Fluorescent Labels and Techniques
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Questions and Answers

What are the main characteristics of organic fluorophores that make them suitable for multiplex assays?

Organic fluorophores contain aromatic groups and conjugated bonds, which allow for easy excitation and specific emission wavelengths.

How do fluorescent proteins differ from traditional fluorophores in applications?

Fluorescent proteins, such as GFP from jellyfish, are used as fusion proteins and exhibit natural bioluminescence.

What is the role of enzymes in fluorometric ELISA?

Enzymes in fluorometric ELISA convert non-fluorescent substrates into fluorescent products, enabling detection.

What are the drawbacks associated with fluorescent labels used in assays?

<p>Drawbacks include a background signal, self-quenching at high concentrations, and a short fluorescence lifetime.</p> Signup and view all the answers

Identify the common lanthanide elements used in immunoassays and their significance.

<p>Common lanthanide elements include Europium (Eu), Terbium (Tb), Samarium (Sm), and Dysprosium (Dy), notable for their intense fluorescence.</p> Signup and view all the answers

What mechanism allows the fluorescence signal of lanthanides to be observed?

<p>The fluorescence signal from lanthanides is observed when they are firmly bound to an organic ligand that shields them from water.</p> Signup and view all the answers

Explain the advantages of using lanthanide ions in immunoassays.

<p>Lanthanide ions provide intense fluorescence, a wide stoke shift, sharp emission bands, and long-lived fluorescence.</p> Signup and view all the answers

What are non-fluorescent chelates and their role in the context of lanthanide ions?

<p>Non-fluorescent chelates are structures that bind lanthanide ions but do not emit fluorescence themselves.</p> Signup and view all the answers

What happens to the AEB analogue with an increase in the number of 'on beads'?

<p>The AEB analogue increases as the number of 'on beads' rises.</p> Signup and view all the answers

How is AEB digital defined in relation to 'on beads'?

<p>AEB digital is defined as the negative natural logarithm of 1 minus 'on beads'.</p> Signup and view all the answers

What is one major advantage of digital ELISA over chemiluminescence and analogue fluorescence?

<p>Digital ELISA provides better sensitivity than chemiluminescence or analogue fluorescence.</p> Signup and view all the answers

In multiplex ELISA, how are different analytes distinguished?

<p>Different analytes are distinguished using color-coded, fluorescence-labeled beads.</p> Signup and view all the answers

List two potential causes for background interference in digital ELISA.

<p>Tracer binding to solid phase and cross-reacting substances blocking the antibodies.</p> Signup and view all the answers

What is the necessary condition regarding oxidation and reduction for an electrochemical immunoassay?

<p>A reaction requires that something must be reduced and something must be oxidized.</p> Signup and view all the answers

What specific instrument types are used to measure changes in electric current in electrochemical immunoassays?

<p>Cyclic voltammetry or amperometry are used to measure current changes.</p> Signup and view all the answers

How is an electrochemical ELISA distinguished from standard ELISA?

<p>In electrochemical ELISA, the antibody is conjugated with HRP enzyme and requires oxidizable substrates.</p> Signup and view all the answers

What is the main advantage of inherently fluorescent chelates over traditional ones in immune assays?

<p>Inherently fluorescent chelates do not require a development step, thus simplifying the assay process.</p> Signup and view all the answers

Describe the purpose of the acidic buffer in the DELFIA enhancement solution.

<p>The acidic buffer's purpose is to dissociate the ions, facilitating the formation of new fluorescent chelates.</p> Signup and view all the answers

List two key criteria that determine a good lanthanide chelate reporter.

<p>High fluorescence and good stability are two key criteria for an effective lanthanide chelate reporter.</p> Signup and view all the answers

What is the potential drawback of using lanthanide chelates in blood plasma assays?

<p>The presence of EDTA in blood plasma can interfere with the assay, making it unsuitable for this sample type.</p> Signup and view all the answers

Explain the significance of time-resolved fluorescence in the context of lanthanide chelates.

