Expanding the Chemical Diversity of DNA

Chun Guo; Dehui Kong; Yi Lei; Ryan Hili

doi:10.1055/s-0036-1591959

Synlett, Table of Contents

Synlett 2018; 29(11): 1405-1414
DOI: 10.1055/s-0036-1591959

synpacts

Expanding the Chemical Diversity of DNA

Authors

Chun Guo

^aDepartment of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia, 30602, USA
Dehui Kong

^aDepartment of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia, 30602, USA
Yi Lei

^aDepartment of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia, 30602, USA
Ryan Hili *

^aDepartment of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia, 30602, USA

^bDepartment of Chemistry and Centre for Research on Biomolecular Interactions, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada Email: rhili@yorku.ca

Abstract

All articles of this category

Abstract

Nucleic acid polymers can be evolved to exhibit desired properties, including molecular recognition of a molecular target and catalysis of a specific reaction. These properties can be readily evolved despite the dearth of chemical diversity available to nucleic acid polymers, especially when compared to the rich chemical complexity of proteins. Expansion of nucleic acid chemical diversity has therefore been an important thrust for improving their properties for analytical and biomedical applications. Herein, we briefly describe the current state-of-the-art for the sequence-defined incorporation of modifications throughout an evolvable nucleic acid polymer. This includes contributions from our own lab, which have expanded the chemical diversity of nucleic acid polymers closer to the level observed in proteinogenic polymers.

1 Introduction

2 Polymerase-Catalyzed Synthesis of Modified Nucleic Acid Polymers

3 Ligase-Catalyzed Oligonucleotide Polymerization (LOOPER)

4 LOOPER with Small Modifications

5 LOOPER with Large Modifications

6 Evolution of Aptamers Derived from LOOPER Libraries

7 Outlook

Key words

modified nucleic acids - modified aptamers - sequence-defined polymers - ligase - in vitro selection - molecular evolution

Full Text

References

References
1 Chen K. Zhao BS. He C. Cell Chem. Biol. 2016; 23: 74
2 Batey RT. Rambo RP. Doudna JA. Angew. Chem. Int. Ed. 1999; 38: 2326
3 Serganov A. Patel DJ. Nat. Rev. Genet. 2007; 8: 776
4 Nissen P. Hansen J. Ban N. Moore PB. Steitz TA. Science 2000; 289: 920
5 Tuerk C. Gold L. Science 1990; 249: 505
6 Ellington AD. Szostak JW. Nature 1990; 346: 818
7 Liu J. Cao Z. Lu Y. Chem. Rev. 2009; 109: 1948
8 Silverman SK. Cell 2016; 41: 595
9 Dunn MR. Jimenez RM. Chaput JC. Nat. Rev. Chem. 2017; doi:
10 Kong D. Yeung W. Hili R. ACS Comb. Sci. 2016; 18: 355
11 Lipi F. Chen S. Chakravarthy M. Rakesh S. Veedu RN. RNA Biol. 2016; 13: 1232
12 Tolle F. Brändle GM. Matzner D. Mayer G. Angew. Chem. Int. Ed. 2015; 54: 10971
13 Welter M. Verga D. Marx A. Angew. Chem. Int. Ed. 2016; 55: 10131
14 Meek KN. Rangel AE. Heemstra JM. Methods 2016; 106: 29
15 Rohloff JC. Gelinas AD. Jarvis TC. Ochsner UA. Schneider DJ. Gold L. Janjic N. Mol. Ther.-Nucleic Acids 2014; 3: No. e201

16a Perrin DM. Garestier T. Helene C. J. Am. Chem. Soc. 2001; 123: 1556
16b Hollenstein M. Hipolito CJ. Lam CH. Perrin DM. Nucleic Acids Res. 2009; 37: 1638
16c Hollenstein M. Hipolito CJ. Lam CH. Perrin DM. ACS Comb. Sci. 2013; 15: 174
16d Thomas JM. Yoon JK. Perrin DM. J. Am. Chem. Soc. 2009; 131: 5648

17 Zhou C. Avins JL. Klauser PC. Brandsen BM. Lee Y. Silverman SK. J. Am. Chem. Soc. 2016; 138: 2106
18 Jager S. Rasched G. Kornreich-Leshem H. Engeser M. Thum O. Famulok M. J. Am. Chem. Soc. 2005; 127: 15071
19 Malyshev DA. Romesberg FE. Angew. Chem. Int. Ed. 2015; 54: 11930
20 Hili R. Niu J. Liu DR. J. Am. Chem. Soc. 2013; 135: 98
21 Guo C. Watkins CP. Hili R. J. Am. Chem. Soc. 2015; 137: 11191
22 Lei Y. Kong D. Hili R. ACS Comb. Sci. 2015; 17: 716
23 Kong D. Lei Y. Yeung W. Hili R. Angew. Chem. Int. Ed. 2016; 55: 13164
24 Guo C. Hili R. Bioconjugate Chem. 2017; 28: 314
25 Lei Y. Hili R. Org. Biomol. Chem. 2017; 15: 2349
26 Schmitt MW. Kennedy SR. Salk JJ. Fox EJ. Hiatt JB. Loeb L. Proc. Natl. Acad. Sci. USA 2012; 109: 14508
27 Eckert KA. Kunkel TA. PCR Methods Appl. 1991; 1: 17
28 Kong D. Yeung W. Hili R. J. Am. Chem. Soc. 2017; 139: 13977
29 Bock LC. Griffin LC. Latham JA. Vermaas EH. Toole JJ. Nature 1992; 355: 564
30 Tasset DM. Kubik MF. Steiner WJ. J. Mol. Biol. 1997; 272: 688
31 Woodson SA. Curr. Opin. Chem. Biol. 2005; 9: 104
32 Hottin A. Marx A. Acc. Chem. Res. 2016; 49: 418
33 Thirunavukarasu D. Chen T. Liu Z. Hongdilokkul N. Romesberg FE. J. Am. Chem. Soc. 2017; 139: 2892
34 Rydel TJ. Ravichandran KG. Tulinsky A. Bode W. Huber R. Roitsch C. Fenton II J. W. Science 1990; 249: 277