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?