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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) , PNAS - PowerPoint PPT Presentation
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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