Abstract
Nucleic acid mutations are of tremendous importance in modern clinical work, biotechnology and in fundamental studies of nucleic acids. Therefore, rapid, cost-effective and reliable detection of mutations is an object of extensive research. Today, Förster resonance energy transfer (FRET) probes are among the most often used tools for the detection of nucleic acids and in particular, for the detection of mutations. However, multiple parameters must be taken into account in order to create efficient FRET probes that are sensitive to nucleic acid mutations. In this review; we focus on the design principles for such probes and available computational methods that allow for their rational design. Applications of advanced, rationally designed FRET probes range from new insights into cellular heterogeneity to gaining new knowledge of nucleic acid structures directly in living cells.
Highlights
Nucleic acids are essential for all known forms of life
Attachment of Förster resonance energy transfer (FRET) pairs to deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) probes is an attractive strategy for measuring hybridization of two strands in vitro, in cell lines and in vivo
Larsen et al increased the brightness of nucleobase analogues stranded linear, hairpin-shaped or double-stranded probes are most often applied
Summary
Nucleic acids are essential for all known forms of life. In the form of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), they function in encoding, transmitting and expressing genetic information [1]. Nucleic acid modifications are finding growing applications in the preparation of target-specific probes [4] This theoretical framework is confirmed by extensive experimental data in vitro, at concentrations above 50 nM and for unmodified and modified sequences [5]. Far, diverse parameters modified oligonucleotideshave havebeen beenaddressed addressedseparately This includes binding affinity assessments by thermodynamic models [6], SNP detection. Among other optical effects applied in nucleic acid studies, Förster resonance energy transfer (FRET). Is a quantum phenomenon applied in nucleic acid studies, Förster resonance energy transfer (FRET) is a quantum phenomenon occurring between two dye molecules, a donor and anan acceptor, which are inin close proximity An important and novel aspect of this review is the description of recent advances of molecular modeling and quantum chemical approaches for design of effective FRET probes. Förster Resonance Energy Transfer-Based Probes in Nucleic Acid Research and Molecular Diagnostics
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