Download PDF
Synlett 2018; 29(11): 1405-1414
DOI: 10.1055/s-0036-1591959
synpacts
© Georg Thieme Verlag Stuttgart · New York

Expanding the Chemical Diversity of DNA

Chun Guo
a   Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia, 30602, USA
,
Dehui Kong
a   Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia, 30602, USA
,
Yi Lei
a   Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia, 30602, USA
,
Ryan Hili  *
a   Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia, 30602, USA
b   Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada   Email: rhili@yorku.ca
› Author AffiliationsFinancial support for this work was provided by the National Science Foundation (1506667), the National Institutes of Health (­R21CA207711), the University of Georgia, and York University.
Further Information

Publication History

Received: 04 January 2018

Accepted after revision: 21 February 2018

Publication Date:
20 March 2018 (online)

    Permissions and Reprints 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
 

  • References

  • 1 Chen K. Zhao BS. He C. Cell Chem. Biol. 2016; 23: 74
    PubMed
  • 2 Batey RT. Rambo RP. Doudna JA. Angew. Chem. Int. Ed. 1999; 38: 2326
    CrossrefPubMed
  • 3 Serganov A. Patel DJ. Nat. Rev. Genet. 2007; 8: 776
    CrossrefPubMed
  • 4 Nissen P. Hansen J. Ban N. Moore PB. Steitz TA. Science 2000; 289: 920
    CrossrefPubMed
  • 5 Tuerk C. Gold L. Science 1990; 249: 505
    CrossrefPubMed
  • 6 Ellington AD. Szostak JW. Nature 1990; 346: 818
    CrossrefPubMed
  • 7 Liu J. Cao Z. Lu Y. Chem. Rev. 2009; 109: 1948
    CrossrefPubMed
  • 8 Silverman SK. Cell 2016; 41: 595
  • 9 Dunn MR. Jimenez RM. Chaput JC. Nat. Rev. Chem. 2017; doi: DOI: 10.1038/s41570-017-0076.
    Crossref
  • 10 Kong D. Yeung W. Hili R. ACS Comb. Sci. 2016; 18: 355
    CrossrefPubMed
  • 11 Lipi F. Chen S. Chakravarthy M. Rakesh S. Veedu RN. RNA Biol. 2016; 13: 1232
    CrossrefPubMed
  • 12 Tolle F. Brändle GM. Matzner D. Mayer G. Angew. Chem. Int. Ed. 2015; 54: 10971
    CrossrefPubMed
  • 13 Welter M. Verga D. Marx A. Angew. Chem. Int. Ed. 2016; 55: 10131
    CrossrefPubMed
  • 14 Meek KN. Rangel AE. Heemstra JM. Methods 2016; 106: 29
    CrossrefPubMed
  • 15 Rohloff JC. Gelinas AD. Jarvis TC. Ochsner UA. Schneider DJ. Gold L. Janjic N. Mol. Ther.-Nucleic Acids 2014; 3: No. e201
    PubMed
    • 16a Perrin DM. Garestier T. Helene C. J. Am. Chem. Soc. 2001; 123: 1556
      CrossrefPubMed
    • 16b Hollenstein M. Hipolito CJ. Lam CH. Perrin DM. Nucleic Acids Res. 2009; 37: 1638
      CrossrefPubMed
    • 16c Hollenstein M. Hipolito CJ. Lam CH. Perrin DM. ACS Comb. Sci. 2013; 15: 174
      CrossrefPubMed
    • 16d Thomas JM. Yoon JK. Perrin DM. J. Am. Chem. Soc. 2009; 131: 5648
      CrossrefPubMed
  • 17 Zhou C. Avins JL. Klauser PC. Brandsen BM. Lee Y. Silverman SK. J. Am. Chem. Soc. 2016; 138: 2106
    CrossrefPubMed
  • 18 Jager S. Rasched G. Kornreich-Leshem H. Engeser M. Thum O. Famulok M. J. Am. Chem. Soc. 2005; 127: 15071
    CrossrefPubMed
  • 19 Malyshev DA. Romesberg FE. Angew. Chem. Int. Ed. 2015; 54: 11930
    CrossrefPubMed
  • 20 Hili R. Niu J. Liu DR. J. Am. Chem. Soc. 2013; 135: 98
    CrossrefPubMed
  • 21 Guo C. Watkins CP. Hili R. J. Am. Chem. Soc. 2015; 137: 11191
    CrossrefPubMed
  • 22 Lei Y. Kong D. Hili R. ACS Comb. Sci. 2015; 17: 716
    CrossrefPubMed
  • 23 Kong D. Lei Y. Yeung W. Hili R. Angew. Chem. Int. Ed. 2016; 55: 13164
    CrossrefPubMed
  • 24 Guo C. Hili R. Bioconjugate Chem. 2017; 28: 314
    CrossrefPubMed
  • 25 Lei Y. Hili R. Org. Biomol. Chem. 2017; 15: 2349
    CrossrefPubMed
  • 26 Schmitt MW. Kennedy SR. Salk JJ. Fox EJ. Hiatt JB. Loeb L. Proc. Natl. Acad. Sci. USA 2012; 109: 14508
    CrossrefPubMed
  • 27 Eckert KA. Kunkel TA. PCR Methods Appl. 1991; 1: 17
    CrossrefPubMed
  • 28 Kong D. Yeung W. Hili R. J. Am. Chem. Soc. 2017; 139: 13977
    CrossrefPubMed
  • 29 Bock LC. Griffin LC. Latham JA. Vermaas EH. Toole JJ. Nature 1992; 355: 564
    CrossrefPubMed
  • 30 Tasset DM. Kubik MF. Steiner WJ. J. Mol. Biol. 1997; 272: 688
    CrossrefPubMed
  • 31 Woodson SA. Curr. Opin. Chem. Biol. 2005; 9: 104
    CrossrefPubMed
  • 32 Hottin A. Marx A. Acc. Chem. Res. 2016; 49: 418
    CrossrefPubMed
  • 33 Thirunavukarasu D. Chen T. Liu Z. Hongdilokkul N. Romesberg FE. J. Am. Chem. Soc. 2017; 139: 2892
    CrossrefPubMed
  • 34 Rydel TJ. Ravichandran KG. Tulinsky A. Bode W. Huber R. Roitsch C. Fenton II J. W. Science 1990; 249: 277
    CrossrefPubMed