformed Length (nm)
Forc
e (p
N)
Sticky Ends with Different Lengths
2bp GC Sticky End Replica2
4bp Sticky End Replica 24bp Sticky End
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6.5 8.5 10.5 12.5 14.5 16.5 18.5 20.5 22.5
-200
0
200
400
600
800
1000
1200
1400
1600
1800
Deformed Length (nm)
Forc
e (p
N)
F-D Diagram of The Sticky Ends Compared to dsDNA
4bp Sticky End
2bp GC Sticky End
dsDNA
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Conclusions
• The sequence of bases at the sticky end does not have a major effect on their axial strength.
• The number of bases in the sticky end controls the strength.
• Thermal fluctuations play a large role in failure and hence influence the failure strength.
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Thank you for your attention.
Simulations are performed using NAMD and RPI Scorec Blue gene.Molecules are visualized using VMD.
Also used extensively are Notepad++ and Tcl scripting with VMD Tk Console.