Computational Modeling of DNA Binding Molecules

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Computational Modeling of DNA Binding Molecules

• Heather Hill
• Department of Chemistry and Biochemistry
• University of North Carolina at Wilmington
• Wilmington, NC 28403

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• Molecules being constructed in our lab

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• This molecule binds in the groove of DNA

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• Crystal Structure of DNA with molecule
  (modified in Titan)

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• DNA with molecule and an attached linker and
• glucose ring (modified in Insight II)

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Methods

• Build/model molecules with two different
  targeting molecules and several different linkers
• Submit for calculations
• Compare to lab results

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Benefits of Project

• Save time
• Save money
• Identify possible candidates and eliminate those
  that do not work

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References

• Zhang, Y., Chen, F.-X., Mehta, P., and Gold, B.
  (1993) Biochemistry 32, 7954-7965.
• Varadarajan, S., Dharini, S., Dande, P., Settles,
  S., Chen, F.-X., Gilberto, F., and Gold, B.
  (2003) Biochemistry 42, 14318-14327.

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Acknowledgements

• Dr. Varadarajan
• Dr. Martin
• Dr. Bartolotti ( East Carolina University)