182
M. Irfan et al.
step is required for amplification. In contrast, for ‘RNA SELEX’, several steps are
involved, including in vitro transcription followed by RT-PCR [21, 22].
DNA and RNA aptamers are analogous in terms of functions, but possess different
physiochemical properties. The presence of a deoxyribose sugar in the DNA makes
DNA aptamers chemically stable and naturally resistant to serum nucleases (e.g.
RNAse A); in contrast, RNA aptamers are prone to degradation owing to their scissile 2
-hydroxyl group (2
-OH) in the ribose. To overcome the intrinsic chemical
instability of RNA, several sugar modifications are added to RNA aptamers. Specifically, 2
ribose sugar modifications, such as 2
-fluoro (2
-F) or 2
-amino (2
-NH 2 ) on
pyrimidine residues of RNA or 2
-O-methoxy motifs, and/or changes to the phosphodiester backbone with boranophosphate or phosphorothioate are the regularly used
modifications to furnish nuclease stability in RNA aptamers. Although the hydroxyl
group in the ribose sugar of RNA confers instability, it plays an important role in
RNA folding. The 2
-OH groups on the ribose sugar engage in intra-strand hydrogen
bond interactions and provide the RNA with more structural diversity. The 2
-OH
group and non-Watson–Crick base pairing in RNA enable RNA aptamers to fold
into more complex 3D structures compared with single-stranded DNA (ssDNA)
aptamers. Despite physiochemical differences, DNA and RNA aptamers exhibit
similar affinities and specificities for cognate targets [23, 24].
7.1.3 Therapeutic Aptamers
In the modern era of science, targeted therapy has become an essential part of cancer
treatment. Aptamer-based therapeutic approaches in cancer include hindering the
interaction between receptor and ligand and protein–protein, protein–ligand interactions. For cancer treatment, a number of aptamers have been isolated against the
cancer cell surface proteins [25, 26]. AS141 aptamer is a guanine-rich oligonucleotide which binds with nucleolin protein specifically and was generated without
commonly used SELEX [27, 28]. Nucleolin is a cancer biomarker and is highly
expressed in different kinds of cancer cells [29]. Due to the rigid structure provided
by G-quartets, this aptamer has higher stability in contrast with other non-modified
aptamers which are generally degraded in a few minutes. A number of other aptamers
showing significant anticancer effects have been reported in a number of murine
models. Angiopoietin-2 is involved in modulating angiogenesis and identified as
one of the potential cancer drug targets. Aptamer has also been selected against
angiopoietin-2 [30, 31]. Similarly, a number of aptamers are being used for their
therapeutic properties and many of them in clinical trials (Table 7.1).
M. Irfan et al.
step is required for amplification. In contrast, for ‘RNA SELEX’, several steps are
involved, including in vitro transcription followed by RT-PCR [21, 22].
DNA and RNA aptamers are analogous in terms of functions, but possess different
physiochemical properties. The presence of a deoxyribose sugar in the DNA makes
DNA aptamers chemically stable and naturally resistant to serum nucleases (e.g.
RNAse A); in contrast, RNA aptamers are prone to degradation owing to their scissile 2
-hydroxyl group (2
-OH) in the ribose. To overcome the intrinsic chemical
instability of RNA, several sugar modifications are added to RNA aptamers. Specifically, 2
ribose sugar modifications, such as 2
-fluoro (2
-F) or 2
-amino (2
-NH 2 ) on
pyrimidine residues of RNA or 2
-O-methoxy motifs, and/or changes to the phosphodiester backbone with boranophosphate or phosphorothioate are the regularly used
modifications to furnish nuclease stability in RNA aptamers. Although the hydroxyl
group in the ribose sugar of RNA confers instability, it plays an important role in
RNA folding. The 2
-OH groups on the ribose sugar engage in intra-strand hydrogen
bond interactions and provide the RNA with more structural diversity. The 2
-OH
group and non-Watson–Crick base pairing in RNA enable RNA aptamers to fold
into more complex 3D structures compared with single-stranded DNA (ssDNA)
aptamers. Despite physiochemical differences, DNA and RNA aptamers exhibit
similar affinities and specificities for cognate targets [23, 24].
7.1.3 Therapeutic Aptamers
In the modern era of science, targeted therapy has become an essential part of cancer
treatment. Aptamer-based therapeutic approaches in cancer include hindering the
interaction between receptor and ligand and protein–protein, protein–ligand interactions. For cancer treatment, a number of aptamers have been isolated against the
cancer cell surface proteins [25, 26]. AS141 aptamer is a guanine-rich oligonucleotide which binds with nucleolin protein specifically and was generated without
commonly used SELEX [27, 28]. Nucleolin is a cancer biomarker and is highly
expressed in different kinds of cancer cells [29]. Due to the rigid structure provided
by G-quartets, this aptamer has higher stability in contrast with other non-modified
aptamers which are generally degraded in a few minutes. A number of other aptamers
showing significant anticancer effects have been reported in a number of murine
models. Angiopoietin-2 is involved in modulating angiogenesis and identified as
one of the potential cancer drug targets. Aptamer has also been selected against
angiopoietin-2 [30, 31]. Similarly, a number of aptamers are being used for their
therapeutic properties and many of them in clinical trials (Table 7.1).