1. Correlation of DNA structural features with internal dynamics and conformational flexibility H. Peter Spielmann University of Kentucky Dept. of Molecular and Cellular Biochemistry

2. Molecular Structure From NMR Average inter-atomic distances measured for non-exchangeable hydrogens Refined solution structure of self-complementary DNA molecule containing G-T mismatches 5’-CCATGCGTGG-3’ 3’-GGTGCGTACC-5’

3. Dynamic Processes on the ps-ns Timescale Deoxyribose Re-puckering Phosphate B I - B II Exchange Internal Vibrational Modes

4. C2’-endoC3’-endo Also less well characterized motions Bases also move, but less than backbone Spontaneous base pair opening (“breathing”) Rocking about the glycosidic linkage (  ) What is DNA “Flexibility”

5. Internal Vibrational Modes Order Parameters (S 2 ) Methine 13 C Relaxation Modelfree Analysis

6. Methine Carbons in DNA

8. How to Combine Disparate Dynamic Data to Obtain Information on Specific Motional Modes in DNA?

9. Molecular Dynamics Simulation Newtonian model of a quantized system Atomic positions/velocities change in femtosecond steps, based on current velocities and inter-nuclear interactions, dependent on force field equations: Parameterized to reproduce experimental measurements of gross structural features

10. Time-Averaged Restraints Different than conventional restraints, in that deviations are allowed as long as the restraint is satisfied on average over a particular time frame (10-50 ps)

11. Effects of Smoothing = No smoothing = 5 ps interval smoothing

12. Computing Dynamics from MD Autocorrelation function: Lipari-Szabo modelfree formalism: Clore et al. extended model:

13. Effect of Smoothing on T8:C1’ C(t) t (ps) Data 2-parameter 4-parameter C(t) t (ps) Before After

14. Dynamics Correlations from NMR Correlations between S 2, phosphate population, deoxyribose ring population, helical parameters 3’ 5’ %B I vs. C1’ 5’ & %S 5’ R 2 = 0.79 Correlations not evident in MD trajectories

15. Dynamics Relate to Recognition FlexibilityDynamics NMR & MD Deformability Sequence (Damage?) Specific

16. NormalMismatch Biological Relevance MutS: Mismatch Recognition Deformation: -Bend -Compressed, Deepened Major Groove -Widened Minor Groove

17. CGGCATGCTG CGGCATGCTG GT-2 GT-5 CGGCACGCTG CGGCACGCTG

18. Normal vs. Mismatch

19. Major Groove Width (Å) Minor Groove Width (Å) = Normal = Mismatch Groove Widths & Flexibility Mismatched DNA has more flexibility in major groove width

20. 5’-CCATCGCTACC-3’ 3’-GGTAGCGATGG-5’

21. Conclusions Mechanical coupling exists in DNA Structure and dynamics are related Time-averaged restrained MD simulations are more accurate than are unrestrained MD simulations Smoothing improves accuracy of tarMD tarMD can reveal dynamic features of biological relevance

22. Acknowledgements Richard J. Isaacs William Rayens NSF Kentucky Center for Computational Sciences NCSA