1. Cristiano De Michele cristiano.demichele@roma1.infn.it Hierarchical propagation of chirality through reversible polymerization: the cholesteric phase of DNA oligomers Tommaso Bellini Giuliano Zanchetta Elisa Frezza Alberta Ferrarini

2. OUTLINE MOTIVATION OF THIS WORK MODELS MOLECULAR THEORY PARAMETERIZATION COMPARISON WITH EXPERIMENTS CONCLUSIONS

3. SHORT DNA DUPLEXES EXPERIMENTAL SYSTEM WATER

4. Building Block (monomer) Short DNA Duplex (nanoDNA) 6 to 20 bp in length SHORT DNA DUPLEXES Sugar-phosphate backbone Base stacking Base pairing 12 bp Nb=Nb=

5. nanoDNA SELF-ASSEMBLY semi-flexible reversible polymers

6. nanoDNA SELF-ASSEMBLY ISOTROPIC CHIRAL NEMATIC semi-flexible reversible polymers

7. CHOLESTERIC nanoDNA CHOLESTERIC nanoDNA PERIODIC ROTATION OF NEMATIC DIRECTOR PERIOD = CHOLESTERIC PITCH (p) NEMATICCHOLESTERIC

8. AN ITALIAN THREE-COURSE MEAL AN ITALIAN THREE-COURSE MEAL ISOTROPIC NEMATIC CHOLESTERIC long holed fusilli of Gragnano fusilli helical axis

9. \ p NEW PITCH MEASUREMENT FOR DICKERSON DODECAMER (CGCGAATTCGCG)

10. MODELS EXPERIMENTS THEORY SIMULATIONS comparison to optimize input parameteres STRATEGY: MULTISCALE BOTTOM-UP APPROACH Input parameters Comparison to check theoretical predictions NO THEORETICAL OR COMPUTATIONAL APPROACH WHICH ACCOUNTS FOR BOTH SELF-ASSEMBLY AND HELICAL ORDERING

11. OUTLINE MOTIVATION OF THIS WORK MODELS MOLECULAR THEORY PARAMETERIZATION COMPARISON WITH EXPERIMENTS CONCLUSIONS

12. Sugar- phosphate backbone Base stacking Base pairing 12 bp OXFORD MODEL CDM, L. Rovigatti, T. Bellini and F. Sciortino, Soft Matter 8, 8388 (2012) rigid body (nucleotide) Nb=Nb= realistic and parameter free

13. HARD CYLINDERS MODEL Sugar- phosphate backbone Base stacking Base pairing 12 bp K. T. Nguyen, F. Sciortino and CDM, Langmuir 30, 4814 (2014) Nb=Nb= simplistic model to test theory

14. BENT CYLINDER MODEL K. T. Nguyen, A. Battisti, D. Ancora, F. Sciortino and CDM, Soft Matter 11, 2934 (2015) N b = 12 θbθb accounts for structural bending of short duplexes

15. STERIC MODEL OF DICKERSON DODECAMER nucleobase sugar phosphate E. Frezza, F. Tombolato and A. Ferrarini, Soft Matter 7, 9291 (2011) WE IGNORE ELECTROSTATICS RIGID STRUCTURE HARD CORE INTERACTIONS

16. OUTLINE MOTIVATION OF THIS WORK MODELS MOLECULAR THEORY PARAMETERIZATION COMPARISON WITH EXPERIMENTS CONCLUSIONS

17. FREE ENERGY In our approach: CDM, T. Bellini and F. Sciortino, Macromolecules 45, 1090-1106 (2012) Onsager-like theory

18. FREE ENERGY In our approach: CDM, G. Zanchetta, T. Bellini, E. Frezza and A. Ferrarini, submitted (2015)

19. OUTLINE MOTIVATION OF THIS WORK MODELS MOLECULAR THEORY PARAMETERIZATION COMPARISON WITH EXPERIMENTS CONCLUSIONS

20. ESTIMATE OF STACKING FREE ENERGY G ST AND l 0 OXFORD MODEL STACKING FREE ENERGY G ST HARD CYLINDER MODEL l0l0 BENT CYLINDER MODEL PERSISTENCE LENGTH l p STERIC MODEL