<p>Time-resolved fluorescence allows for long-lived fluorescence, enabling precise timing in measurement for enhanced sensitivity.</p> Signup and view all the answers

What is a key difference between DELFIA and direct TRF assays when it comes to washing steps?

<p>Direct TRF assays do not require a washing step, unlike DELFIA which requires careful washing before measurement.</p> Signup and view all the answers

Why is Triton X-100 included in the DELFIA enhancement solution?

<p>Triton X-100 is included to stabilize the chelates and form hydrophobic pockets to shield them from water.</p> Signup and view all the answers

Identify a challenge associated with the timing of measurements in DELFIA and its consequences.

<p>Measurement timing must be precise; otherwise, it can lead to inaccurate signal readings.</p> Signup and view all the answers

What is the primary purpose of the conjugate application buffer in the creation of a conjugated pad?

<p>The conjugate application buffer facilitates the addition of the conjugate by providing necessary agents like proteins, polymers, and surfactants.</p> Signup and view all the answers

Describe the role of the wicking pad in an assay.

<p>The wicking pad pulls fluid upstream through the strip and prevents back flow, acting as the engine of the assay.</p> Signup and view all the answers

What are the primary materials used for backing material in the assay strips?

<p>Backing materials are typically made of plastic, commonly polystyrene, and are coated with pressure sensitive adhesive.</p> Signup and view all the answers

List the main characteristics that an optimal analytical membrane should possess.

<p>An optimal analytical membrane must allow liquid movement through capillary forces and bind proteins irreversibly on test and control lines only.</p> Signup and view all the answers

What are the two primary issues associated with the use of nitrocellulose membranes?

<p>Nitrocellulose membranes face high non-specific binding due to their high protein binding capacity and variability in performance under different environmental conditions.</p> Signup and view all the answers

Explain how pore size affects the performance of a nitrocellulose membrane in assays.

<p>Larger pore sizes allow for faster liquid flow but may compromise the sensitivity of the assay due to reduced interaction opportunities with target proteins.</p> Signup and view all the answers

Identify the main types of forces at play in different polymer membranes, such as polyvinylidene fluoride and Nylon.

<p>Polyvinylidene fluoride uses hydrophobic forces, while Nylon operates through ionic electrostatic forces.</p> Signup and view all the answers

How is flow time defined in the context of membrane assays?

<p>Flow time is defined as the number of seconds it takes for liquid to cross 4 centimeters of the membrane.</p> Signup and view all the answers

How does the threshold cycle in qPCR relate to the starting quantity of the analyte?

<p>The threshold cycle indicates the point at which the signal surpasses the background, with a higher quantity of analyte leading to a quicker approach to this cycle.</p> Signup and view all the answers

What might happen if the TaqMan probe does not have a strong enough specificity?

<p>It may bind to non-target sequences like primer dimers, resulting in inaccurate measurements.</p> Signup and view all the answers

What factors should be considered in the design of primers for optimal qPCR performance?

<p>The ratio of adenine-thymine (A-T) to guanine-cytosine (G-C) pairs, ensuring no secondary structures, and a length between 18 to 24 nucleotides.</p> Signup and view all the answers

In molecular beacons, how is the fluorescent signal produced during the assay?

<p>The probe binds to the target sequence, separating the reporter from the quencher, which allows the signal to be detected.</p> Signup and view all the answers

Explain how scorpion primers function during the qPCR process.

<p>They exist in a hairpin structure that opens during denaturation, allowing the reporter to bind to the amplicon while being separated from the quencher.</p> Signup and view all the answers

What is the main advantage of using dual hybridization probes in qPCR?

<p>They enhance signal strength through FRET by having a donor and an acceptor probe that are positioned closely during annealing.</p> Signup and view all the answers

Describe the importance of avoiding mononucleotide or dinucleotide repeats in primer design.

<p>These repeats can lead to mispriming or the formation of secondary structures, compromising the efficiency of the PCR.</p> Signup and view all the answers

What distinguishes TaqMan probes from other fluorescent probe types used in qPCR?

