Cyanine Dyes for RNA Labeling

Cyanine is a class of organic dyes with unique optical properties, which are widely used in biomedicine and biotechnology. Its fundamental structure is a polyene chain made up of two aromatic rings joined by a conjugated double bond chain. Particularly popular for use in RNA labeling are cyanine dyes. Researchers can track and quantify RNA molecules quantitatively by using cyanine dyes to link them to RNA molecules by chemical coupling or covalent bonding technologies. The study of RNA distribution, dynamic changes, and interactions has benefited immensely from this technique.

Ribonucleic Acid

Ribonucleic acid (RNA) is a biological macromolecule composed of nucleotides, which plays a vital role in the transmission and expression of genetic information. RNA therapy is a newly developed therapeutic approach that targets RNA molecules to treat a range of illnesses, including viral infections, cancer, and genetic disorders. Antisense oligonucleotide (ASO) therapy, small interfering RNA (siRNA) therapy, messenger RNA (mRNA) therapy, and ribozyme therapy are some of the key tactics that are included in it. Cyanine dyes are a class of fluorescent dyes widely used for RNA labeling. Fluorescent RNA labeling can be achieved in RNA labeling by conjugating cyanine dyes to nucleotides or nucleic acid probes and linking them to RNA molecules through a chemical process. This labeling technique offers a potent tool for researching the composition, dynamics, and interactions of RNA by precisely tracking and locating the distribution and changes in RNA molecules. For instance, fluorescence microscopy can be used to study the location and transit process of RNA in cells, providing insight into the biological functions of cells.

Ribonucleic Acid Types

RNA molecules can be divided into several types according to their functions, such as messenger RNA (mRNA), transfer RNA (tRNA) and ribosomal RNA (rRNA). RNA has a wide range of applications in biology. It plays a key role in gene expression, converting DNA sequences into information that can be used for protein synthesis through transcription. In addition, RNA technology is used in vaccine development, gene therapy and disease diagnosis, such as the prevention of new coronavirus by mRNA vaccines. RNA interference technology (RNAi) is also used to study gene function and treat gene-related diseases.

• Messenger RNA

mRNA is a type of RNA transcribed from a DNA template that carries genetic information and guides protein synthesis. In vivo, mRNA transports genetically encoded information from the cell nucleus to the ribosomes in the cytoplasm, thereby guiding protein synthesis. In vitro, the application of mRNA includes the prevention of disease through mRNA vaccines, such as the current COVID-19 vaccine, which uses synthetic mRNA to guide human cells to produce antigenic proteins and induce immune responses.

• Transfer RNA

tRNA plays an important role in the protein synthesis process, responsible for transporting amino acids to the ribosome and accurately matching the codons on the mRNA. In vivo, tRNA pairs with the codons of mRNA through anticodons to determine the order of each amino acid in the peptide chain. In vitro, tRNA can be used in gene expression and translation studies, and is also commonly used in protein synthesis studies in the laboratory.

• Ribosomal RNA

rRNA is one of the main components of ribosomes and is involved in the structural formation and functional realization of ribosomes. In vivo, rRNA and proteins together form ribosomes, which are the "factories" for protein synthesis. Ribosomes catalyze the formation of peptide bonds by binding to mRNA and tRNA. In vitro, rRNA is used to study the structure and function of ribosomes and explore their specific mechanisms in protein synthesis.

• Small RNA

These small RNA molecules (such as miRNA and siRNA) play an important role in gene regulation. miRNA can regulate gene expression by binding to mRNA to inhibit its translation or promote its degradation. In vivo, miRNA plays a key role in processes such as cell differentiation, proliferation and apoptosis. In vitro, miRNA and siRNA are widely used in gene silencing studies to inhibit the expression of specific genes by specifically binding to and degrading target mRNA to study their biological functions.