21. OUTLINE MOTIVATION OF THIS WORK MODELS MOLECULAR THEORY PARAMETERIZATION COMPARISON WITH EXPERIMENTS CONCLUSIONS

22. DICKERSON DODECAMER PHASE DIAGRAM I + N * N*N* I N*N*

23. THEORETICAL AND EXPERIMENTAL PITCH \ p 20 µm 750 mg/ml, 289 K 750 mg/ml, 301 K 20 µm no fitting/adjustable parameters

24. OUTLINE MOTIVATION OF THIS WORK MODELS MOLECULAR THEORY PARAMETERIZATION COMPARISON WITH EXPERIMENTS CONCLUSIONS

25. We developed a parameter free theoretical approach for self-assembly-driven cholesteric liquid crystals Our molecular theory is rather general and it accounts for helical ordering in self-assembly-driven cholesteric phases Hallmark of self-assembly: pitch dependence on ρ and T, which is in good agreement with experiments

26. THANK YOU FOR YOUR ATTENTION

28. CHOLESTERIC CONTRIBUTIONS TO FREE ENERGY CHOLESTERIC CONTRIBUTIONS TO FREE ENERGY twist elastic constantchiral strength CDM, G. Zanchetta, T. Bellini, E. Frezza and A. Ferrarini, submitted (2015)

29. CHOLESTERIC CONTRIBUTIONS TO FREE ENERGY CHOLESTERIC CONTRIBUTIONS TO FREE ENERGY twist elastic constant chiral strength cholesteric (N * ) pitch CDM, G. Zanchetta, T. Bellini, E. Frezza and A. Ferrarini, submitted (2015)

30. SOME INSIGHT FROM THEORETICAL RESULTS

31. isoM

32. 1 2 3 4 5 6 7 1 2 3 4 5 6 8 7 8 SELF-ASSEMBLED CHAINS OF FUSILLI UNBONDED FUSILLI M=1 M=4 THEORETICAL RESULTS FOR STIFF CHAINS

33. 1 2 3 4 5 6 7 1 2 3 4 5 6 8 7 8 SELF-ASSEMBLED CHAINS OF FUSILLI UNBONDED FUSILLI M=1 M=4 #contacts = 4 #contacts = 1 THEORETICAL RESULTS FOR STIFF CHAINS

34. 1 2 3 4 5 6 7 1 2 3 4 5 6 8 7 8 SELF-ASSEMBLED CHAINS OF FUSILLI UNBONDED FUSILLI M=1 M=4 #contacts = 4 #contacts = 1 THEORETICAL RESULTS FOR STIFF CHAINS

35. CHIRAL AND ELASTIC GENERALIZED EXCLUDED VOLUMES CHIRAL AND ELASTIC GENERALIZED EXCLUDED VOLUMES α is the parameter associated to Onsager distribution

36. CHOLESTERIC CONTRIBUTIONS TO FREE ENERGY CHOLESTERIC CONTRIBUTIONS TO FREE ENERGY CDM, G. Zanchetta, T. Bellini, E. Frezza and A. Ferrarini, submitted (2015) Parsons-Lee factorchain length distribution generalized excluded volumes

37. CHOLESTERIC CONTRIBUTIONS TO FREE ENERGY CHOLESTERIC CONTRIBUTIONS TO FREE ENERGY CDM, G. Zanchetta, T. Bellini, E. Frezza and A. Ferrarini, submitted (2015) Parsons-Lee factorchain length distribution generalized excluded volumes

38. HARD CYLINDERS MODEL

39. ESTIMATE OF BENDING ANGLE θbθb BENDING ANGLE

40. EFFECTIVE PERSISTENCE LENGTH

41. G ST ESTIMATE: RB MODEL NO FITTING PARAMETERS

42. ESTIMATE OF l 0 ESTIMATE OF l 0 no fitting parameters