ee-motif structures in dna kathryn iverson usc health sciences center and school of pharmacy...
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eE-Motif Structures in DNA
Kathryn Iverson
USC Health Sciences Center
and School of Pharmacy
SoCalBSI 2007
Outline
• E-motif structure
• Project objectives
• Methods
• Working results
5’
5’
CCGCCGCCG CGCCGCCG CCGCCGCC G C C GCCGCCG
GCGGCGGCGGCGGCGG CGGCGGCGGCGGCGGCGGCG
C C
G C
GCG C
C G
CC
CG
GG
GGC
CG
GC
G
Hairpins formed by GCC repeats
5’ C GC CGGC CGC5’
C
C
E-motif Structure
• Extra-helical cytosines
• Extra-helical cytosines from first GCC and third GCC repeats are interacting
• Stacking between G-C
Fragile X
• Is the most common forms of inherited mental retardation. 1 in 2000 boys and 1 in 4000 girls are afflicted and 1 in 260 women are carriers1
• July 22, National Fragile X Awareness Day• Characterized by the expansion of GCC repeat in the
5’ untranslated region of the FMR1 gene
1. http://www.conquerfragilex.org/about.php
Objectives of Project
• Accurate model of eE-motif structure
• Knowledge of extra-helical cytosine structures
• Insight into Fragile X syndrome
• Therapeutic targets
Methods
• Generate NASDAC input files
• Run energy minimization on the structures using AMBER
• Molecular dynamics modeling with restraints in AMBER
Generation of pdb files
• User enters how many GCC repeats
• Option to protonate one of cytosines
• What parameter to vary and within what range
• Create data.in file, run NASDAC and produce .pdb file
Minimization Without Restraints
• G-C base pairs no longer close enough to hydrogen bond
• Stacking of extra-helical cytosines
Restraints
• Hydrogen bonding distance between G and C base pairs
• Distance between N2 atoms in G-C base pairs
• Torsion angle for G-C base pairs
• Distance between extra-helical cytosines
eE-Motif with Restraints
• Extra-helical cytosines are in the same plane
• Hydrogen bonding
Acknowledgements
• Thank you to Dr. Ian Haworth and Dr. Rebecca Romero for their guidance and advice throughout the project
• USC Health Sciences Center and School of Pharmacy
• Program leaders and faculty of SoCalBSI
• SoCalBSI participants
• Cal State LA
Questions?