3.1 Development of Electrochemical Sensors for DNA Analysis
The electrochemical genosensors introduced in this chapter are classified into two groups, based on the sensing strategy: genosensors in which direct reduction and oxidation of DNA bases as a recognition event is used; and genosensors in which the sensing strategy is based on complementary base paring between the sensor's nucleic acid sequence and the analyte of interest. The DNA sensing procedures based on direct redox reaction of nucleic bases are fairly sensitive and selective, but their applicability is rather limited. One of the methods is based on direct electroactivity of nucleic bases, which takes into account the limitations of genosensors and improves their application, relies on of the same electrochemical mediators that facilitate electron transfer between the electro‐active base and the electrode surface. Today, particularly in medical diagnoses, an ideal biosensor is required not only to be miniaturized and cost effective, but also capable of simultaneous detection of multiple analytes.
3.2 Oligonucleotide Based Artificial Ribonucleases (OBANs)
Artificial ribonucleases can be visualized as molecular scissors cleaving ribonucleic acids, typically at the internucleoside phosphodiester linkages. Synthetic nucleic acids have been, and still are, crucial for the development of life sciences research. Modified oligonucleotides (ONs) and/or conjugates are not only used for research but are also used for diagnostics and have been developed as drugs for the treatment of patients with diseases of genetic origin. Use of an oligonucleotide based artificial nuclease (OBAN) could then lead to recognition and cleavage of RNA sequences responsible for genetic or viral diseases. Double‐stranded RNA is considerably less susceptible to cleavage than single‐stranded RNA. Komiyama is one of the true pioneers, with many contributions to the field of artificial RNA cutters. Peptide nucleic acids (PNA) is readily conjugated through peptide‐type chemistry, but has been used sparingly as a carrier for RNA cleaving agents.
3.3 Exploring Nucleic Acid Conformations by Employment of Porphyrin Non‐covalent and Covalent Probes and Chiroptical Analysis
The porphyrin–DNA binding modes depend on both the structural properties of the porphyrinoid derivatives and the DNA sequences and conformations. The experimental conditions, that is, the molar ratio of porphyrin to DNA and the ionic strength also influence the binding mode. This chapter explores the non‐covalent interactions of porphyrins with different conformations of DNA. It presents only one example of an interaction of porphyrins with a double helix with respect to the aggregation process on DNA. This aspect excites interested investigators due to the photochemical and photophysical properties of the aggregate chromophores. For extended, electronically interacting chromophore arrays, a remarkable enhancement of light scattering is observed within these absorption envelopes. These so called enhanced RLS signals are useful not only for identifying such assemblies, but for characterizing them as well. As porphyrin derivatives, porphyrinoids are also employed as probes for single stranded nucleic acids.
3.4 Chemical Reactions Controlled by Nucleic Acids and their Applications for Detection of Nucleic Acids in Live Cells
Nucleic acid controlled chemical reactions of various types are known. They include enantioselective transformations using DNA‐based catalysts, DNA‐induced formation of nanoparticles consisting, for example, of silver nanoclusters, and other hybridization‐triggered or templated reactions. This chapter focuses on the templated reactions, which are applicable for detection of nucleic acids in live cells. Nucleic acids, including deoxyribonucleic acids (DNAs) and ribonucleic acids (RNAs), are ubiquitous biomolecules playing a number of roles in Nature. Monitoring RNAs in live cells is of great value and can help to better understand numerous RNA‐dependent intra‐ and extra‐cellular biochemical processes. The chemical reactions reviewed here are found to be suitable for the detection of nucleic acids in live cells. They can all be used for the analysis of fairly abundant nucleic acids, such as 28S RNA and β‐actin‐mRNA.
3.5 The Biotechnological Applications of G‐Quartets
At present the origins of the elevated stability of G‐quartets remain unclear: when a guanine becomes involved in a quartet, the rearrangement of its electron density is a phenomenon referred to as resonance‐assisted hydrogen bonding (RAHB), G‐quartet stability is assumed to originate in an electronic redistribution ascribed to interplay between H‐bond formation and delocalization of the nucleobase p‐electrons (resonance). The external G‐quartet– small molecule interaction is a pivotal event in the aim of using quadruplexes as structural switches to control all aforementioned DNA–RNA transactions. The knowledge of the nucleic acid community combined with the techniques of chemistry, molecular biology, surface, and biophysical sciences have unambiguously yielded real biotechnological dividends, as vividly demonstrated by the versatility of the selected examples reported in this chapter. The emerging field of synthetic G‐quartets is providing not only preliminary but also invaluable solutions that help address these issues.