Recent Advances in DNA Biosensor - International Frequency ...

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Sensors & Transducers Journal, Vol. 92, Issue 5, May 2008, pp. 122-133 Table 1. Advantage and disadvantage of different types of DNA based biosensors. 1. Optical a Fiber optics Type Principle Advantage Disadvantages Evanescent wave based, allows measurement of binding at the fiber surface Remote in-situ measurement, inherent sensitivity of optical approaches Costly equipment and not portable, b. Laser interferometry 2. Electrochemical a. Conductometric b. Potentiometric c. Amperometric 3.Piezoelectric 4. Colorimetric/Strip 5. DNA biochip Planar waveguides have evanescent field responsible to change in index of refraction Change in conductance Electric potential Oxidation/reduction Quartz crystals oscillation at defined frequency, binding of an analyte to it changes the mass of crystal hence oscillation frequency Color development Array based Highly sensitive, detect up to 1 cell Fast, low cost High sensitive, fast Not required any instruments Instrument required Susceptibility to turbidity interference Highly buffered solution may interfere Sensitivity level up to 1 cell have not demonstrated Not quantitative Quantitative 3. Optical DNA Biosensors Optical methods are the most frequently used in detection of analytes. The simplest detection units are spectrophotometer and fluorometers, which can be used for spectroscopic or fluorescence detection. Since nucleic acids do not have intrinsic properties that are functional in direct detection, many of the nucleic acid-based assays, especially optical setups, require a label for detection. The choice of label is based on stability, sensitivity and its convenience. DNA optical biosensors are based on a fiber optic to transducer the emission signal of a fluorescent label. Fiber optics are devices that carry light from one place to another by a series of internal inflections. The operation of fiber-optic DNA biosensors involves placement of an ssDNA probe at the end of the fiber and monitoring the fluorescent changes resulting from the association of a fluorescent indicator with the double-stranded (ds) DNA hybrid [30-31]. The first DNA optical biosensor, developed by Krull and coworkers using fluorescent indicator ethidium bromide [30, 32].Watts group developed a fiber-optic DNA sensor array for the simultaneous detection of multiple DNA sequences [33].The hybridization of fluorescent labeled complementary olgonucleotides was monitored by observing the increase in fluorescence. A different optical transduction, based on evanescent wave devices, can offer real-time label-free optical detection of DNA hybridization. The different types of optical biosensors are as follows: 124
3.1. Molecular Beacons (MBs) Sensors & Transducers Journal, Vol. 92, Issue 5, May 2008, pp. 122-133 MBs are oligonucleotides with a stem-and-loop structure, labeled with a fluorophore at one end and a quencher on the other end of the stem that become fluorescent upon hybridization. In addition to their direct monitoring capability, MB probes offer high sensitivity and specificity. A biotinylated molecular beacon probe was developed to prepare a DNA biosensor using a bridge structure. MB was biotinylated at quencher site of the stem and linked on a biotinylated glass through strepatavidin, which acted as bridge between MB and glass matrix. The fluorescence change was measured by confirmation change of MB in the presence of complementary target DNA [34, 35]. 3.2. Surface Plasmon Resonance (SPR) Surface plasmon resonance (SPR) is an quantum optical-electrical phenomenon arising from the interaction of light with metal surface. Under specific conditions the energy carried by photons of light is transferred to packets of electrons (photons) on a metal surface. Energy transfer occurs only at specific resonance wavelength of light [33]. These biosensors are based on monitoring changes in surface optical properties (change in resonance angle due to change in the interfacial refractive index) resulting from the surface binding reaction. Such devices thus combine the simplicity of SPR with the sensitivity of wave guiding devices. The resonance conditions are influenced by the material adsorbed onto the thin metal film. A linear relationship is found between resonance energy and mass concentration of molecules such as proteins, sugars and DNA. The SPR signal which is expressed in resonance units is therefore a measure of mass concentration at the sensor chip surface [36-38].It has been reported that alkane thiol modified oligonucleotide can be immobilized onto gold surface to detect DNA hybridization using SPR based detection in agro food industry [39]. 3.3. Quantum–Dot An ultrasensitive nanosensor based on fluorescence resonance energy transfer (FREET) can detect very low concentration of DNA and do not require separation of unhybridized DNA. Such type of technique is based on quantum-dots (QDs) which are linked to specific DNA probes to capture target DNA. The target DNA strand binds to a fluorescent-dye (fluorophore) labeled reporter strand and thus forming FREET donor-acceptor assembly. Quantum dot also functions as to concentrate the signal by confining several targets at nanoscale domain. Unbound DNA strand produce no fluorescence but on biding of even small amount of target DNA (≤ 50 copies) may produce very strong FREET signal. Several FREET based DNA probes (molecular beacons and TaqMan probes) whose fluorescence signals change as a result of hybridization or enzymatic reactions have been developed for separation free (unhybridized DNA strand) detection of target DNA [40-43]. DNA nanosensor consists of two target specific DNA probes i.e. reporter and capture probe. The reporter probe is labeled with fluorophore whereas capture probe is labeled with biotin which binds with streptavidin conjugated with QD. The QD functions as target concentrator as well as FREET energy donor. When target DNA is present in solution, it becomes sandwiched by reporter and capture probes. Several sandwiched hybrids are then captured by a single QD through biotin-streptavidin binding and concentrate at nanoscale domain [44]. The fluorophore acceptor and QD donor close proximity causing fluorescence from acceptor by means of FREET on illumination of the donor. The detection of acceptor emission indicates the presence of target DNA. The unhybridized probe do not participate in FREET and do not give fluorescence, therefore, it is not necessary to remove. The CdSe- 125
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