Week 2 : Optical biosensors Flashcards
What is the difference between background fluorescence and autofluorescence?
autofluorescence originate from endogenous sample constituent in which naturally fluorescent molecules are present.
background fluorescence originates from unbound or nonspecifically bound probes
how to increase fluorescence detection sensitivity and decrease Background Fluorescence and Autofluorescence?
(1) Minimize this signal distortion by probes excited at longer wavelengths (>500nm) e.g. Alexa 647
(2) Extract the biomarkers from their original environment prior to analysis. Note: this extra sample processing step can result in error and variability, dependent on extraction efficiency, and biomarker purity
(3) Fluorescence lifetime imaging (FLIM): the chances of your signal and sample autofluorescence having the same lifetime signal are smaller than the chances of spectral overlap
Give an example of common autofluorescent molecules in cell.
DNA, Folic acid, retinol.
What are the sources of fluorescent molecules?
(1) Naturally occurring fluorescent small molecules or proteins. DISADVANTAGES: low fluorescence quantum yield & low excitation/emission wavelengths.
(2) There are also synthetic fluorescent molecules:
engineered small molecules or engineered nanoparticles.
How can you use Fluorescent Small Molecules in biosensing?
(1) can be designed to bind preferentially to cancer biomarkers (2) can be attached to receptors/probes to target them
How can you use Fluorescent nanomaterials in biosensing?
require surface to be functionalized with
receptors to confer biomarker specificity.
How can you use Fluorescent nanomaterials in biosensing?
by functionalizing the surface with receptors to confer biomarker specificity.
Give an example of fluorescent nanomaterilas.
Carbon dots, Quantum dots, metal nanoclusters, polymer NPS
What are the types of fluorescent small molecule-based probes, in terms of mechanisms?
1) Labels
2) Molecular Beacons
3) Intercalator Dyes
4) Molecular Rotors
Explain Molecular Beacons
Typically single-stranded oligonucleotide hybridization probes that can adopt a stable stem-and-loop structure in solution.
•loop contains a probe sequence that is complementary to that of the nucleic acid biomarker, and stem is formed by annealing of two complementary “arm” sequences located on either side of the probe sequence (i.e., 3’ and 5’ ends).
• fluorophore is covalently linked to the end of one arm and a quencher is covalently linked to the end of the other arm.
How do Molecular beacons function?
MBs do not fluoresce when they are free in solution, but when they hybridize to a target sequence they undergo a conformational change that enables them to fluoresce brightly
Explain Intercalating Dye.
small molecules that can intercalate between Watson-Crick
base pairs of double-stranded DNA and emit fluorescence of intensity orders of magnitude greater than when the dye is free in solution.
Give an example of Intercalating Dye
(1) SYBR Green (SG)
(2) picoGreen (PG)
(3) SYBR Gold
(4) YOYO dyes
Give an example of Intercalating Dye
DAPI
(1) binds to A-T regions (Major groove)
(2) used in fluorescence microscopy
(3) can be used in live and fixed cells
(4) passes through the membrane less efficiently in live
cells and therefore provides a marker for membrane viability
Explain Molecular Rotors
probes known to form twisted intramolecular charge transfer (TICT) complexes in the excited state producing a fluorescence quantum yield that is dependent on the surrounding environment
How do Molecular Rotors function?
Following photoexcitation, this motif can relax via fluorescence emission or internal nonradiative process that involves molecular rotation between the donor and the acceptor
• When rotation is hindered (e.g., because dye is intercalated between base pairs), relaxation occurs via an increased fluorescence emission
• When the dye is in solution, relaxation proceeds mainly via a nonradiative pathway, meaning no (or lower) emission of fluorescence.
Give an example (type) of fluorescent nanomaterials
1) Quantum Dots (QDs)
2) Gold Nanoparticles (AuNPs)
Describe Quantum dots
• Composed of a semiconductor core capped with a shell for stability
• surface can be coated with hydrophilic, hydrophobic, or amphiphilic ligands which can be further linked with proteins, drugs, antibodies, and other bioreceptors
• emission spectra can be tuned by adjusting the size
What are the advantages of NP probes?
(1) high quantum yeild
(2) more photostable
(3) longer fluorescence lifetime
(4) have broader absorption spectra
Explain gold NPs.
1) diameter of 1 to 100nm
2) rely on fluorescence quenching
3) emission spectra varies based on size
Give an example of using gold NPS.
Nanoflare; functionalized AuNPs with ssDNA that are complemntry to the target sequence and a reporter sequnce. when the target is not presented, the reporter sequnce contianng the flurofre is quenched.
Draw and explain Jablonski Diagram
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Why Fluorescence-based sensors are common? (Features)?
1) dynamic range,
2) high sensitivity, multiplexing capabilities
3) ability to measure multiple fluorescence properties (e.g. fluorescence intensity and fluorescence lifetime).
4) allows the detection single molecules
What Challenges are there for Fluorescence-based sensors
1) Background autofluorescence
2) photobleaching