Cyanine Dyes

Cyanine (Cy), also known as cyanine dyes, or anthocyanin series fluorescent dyes, is a class of synthetic fluorescent dyes with the chemical structure characteristics of a polymethylenyl bridge chain. The two ends of the methylenyl bridge chain (1-7 methylenyl groups) of Cy dyes are often connected to two nitrogen atoms, one of which is positively charged, so that Cy dyes form interionic compounds with a delocalized positive charge effect. Because of this structural feature, the extinction coefficient of Cy dyes is very high. The length of the bridge chain and the chromophores at both ends directly control the absorption and emission peaks of the dyes, allowing the Cy series dyes to cover almost all commonly used fluorescence bands from ultraviolet to far infrared. The length of the bridge chain and the chromophores at both ends directly control the absorption and emission peaks of the dyes, allowing the Cy series dyes to cover almost all commonly used fluorescence bands from ultraviolet to far infrared. The Cy series of cyanine dyes are often divided into fat-soluble Cy dyes and water-soluble Cy dyes.

• Lipid-Soluble Cy Dyes

Lipid-soluble Cy dyes include Cy3, Cy3.5, Cy5, Cy5.5, Cy7 and Cy7.5. The chromophores of Cy3, Cy5 and Cy7 are indolenine, while those of Cy3.5, Cy5.5 and Cy7.5 are benzoindole. Benzoindole has only one more benzene ring than indolenine. This extra benzene ring red-shifts the absorption and emission peaks of the entire dye, allowing the Cy dye series to cover a wide range of fluorescence spectra. The structure of Cy dyes is almost symmetrical. In order to make the dye labelable, a 6-carbon chain carboxyl group is extended from one of the chromophores to activate the label. Although they carry a positive charge, the water solubility of lipophilic Cy dyes is relatively low. When labeling biomolecules (usually in a buffer solution), it is often necessary to add an organic solvent (usually 5-20% DMF or DMSO) to help dissolve. Conventionally, the dye is first dissolved in an organic solvent, then added to the aqueous solution of the biomolecule in proportion for reaction, and the precipitated dye is removed by centrifugation after the reaction is completed. Of course, lipid-soluble Cy dyes can also directly react with organic small molecules in organic solvents to label small molecules or polymer materials.

• Water-Soluble Cy Dyes

Water-soluble Cy dyes (sulfo-Cyanine) are obtained by adding sulfonic acid groups to the chromophore of lipid-soluble Cy dyes, which greatly increases the water solubility of the dyes and slightly improves the optical stability and quantum yield of the dyes. Therefore, water-soluble dyes are more resistant to light and emit slightly stronger fluorescence. Due to the sulfonate, this type of dye has a very high water solubility and does not require any organic solvent to assist in the labeling reaction. In addition, the labeled dye molecules will not aggregate due to their good water solubility, nor will they affect the stability of the labeled macromolecules. This is very important, especially when multiple dye molecules need to be labeled on each target biomacromolecule, or when the target biomacromolecule has low solubility and poor stability.

Cyanine for RNA Labeled

Cyanine dyes have high brightness, high sensitivity, and good photostability, which makes them ideal for labeling RNA. When labeling RNA, cyanine dyes can be attached to RNA molecules through covalent or non-covalent bonds. Common methods include using fluorescence in situ hybridization (FISH) technology or incorporation of chemically modified nucleoside triphosphates (NTPs) during RNA synthesis. In terms of spectral properties, cyanine dyes have strong fluorescence emission in different wavelength ranges. For example, Cyanine 3 and Cyanine 5 emit orange-red and infrared light, respectively. These two dyes are often used in multiple labeling experiments, which can simultaneously label different RNA molecules for joint detection.

Cyanine-labeled RNA shows good performance in many applications, such as fluorescence confocal microscopy, flow cytometry, fluorescence in situ hybridization, and northern hybridization. In addition, the combination of cyanine dyes with modern imaging techniques, such as super-resolution microscopy and two-photon microscopy, enables researchers to observe the behavior of RNA at the single-molecule level. In biomedical research, cyanine RNA labeling technology helps to gain a deeper understanding of the expression, localization, and interaction of disease-related RNA molecules. For example, studying specific RNA markers in tumor cells can reveal changes in gene expression during carcinogenesis, which can help develop new diagnostic tools and treatments. In addition, the labeling and detection of viral RNA can help reveal the mechanisms of viral infection and replication, providing important information for the development of antiviral drugs.

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