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BDNA/ZDNA FRET efficiency

This study investigates the significance of Z-DNA in the transcription process, utilizing fluorescence resonance energy transfer (FRET) to assess efficiency in biophysical experiments. By employing molecular dynamics simulations and analyzing donor fluorescence characteristics, we explore the dynamics and geometric constraints of Z-DNA compared to B-DNA. The findings suggest that Z-DNA exhibits distinct kinematic and conformational behaviors, impacting dye orientations and resulting FRET efficiencies. This research sheds light on the structural intricacies of Z-DNA and its potential roles in biological functions.

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BDNA/ZDNA FRET efficiency

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  1. BDNA/ZDNA FRET efficiency SNU Compbio. 이 윤 경

  2. Introduction : Z-DNA Is this a proper model for transcription process?

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

  4. Introduction : Z-DNA

  5. Introduction : FRET • Experiment

  6. Introduction : FRET - Donor fluorescence lifetime/quantum yield/ intensity

  7. FRET Efficiency from MD Kappa^2 R

  8. 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

  9. MD simulation preparation • Geometry optimization and charge derivation • B3LYP/6-31G* including solvent effect -> RESP Cy3 Cy5

  10. MD simulation preparation

  11. MD simulation preparation

  12. MD simulation • Weak harmonic potential on DNA • Weak dihedral angle restraint on Dyes • Explicit water solvation • 300K • 3ns Z-DNA

  13. FRET Efficiency from MD R Kappa^2 Efficiency Static isotropic dynamic BDNA 0.498 0.739 0.608 ZDNA 0.088 0.286 0.101 ratio 0.177 0.391 0.166 0.371 45.294 BDNA ZDNA 0.197 63.055

  14. Distance distribution

  15. Distance Distribution B-DNA : 45.294 Z_DNA : 63.055 distance Time step

  16. Distance Distribution B-DNA : 45.294 Z_DNA : 63.055 frequency distance

  17. Kappa distribution <- Kappa=0.01 Kappa=3.6 ->

  18. Kappa Distribution B-DNA : 0.371 Z_DNA : 0.197 frequency kappa

  19. Static average distribution B-DNA : 0.498 Z-DNA : 0.088 frequency E_stat

  20. 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

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