BDNA/ZDNA FRET efficiency

SNU Compbio.이 윤 경

Introduction : Z-DNA

Is this a proper model for transcription process?

Introduction : Z-DNA

Supercoiling of the DNA template during transcription, LEROY F. LIU & JAMES C. WANG, June 17, 7024 (1987) , PNASZ-DNA : the long road to biological function, Alexander Rich and Shunguang Zhang, July 2003, Vol 4, Nature

Introduction : Z-DNA

Introduction : FRET

• Experiment

Introduction : FRET

- Donor fluorescence lifetime/quantum yield/ intensity

FRET Efficiency from MDKappa^2

R

Orientation Dependence in FRET Efficiency

ZDNA BDNA Single-molecule FRET measures bends and kinks in DNA, Anna K. Wozniak, Gunnar F. Schroder, Helmut Grubmuller, Claus A. M. Seidel, and Filipp Oesterhelt, September 24, 2008, PNAS

MD simulation preparation

• Geometry optimization and charge derivation– B3LYP/6-31G* including solvent effect -> RESP

Cy5Cy3

MD simulation preparation

MD simulation preparation

MD simulation

• Weak harmonic potential on DNA• Weak dihedral angle restraint on Dyes• Explicit water solvation• 300K• 3ns

Z-DNA

FRET Efficiency from MD

Kappa^2

R

EfficiencyEfficiency

BDNA

ZDNA

BDNA

ZDNA

ratio

Static isotropic

0.498

0.2860.088

0.739

0.177 0.391

0.371 45.294

0.197 63.055

dynamic

0.608

0.101

0.166

Distance distribution

Distance Distribution

B-DNA : 45.294 Z_DNA : 63.055

dista

nce

Time step

Distance Distribution

distance

frequenc

y

B-DNA : 45.294 Z_DNA : 63.055

Kappa distribution

Kappa=3.6 ->

<- Kappa=0.01

Kappa Distribution

B-DNA : 0.371 Z_DNA : 0.197

frequ

ency

kappa

Static average distribution

E_stat

frequ

ency

B-DNA : 0.498 Z-DNA : 0.088

Summary

- Kappa value : far from the isotropic assumption (BDNA 0.4; ZDNA 0.2)

- Difference in kappa^2 value between two form of DNA : affects relative orientation between two dyes

- Average scheme : incomplete description for the movement of two dyes

- Insufficient conformational space search