cations such Mg
2+ are crucial for RNA conformational stability and functionality
[37].
Except the well known compositional and structural differences, RNA is also
capable, conversely to DNA, to have long range interaction such as the
kissing-loop. The knowledge of these biophysical properties have to be considered
in the of RNA origami technique.
The term “RNA tectonics” [38] indicates the modularity of RNA structure that
can disassembled and then reorganized into new units called “tecto RNA”. These
new module are capable to assembly themselves into more complex nanoparticles.
The shape and dimension of new RNA objects can be designed in advance. The
tecto RNA is often the result of computational simulations. This procedure consent
to allocate in precise way the fragments, estimate and correct the distances among
the elements. It is possible to control the supramolecular assembly of tecto RNAs in
order to minimize the set of alternatively folded structures. The nucleic acid based
nanotechnology is a fast evolving research area, triggered by the synthetic biology
requirements [39], now utilized in several different advanced applicative sectors.
2.2 A Survey of Computational Tools for Nucleic Acid
Based Biosensor Development
The design of bio-receptor and its interaction with the transducer material is an ICT
complex task because it need the employ of bioinformatics, chemo-informatics and
nanoinformatics tools into a automated and reusable computational pipeline: the
workflow. Workflow management systems, initially developed for different
industrial applications, has been recently also applied to nanotechnology [40]. Good
workflows have to include advance Machine Learning tools to optimize the quality
of the biosensing module (bioreceptor and transducer system). Three workflow
management systems that could be considered for the design biosensing module:
(1) KEPLER that can work on biophysical and genomic data [41]; (2) GALAXY
that can operate on molecular biology, image and nanostructures [42]; (3) KNIME
that is a more flexible and general purpose system [43]. The design of a biosensor,
for environmental monitoring, can starts from the available information about a
specific chemical Specific data mining can also to be used to obtain the maximal
amount of chemical, biological and toxicological. Conformational characteristics
are the core theme for each possible application of nucleic acid-based biosensors.
There are different tools to design simple nucleic acid structure or supramolecular
complexes. The repository more helpful to design a bio-receptor are: (1) the
Nucleic Acid database (NDB) containing nucleic acid experimentally solved
structures [44, 45] and the collection of 3D structural motifs of RNA; (2) G4RNA
that contain information about these structural motifs in RNA [46]; (3) G4IPDB a
more general repository encompassing the solved structure of G-quadruplex [47];
(4) MODOMICS database includes information about modified ribonucleosides
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P. Arrigo and D. Baroni
2+ are crucial for RNA conformational stability and functionality
[37].
Except the well known compositional and structural differences, RNA is also
capable, conversely to DNA, to have long range interaction such as the
kissing-loop. The knowledge of these biophysical properties have to be considered
in the of RNA origami technique.
The term “RNA tectonics” [38] indicates the modularity of RNA structure that
can disassembled and then reorganized into new units called “tecto RNA”. These
new module are capable to assembly themselves into more complex nanoparticles.
The shape and dimension of new RNA objects can be designed in advance. The
tecto RNA is often the result of computational simulations. This procedure consent
to allocate in precise way the fragments, estimate and correct the distances among
the elements. It is possible to control the supramolecular assembly of tecto RNAs in
order to minimize the set of alternatively folded structures. The nucleic acid based
nanotechnology is a fast evolving research area, triggered by the synthetic biology
requirements [39], now utilized in several different advanced applicative sectors.
2.2 A Survey of Computational Tools for Nucleic Acid
Based Biosensor Development
The design of bio-receptor and its interaction with the transducer material is an ICT
complex task because it need the employ of bioinformatics, chemo-informatics and
nanoinformatics tools into a automated and reusable computational pipeline: the
workflow. Workflow management systems, initially developed for different
industrial applications, has been recently also applied to nanotechnology [40]. Good
workflows have to include advance Machine Learning tools to optimize the quality
of the biosensing module (bioreceptor and transducer system). Three workflow
management systems that could be considered for the design biosensing module:
(1) KEPLER that can work on biophysical and genomic data [41]; (2) GALAXY
that can operate on molecular biology, image and nanostructures [42]; (3) KNIME
that is a more flexible and general purpose system [43]. The design of a biosensor,
for environmental monitoring, can starts from the available information about a
specific chemical Specific data mining can also to be used to obtain the maximal
amount of chemical, biological and toxicological. Conformational characteristics
are the core theme for each possible application of nucleic acid-based biosensors.
There are different tools to design simple nucleic acid structure or supramolecular
complexes. The repository more helpful to design a bio-receptor are: (1) the
Nucleic Acid database (NDB) containing nucleic acid experimentally solved
structures [44, 45] and the collection of 3D structural motifs of RNA; (2) G4RNA
that contain information about these structural motifs in RNA [46]; (3) G4IPDB a
more general repository encompassing the solved structure of G-quadruplex [47];
(4) MODOMICS database includes information about modified ribonucleosides
222
P. Arrigo and D. Baroni