Modified Nucleoside Triphosphates for In-vitro Selection Techniques

Abstract

The development of SELEX (Selective Enhancement of Ligands by Exponential Enrichment) provides a powerful tool for the search of functional oligonucleotides with the ability to bind ligands with high affinity and selectivity (aptamers) and for the discovery of nucleic acid sequences with diverse enzymatic activities (ribozymes and DNAzymes). This technique has been extensively applied to the selection of natural DNA or RNA molecules but, in order to improve chemical and structural diversity as well as for particular applications where further chemical or biological stability is necessary, the extension of this strategy to modified oligonucleotides is desirable. Taking into account these needs, this review intends to collect the research carried out during the past years, focusing mainly on the use of modified nucleotides in SELEX and the development of mutant enzymes for broadening nucleoside triphosphates acceptance. In addition, comments regarding the synthesis of modified nucleoside triphosphate will be briefly discussed.

Keywords: DNAzymes; SELEX; aptamers; functional oligonucleotides; modified nucleotides; ribozymes.

Figure 1

Schematic representation of the alternative routes to obtain modified functional oligonucleotides.

Figure 2

Modified nucleoside triphosphates used in SELEX experiments. References: 1: (Jhaveri et al., ; Somasunderam et al., ; Higashimoto et al., 2013); 2: (Lato et al., 2002); 3: (Lin et al., ; Green et al., ; Jellinek et al., 1995); 4: (Svobodova et al., ; Dupont et al., 2010); 5: (Burmeister et al., 2005); 6: (Pagratis et al., 1997); 7: (Friedman et al., 2015); 8: (Latham et al., 1994); 9: (Li et al., 2008); 10: (Vaught et al., ; Ochsner et al., 2013, 2014); 11: (Tarasow et al., 1997); 12: (Battersby et al., 1999); 13: (Vaish et al., 2003); 14: (Masud et al., ; Shoji et al., 2007); 15: (Santoro et al., ; Sidorov et al., 2004); 16: (Wiegand et al., 1997); 17: (Hollenstein et al., 2009); 18: (Imaizumi et al., 2013); 19: see 9; 20: (Hollenstein et al., 2009); 21: (Sidorov et al., 2004); 22: (Hollenstein et al., 2009); 23: (Liu et al., 2010); 24: (Kasahara et al., 2013); 25: (Minikawa et al., 2008).

Figure 3

Modified nucleoside triphosphates accepted by modified polymerases but not yet used in SELEX protocols.