<p>TaqMan probes undergo hydrolysis during amplification, resulting in the separation of the fluorophore from the quencher, which generates a measurable signal.</p> Signup and view all the answers

Study Notes

Fluorescent Labels

  • Organic fluorophores: contain aromatic groups and conjugated bonds.
  • Aromatic groups are easily excited, each fluorophore has a specific emission wavelength. Used for multiplex assays.
  • Fluorescent proteins: naturally bioluminescent, used in microscopic techniques, mainly as fusion proteins.
  • GFP from jellyfish can be mutated to produce colors other than green.
  • Red algae proteins (APC or PE) are also used.

Fluorometric ELISA

  • Enzyme converts non-fluorescent substrate into a fluorescent product. Different excitation and emission profiles affect sensitivity.
  • Enzymes used: beta galactosidase, HRP, alkaline phosphatase. Each produces different products with defined spectra.
  • Narrow stroke shift - fluorescence signal has a short half-life, measured instantaneously.
  • Background signal due to other molecules or plastic backing.
  • Self-quenching reduces signal at high label concentrations.

Lanthanide Chelates

  • Rare earth elements used in immunoassays: Europium (Eu), terbium (Tb), samarium (Sm), dysprosium (Dy).
  • Lanthanides form ions (La 3+) with aqueous quenching of fluorescence signal.
  • Fluorescence observed when bound to an organic ligand that shields the ion from water and delivers energy.
  • Ligand can be used to attach lanthanide to antigens, antibodies, or nucleic acids.
  • Advantages: intense fluorescence, wide stroke shift, sharp emission bands, long-lived fluorescence.
  • Types of chelates:
    • Non-fluorescent chelates: used as linkers, require a development step to obtain signal from the ion.
    • Inherently fluorescent chelates: do not need a development step.

DELFIA (Dissociation Enhanced Fluoroimmuno Assay)

  • Two-site immune reaction on a solid phase.
  • High sensitivity.
  • Enhancement solution creates fluorescence: acidic buffer to dissociate ions, beta diketone for new chelates, Lewis base to displace water and enhance fluorescence, Triton X-100 to stabilize chelates.
  • Criteria for a good lanthanide chelate reporter:
    • High fluorescence, good protection of the lanthanide, high energy absorption, high quantum yield, good stability, good thermodynamics and kinetics for ion release, coupling properties (hydrophobicity, efficient coupling, mild reaction).
  • Drawbacks:
    • Enhancement solution added, develops for 30 minutes, then measured. Timing is crucial for accurate measurement.
    • Expensive.
    • Can't be used with blood plasma due to EDTA interference.

Direct Trf

  • Uses inherently fluorescent chelates, no washing step required.
  • Water quenching, requires measurement in dried wells.
  • Signal remains for months making storage convenient.

Time-Resolved Fluorometry

  • Lanthanides used in immunoassays have energy levels for time-resolved fluorometry (long-lived fluorescence).
  • Each lanthanide has a different wavelength allowing multiplex assays.

Digital ELISA

  • Higher “on beads” indicates higher analyte concentration, leading to higher AEB (analyte equivalent beads) analogue.
  • AEB digital (negative natural logarithm of 1 – “on beads”) used for low/medium concentrations.
  • Digital ELISA has higher sensitivity compared to chemiluminescence or analogue fluorescence, with a very low LOD.
  • Can be used for multiplex assays using color-coded beads with different labels and excitation wavelengths.
  • Applicable to miRNA detection and single-cell protein counting.

DIGITAL ELISA Troubleshooting

  • False elevation:
    • Tracer binds to solid phase.
    • Tracer binds to capture antibody.
    • Enzyme binds non-specifically.
    • Bridging with heterophile.
    • Cross-reaction with target analyte.
  • False suppression:
    • Heterophile blocks the capture antibody.
    • Heterophile blocks the detection antibody.
    • Cross-reacting substance blocks the detection antibody.
    • Cross-reacting substance blocks the capture antibody.
    • Target is blocked from reacting with the capture antibody.

