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

Chapter 6. Synthetic Receptors for Nucleosides and Nucleotides

Jinrok Oh,a Hyun-Woo Rhee,b and Jong-In Honga*

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: [email protected]

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

Scheme 6.1 General structures of nucleosides and nucleotides.


Scheme 6.2 Structures of redox nucleotides.


Scheme 6.3 Structures of nucleotide messengers in signal transductions.


Scheme 6.4 Structures of artificial nucleosides developed for the treatment of diseases.


Figure 6.1 cAMP recognition by a PKA regulatory subunit (PDB ID: 1RGS).


Figure 6.2 FMN recognition by Flavodoxin (PDB ID: 3FX2).


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)


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)


Scheme 6.5


Scheme 6.6


Scheme 6.7


Scheme 6.8


Scheme 6.9


Scheme 6.10


Scheme 6.11


Scheme 6.12


Scheme 6.13


Scheme 6.14


Scheme 6.15


Scheme 6.16


Scheme 6.17


Scheme 6.18


Scheme 6.19


Scheme 6.20


Scheme 6.21


Scheme 6.22


Scheme 6.23


Scheme 6.24


Scheme 6.25


Scheme 6.26


Scheme 6.27


Scheme 6.28


Scheme 6.29


Scheme 6.30


Scheme 6.31


Scheme 6.32


Scheme 6.33


Scheme 6.34


Scheme 6.35


Scheme 6.36


Scheme 6.37


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)


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)


Scheme 6.38


Scheme 6.39


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)


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)


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)


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)


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)


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)


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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