The main advantage of this methodology is the possibility to develop biosensor
array capable to perform a multiple screening [12]. In this group could be also
include the xeno nucleic acids (XNA). There are several limitations in development
of biosensors which basically depend on the intrinsic characteristics of a biological
element, the production cost, robustness and reusability. The great challenge in
biosensor production is to obtain a system having the maximal sensitivity for a
specific ligand. It is also mandatory to underline the need to optimize the combination between bioreceptor and the material of transducing system.
Biomedicine is one of the fields in which biosensors are widely applied either for
diagnostic and therapy [13]. Defence (bioterrorism) and food security [14] are other
important operational fields of these systems. The use of biosensors in environmental monitoring has been stimulated by the need to design and implement
instrumentation having high efficiency, portability and a rapid response over the
time. The advancement of analytical integrated instrumentation offer the possibility
to develop high-throughput monitoring using platforms with interchangeable
bio-recognition elements robust, easy to use and relatively cheap.
2.1 Overview of Nucleic Acid Characteristics
Previous paragraph has briefly outlined some fundamental elements of biosensor
architecture: this section ids focused on the characteristics of nucleic acids valuable
for a bio-receptor design. A simple survey on Pubmed has found, at the date of this
chapter, 9931 papers. A similar search however using the query “RNA and
Biosensors” has found 2231 papers. A similar survey, adding the term “pollutant
(s)” has identified only 33 papers for RNA and 254 for DNA. In order to offer a
parameter for comparison the query “enzyme and biosensors” has found 19,090
entry and the query with the ad joint of the term pollutant(s) has retrieved 482
entries. This rough empirical survey underlines how the use of nucleic acids for
biosensors, if compared with protein based biosensors, looks to be in the initial
phase. It is necessary to distinguish DNA-, RNA- and XNA-based bio-receptor
because each class of nucleic acid has different biophysical properties that have to
be considered in the biosensor element design. XNAs are completely synthetic
nucleic acids initially developed for xenobiology [15] researches. These macromolecules can be formed by unnatural nucleobases and sugar backbone. The
chemical modifications are designed to increase the stability and their scaffolding
characteristics [16]. The thermodynamical difference, between DNA and RNA, is
the first information to take into account in a bioreceptor design phase. For long
time DNA has been considered more stable than RNA, however several studies [17]
have demonstrated a comparable stability between the two types of nucleic acids.
A drawback that must be considered in the design of RNA biosensors is its higher
sensitivity to enzymatic degradation by RNAses.
Contrarily to DNA, which is less affected by the ionic environment, the RNA
conformation is strongly dependent on the type and distribution of counter-ions
Computational Design of Nucleic Acid-Based Bioreceptor …
217
array capable to perform a multiple screening [12]. In this group could be also
include the xeno nucleic acids (XNA). There are several limitations in development
of biosensors which basically depend on the intrinsic characteristics of a biological
element, the production cost, robustness and reusability. The great challenge in
biosensor production is to obtain a system having the maximal sensitivity for a
specific ligand. It is also mandatory to underline the need to optimize the combination between bioreceptor and the material of transducing system.
Biomedicine is one of the fields in which biosensors are widely applied either for
diagnostic and therapy [13]. Defence (bioterrorism) and food security [14] are other
important operational fields of these systems. The use of biosensors in environmental monitoring has been stimulated by the need to design and implement
instrumentation having high efficiency, portability and a rapid response over the
time. The advancement of analytical integrated instrumentation offer the possibility
to develop high-throughput monitoring using platforms with interchangeable
bio-recognition elements robust, easy to use and relatively cheap.
2.1 Overview of Nucleic Acid Characteristics
Previous paragraph has briefly outlined some fundamental elements of biosensor
architecture: this section ids focused on the characteristics of nucleic acids valuable
for a bio-receptor design. A simple survey on Pubmed has found, at the date of this
chapter, 9931 papers. A similar search however using the query “RNA and
Biosensors” has found 2231 papers. A similar survey, adding the term “pollutant
(s)” has identified only 33 papers for RNA and 254 for DNA. In order to offer a
parameter for comparison the query “enzyme and biosensors” has found 19,090
entry and the query with the ad joint of the term pollutant(s) has retrieved 482
entries. This rough empirical survey underlines how the use of nucleic acids for
biosensors, if compared with protein based biosensors, looks to be in the initial
phase. It is necessary to distinguish DNA-, RNA- and XNA-based bio-receptor
because each class of nucleic acid has different biophysical properties that have to
be considered in the biosensor element design. XNAs are completely synthetic
nucleic acids initially developed for xenobiology [15] researches. These macromolecules can be formed by unnatural nucleobases and sugar backbone. The
chemical modifications are designed to increase the stability and their scaffolding
characteristics [16]. The thermodynamical difference, between DNA and RNA, is
the first information to take into account in a bioreceptor design phase. For long
time DNA has been considered more stable than RNA, however several studies [17]
have demonstrated a comparable stability between the two types of nucleic acids.
A drawback that must be considered in the design of RNA biosensors is its higher
sensitivity to enzymatic degradation by RNAses.
Contrarily to DNA, which is less affected by the ionic environment, the RNA
conformation is strongly dependent on the type and distribution of counter-ions
Computational Design of Nucleic Acid-Based Bioreceptor …
217