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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 Presentation
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Mechanics of DNA Sticky End JointsEhsan Ban & Catalin Picu
APS March 2012
Rensselaer Polytechnic Institute
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
• Unit Cell• Triangles• Holliday Junctions• Sticky Ends
Mechanics of 3D DNA Crystals
Outline
• Molecular Dynamics simulation of DNA
mechanics
• Simulating stretch of dsDNA and sticky ends
• A comparison of stretching different sticky
ends
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
Test Model
Costum DNA pdb genherated by 3D DART server; DNA Chemical Structure Image from Wikipedia
5’
5’
3’
3’
Stretch of dsDNA
6 10 14 18 22-200
800
1800
Deformed Length (nm)
Forc
e (p
N)
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
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
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)
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
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
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
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.
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.