Revealing Nucleic Acid Mutations Using Förster Resonance Energy Transfer-Based Probes

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.

DNA nanotechnology for nucleic acid analysis: multifunctional molecular DNA machine for RNA detection

“…1 a Common challenges of hybridization probes include insufficient sensitivity and selectivity. 1 Detection of specific RNA molecules is particularly challenging due to the stable secondary structures that inhibit or even prevent their interactions with hybridization probes.…”

“…1 a Common challenges of hybridization probes include insufficient sensitivity and selectivity. 1 Detection of specific RNA molecules is particularly challenging due to the stable secondary structures that inhibit or even prevent their interactions with hybridization probes. 2 For example, some molecular beacon probes, fluorophore- and quencher-labelled DNA stem-loop structures, 3 were previously shown to fail in detecting folded RNA and DNA molecules.…”

“…BiDZ can be considered as one of the most promising hybridization probes for homogeneous mix-and-read nucleic acid analysis, since it enables (i) high selectivity of point mutation analysis, 8 (ii) reduced cost, ‡ and (iii) LOD down to 8–20 pM after 60 min of incubation, 8 which is ~50 times lower than that of commercially available fluorescent probes. 1,3 b However, the LOD of BiDZ sensors is compromised when long and highly folded RNA is to be analysed. In this case, the access of the BiDZ probe to the targeted analyte fragment is limited resulting in ~10–25 fold decrease in LOD in comparison to an unstructured analyte.…”

“…8 a,d Moreover, signal amplification approaches are less sensitive to contaminants. 1 d Other advantages of BiDZ-based approaches include: (i) high selectivity towards SNP, which is not provided by amplification techniques directly, but requires additional probe-based assays; (ii) protein enzyme-free format, which potentially enables storage of the reagents at room temperature for a long time.…”

Mechanism of Cellular Uptake to Optimized AuNP Beacon for Tracing mRNA Changes in Living Cells

“…It is well‐acknowledged that the growth and metastasis of tumors are directly correlated with the expression of some important proteins within tumor cells, which are translated from relevant mRNAs . Since the emergence of live cell detection techniques, revolutionary changes in mRNA detection have taken place, and molecular beacon is one of the most promising tools in this field …”