Electrochemical Immunoassay

  • Binding event detected as a change in current due to a redox reaction.
  • Uses biosensors with binding surfaces and electrodes to detect changes in electrical current.
  • Requires reduction and oxidation reactions close to the electrode.
  • Interferences require wash steps.
  • Measured by instruments detecting changes in electrical current, such as cyclic voltammetry or amperometry.

Electrochemical ELISA

  • Antibody conjugated with HRP enzyme, substrate must be oxidizable.
  • Conjugate pad created with buffer containing agents, proteins, polymers, surfactants, sugars, and salts.
  • Conjugate added by immersion or non-contact dispersion.

Wicking Pad (Absorbent Pad)

  • Pulls fluid through the strip and holds it, preventing back flow.
  • The “engine” of the assay as it pulls liquid from the sample pad.
  • Made of high-density cellulose.
  • Length varies based on the volume of fluid added.

Backing Material

  • The platform of the assay.
  • Lamination of all components in their place.
  • Provides rigidity and easy handling.
  • Made from plastic (polystyrene) coated with pressure sensitive adhesive. Adhesive can transfer to the strip cutter.

Analytical Membrane

  • Allows liquid to travel through capillary forces.
  • Binds proteins on test and control lines irreversibly.
  • Shouldn't bind proteins outside test and control lines.
  • Most materials bind proteins nonspecifically or not at all.
  • Polymers used:
    • Nitrocellulose (electrostatic forces)
    • Polyvinylidene fluoride (hydrophobic forces)
    • Nylon (ionic/electrostatic forces)
    • Polyethersulfone (hydrophobic forces)
  • Nitrocellulose is most common, advantages:
    • Low manufacturing costs
    • Liquid flow through capillary forces
    • High protein binding capacity
    • Wide range of commercially available membranes
  • Nitrocellulose disadvantages:
    • High protein binding capacity leads to non-specific binding
    • Imperfect reproducibility of performance
    • Fragile and flammable
    • Performance varies with environmental conditions
  • Different pore sizes affect flow rate and sensitivity (larger pores = faster flow, lower sensitivity).
  • Flow time is measured for each membrane.

qPCR (Quantitative PCR or Real-time PCR)

  • Threshold signal level is distinguished from background noise and represents reactions in the exponential phase.
  • Threshold cycle (Ct) is the cycle at which the signal surpasses the background.
  • Comparing Ct to a standard determines the starting quantity of the analyte. Higher quantity means faster Ct.

TaqMan Probes

  • Bind to target sequence within the amplicon during annealing.
  • Contain a fluorophore near a quencher.
  • DNA polymerase hydrolyses the probe, separating the fluorophore from the quencher.
  • The linker sequence between fluorophore and quencher must be specific.
  • Specific probes don't bind to primer dimers.

Primer Design

  • At/Gc ratio affects melting temperature, must be optimized.
  • Sequence should minimize secondary structures.
  • Length between 18-24 nucleotides for tight binding.
  • Avoid mononucleotide or dinucleotide repeats to prevent mispriming and secondary structures.

Alternative Probe Types

  • Molecular beacons:
    • No hydrolysis of the primer.
    • Hairpin loop with reporter and quencher at the ends.
    • Binds to target sequence during annealing, separating the reporter and quencher.
    • Signal is produced.
  • Dual hybridization probes:
    • FRET-based.
    • Two probes: one with a donor, one with an acceptor.
    • Donor and acceptor bind next to each other during annealing.
    • Donor produces signal at the designed wavelength based on FRET.
  • Scorpion primers:
    • Hairpin conformation with a reporter on one end and a quencher + PCR blocker on the other.
    • Bind as a hairpin loop during annealing.
    • Loop opens during denaturation, allowing the reporter to bind to the amplicon.
    • Reporter is far from the quencher, producing a signal.

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Description

Explore the fascinating world of fluorescent labels and their applications in various biochemical assays. This quiz covers organic fluorophores, fluorescent proteins, and fluorometric techniques like ELISA. Understand the details of fluorescence, signal sensitivity, and the use of rare earth elements in immunoassays.

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