Nucleic acid-based fluorescent probes and their analytical potential

It is well known that nucleic acids play an essential role in living organisms because they store and transmit genetic information and use that information to direct the synthesis of proteins. However, less is known about the ability of nucleic acids to bind specific ligands and the application of oligonucleotides as molecular probes or biosensors. Oligonucleotide probes are single-stranded nucleic acid fragments that can be tailored to have high specificity and affinity for different targets including nucleic acids, proteins, small molecules, and ions. One can divide oligonucleotide-based probes into two main categories: hybridization probes that are based on the formation of complementary base-pairs, and aptamer probes that exploit selective recognition of nonnucleic acid analytes and may be compared with immunosensors. Design and construction of hybridization and aptamer probes are similar. Typically, oligonucleotide (DNA, RNA) with predefined base sequence and length is modified by covalent attachment of reporter groups (one or more fluorophores in fluorescence-based probes). The fluorescent labels act as transducers that transform biorecognition (hybridization, ligand binding) into a fluorescence signal. Fluorescent labels have several advantages, for example high sensitivity and multiple transduction approaches (fluorescence quenching or enhancement, fluorescence anisotropy, fluorescence lifetime, fluorescence resonance energy transfer (FRET), and excimer-monomer light switching). These multiple signaling options combined with the design flexibility of the recognition element (DNA, RNA, PNA, LNA) and various labeling strategies contribute to development of numerous selective and sensitive bioassays. This review covers fundamentals of the design and engineering of oligonucleotide probes, describes typical construction approaches, and discusses examples of probes used both in hybridization studies and in aptamer-based assays

Screening Scheme Based on Measurement of Fluorescence Lifetime in the Nanosecond Domain

The authors demonstrate that the fluorescence lifetime of certain fluorescent labels is a useful parameter to detect affinity binding between biotin and streptavidin, as well as between biotinylated bovine serum albumin and streptavidin. The assay is performed in a microplate format, and lifetimes are determined using dye laser-induced fluorescence. Four fluorescent labels are presented that undergo a significant change in their lifetime upon affinity binding. The scheme, referred to as the fluorescence lifetime affinity assay, has several attractive features in that it requires single labeling only, represents a homogeneous assay, allows each of the 2 binding partners to be labeled, and is compatible with the standard microwell formats used in high-throughput screening

SDS-PAGE of Proteins Using a Chameleon-Type of Fluorescent Prestain

A new prestaining method for protein SDS-PAGE was developed using the fluorogenic amino-reactive label Py-1. This resulted in one of the fastest, most sensitive, and environmentally friendly protocols available. It is mainly due to the unique optical properties of Py-1, which is blue and virtually nonfluorescent but turns to red and becomes much more strongly fluorescent once it is conjugated to the amino group of a protein. Staining times of 30 min are adequate to visualize subnanogram quantities of proteins because pre-electrophoretic labeling Py-1 does not require the time-consuming steps of washing or fixation of gels. LODs as low as 16 pg of protein are found which is better than the best (commercial) poststains and comparable to the best (commercial) prestains. In addition, prestaining requires marginal amounts of staining solution. The change in electrophoretic mobility and band broadening is at a low level because Py-1 causes a mass shift of 288 Da per bound molecule only. By virtue of the small mass shift it causes, this stain is compatible with mass spectrometric protein analysis even though it acts as a covalent label

Chromogenic Sensing of Biogenic Amines Using a Chameleon Probe and the Red−Green−Blue Readout of Digital Camera Images

We report on sensing spots containing an amine reactive chromogenic probe and a green fluorescent (amine insensitive) reference dye incorporated in a hydrogel matrix on a solid support. Such spots enable rapid and direct determination of primary amines and, especially, biogenic amines (BA). A distinct color change from blue to red occurs on dipping the test spots into a pH 9.0 sample containing primary amines. BAs can be determined in the concentration range from 0.01 to 10 mM within 15 min, enabling rapid, qualitative, and semiquantitative evaluation. In the “photographic” approach, the typically 4−7.5-fold increase in fluorescence intensity of the probe at 620 nm along with the constant green fluorescence at 515 nm of a reference dye are used for quantitation of BAs. The sensing spots are photoexcited with high-power 505 nm light-emitting diodes (LEDs) in a black box. A digital picture is acquired with a commercially available digital camera, and the color information is extracted via red−green−blue (RGB) readout. The ratio of the intensities of the red (signal) channel and the green (reference) channel yields pseudocolor pictures and calibration plots

Determination of biogenic amines by capillary electrophoresis using a chameleon type of fluorescent stain

A method was developed for the determination of biogenic amines (BAs) via micellar electrokinetic chromatography along with laser induced fluorescence detection using the amino-reactive chameleon stain Py-1. A labeling protocol was established for seven primary BAs by optimizing the reaction conditions in terms of the amount of reagents, reaction temperature, reaction time and solvent. Derivatization was accomplished within 30 min and is visible by the naked eye because it is accompanied by a color change from blue to red. Separation of the labeled BAs was achieved within 15 min with a background buffer of pH 2.5 containing phosphate, Tween®80, and methanol. The LODs range from 0.1 to 0.9 µmol·L−1, with RSDs ranging from 1.1 to 4.2% at 10 µmol·L−1. The method was applied to the determination of histamine in various fish samples