1 / 15

Mechanics of DNA Sticky End Joints

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.

hedy
Download Presentation

Mechanics of DNA Sticky End Joints

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Mechanics of DNA Sticky End Joints Ehsan Ban & CatalinPicu Rensselaer Polytechnic Institute APS March 2012

  2. Self Assembled DNA Structures • 3D crystals Similar structures include: • 2D crystals • DNA origami structures & • DNA guided crystallized colloidal nanoparticles J Zheng et al. Nature 2009 PWK Rothemund Nature 2006

  3. Mechanics of 3D DNA Crystals • Unit Cell • Triangles • Holliday Junctions • Sticky Ends

  4. Outline • Molecular Dynamics simulation of DNA mechanics • Simulating stretch of dsDNA and sticky ends • A comparison of stretching different sticky ends

  5. 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

  6. Test Model 3’ 5’ 5’ 3’ Costum DNA pdbgenherated by 3D DART server; DNA Chemical Structure Image from Wikipedia

  7. Stretch of dsDNA

  8. Bases’ Configuration and Stretch Total Bases

  9. Comparison with Existing Literature Bottom fig. from PMD Severin et. al. Nucleic Acid Research 2011

  10. Stretch of a Sticky End Link External work:105 * 10-20(J)

  11. Sticky Ends with Different Sequences 2bp GC 2bp AT Replica 2 2bp GC Replica 2

  12. Sticky Ends with Different Lengths 4bp Sticky End 4bp Sticky End Replica 2 2bp GC Sticky End Replica2

  13. F-D Diagram of The Sticky Ends Compared to dsDNA dsDNA 4bp Sticky End 2bp GC Sticky End

  14. 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.

  15. 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.

More Related