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

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Not Paired

Facing Outward

Deformed Length (nm)

Num

ber o

f Bas

es

Total Bases

Comparison with Existing Literature

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Deformed Length (nm)

Forc

e (p

N)

Bottom fig. from PMD Severin et. al. Nucleic Acid Research 2011

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Length (nm)

Forc

e (p

N)

Stretch of a Sticky End Link

External work:105 * 10-20

(J)

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Deformed Length (nm)

Forc

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Sticky Ends with Different Sequences

2bp GC Replica 2

2bp AT Replica 22bp GC

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Deformed Length (nm)

Forc

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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

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Deformed Length (nm)

Forc

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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.