1. Chapter 6. Synthetic Receptors for Nucleosides and Nucleotides Jinrok Oh, a Hyun-Woo Rhee, b and Jong-In Hong a * a Department of Chemistry, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul 151-747, Korea b Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan 689-798, Korea *Email: jihong@snu.ac.kr Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

2. Scheme 6.1 General structures of nucleosides and nucleotides. Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

3. Scheme 6.2 Structures of redox nucleotides. Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

4. Scheme 6.3 Structures of nucleotide messengers in signal transductions. Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

5. Scheme 6.4 Structures of artificial nucleosides developed for the treatment of diseases. Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

6. Figure 6.1 cAMP recognition by a PKA regulatory subunit (PDB ID: 1RGS). Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

7. Figure 6.2 FMN recognition by Flavodoxin (PDB ID: 3FX2). Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

8. Figure 6.3 Structural perturbations near the ATP binding site of GlnK1 before (A) and after (B) ATP binding. (Adapted with permission from EMBO J., 2007, 26, 589, © European Molecular Biology Organization 2007) Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

9. Figure 6.4 Cyclic-di-GMP recognition by type I c-di-GMP riboswitch in two different aspects. (Reprinted with permission from Nat. Struct. Mol. Biol., 2009, 16, 1212, © Macmillan Publishers Ltd 2014) Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

10. Scheme 6.5 Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

11. Scheme 6.6 Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

12. Scheme 6.7 Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

13. Scheme 6.8 Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

14. Scheme 6.9 Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

15. Scheme 6.10 Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

16. Scheme 6.11 Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

17. Scheme 6.12 Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

18. Scheme 6.13 Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

19. Scheme 6.14 Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

20. Scheme 6.15 Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

21. Scheme 6.16 Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

22. Scheme 6.17 Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

23. Scheme 6.18 Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

24. Scheme 6.19 Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

25. Scheme 6.20 Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

26. Scheme 6.21 Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

27. Scheme 6.22 Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

28. Scheme 6.23 Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

29. Scheme 6.24 Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

30. Scheme 6.25 Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

31. Scheme 6.26 Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

32. Scheme 6.27 Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

33. Scheme 6.28 Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

34. Scheme 6.29 Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

35. Scheme 6.30 Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

36. Scheme 6.31 Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

37. Scheme 6.32 Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

38. Scheme 6.33 Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

39. Scheme 6.34 Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

40. Scheme 6.35 Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

41. Scheme 6.36 Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

42. Scheme 6.37 Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

43. Figure 6.5 Structure of 6.37 and its fluorescent behavior upon addition of various analytes. (Adapted with permission from J. Am. Chem. Soc., 2006, 128, 10380, © American Chemical Society 2006) Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

44. Figure 6.6 Structure of 6.38 and heat map obtained from library, especially mercury(II)- complexes. (Adapted with permission from ACS Comb. Sci., 2013, 15, 483, © American Chemical Society 2013 ) Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

45. Scheme 6.38 Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

46. Scheme 6.39 Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

47. Figure 6.7 Schematic representation of fluorescent cAMP sensing with chimeric PKA domains. (Adapted with permission from Integr. Biol., 2010, 2, 77, © Royal Society of Chemistry 2010) Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

48. Figure 6.8 Ribbon representation of GlnK protein either in the absence (gray and blue) or in the presence (gray, green, yellow) of ATP-Mg(II). Blue = flexible T loop, yellow = cpFP inserted region. (Reprinted with permission from Nat. Methods, 2009, 6, 161, © Macmillan Publishers Ltd 2014) Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

49. Figure 6.9 Structure of fluorescent ATP sensing aptamer. MGA and ATP module represent malachite green binding site and ATP binding site, respectively. (Adapted with permission from J. Am. Chem. Soc., 2004, 126, 9266, © American Chemical Society 2004) Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

50. Figure 6.10 Schematic representation for the fluorescent ATP sensing with a molecular beacon strategy. F and Q represent fluorophore and quencher, respectively. (Adapted with permission from J. Am. Chem. Soc., 2008, 130, 11268, © American Chemical Society 2008) Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

51. Figure 6.11 Schematic representation for the fluorescent sensing of either ATP or GTP with corresponding ribonucleopeptides (RNP) and their utilization in in vitro enzyme assay. (Adapted with permission from J. Am. Chem. Soc., 2013, 95, 3465, © American Chemical Society 2013) Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015

52. Figure 6.12 Schematic representation for the fluorescent GTP sensing with GTP-specific deoxyribozyme Dk2. (Adapted with permission from J. Am. Chem. Soc., 2013, 95, 7181, © American Chemical Society 2013) Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015