Editing Biosensor (section)

==Bioreceptors==
[[File:Biosensors used for screening combinatorial DNA libraries.svg|thumb|Biosensors used for screening combinatorial DNA libraries]]

In a biosensor, the bioreceptor is designed to interact with the specific analyte of interest to produce an effect measurable by the transducer. High [[binding selectivity|selectivity]] for the analyte among a matrix of other chemical or biological components is a key requirement of the bioreceptor. While the type of biomolecule used can vary widely, biosensors can be classified according to common types of bioreceptor interactions involving: antibody/antigen,<ref>{{cite journal |title= Highly sensitive electrochemiluminescence detection of a prostate cancer biomarker |year=2017 |last1= Juzgado |first1=A. |last2= Solda |first2=A. |last3=Ostric |first3=A. |last4=Criado |first4=A. |last5=Valenti |first5=G. |last6=Rapino |first6=S. |last7=Conti |first7=G. |last8=Fracasso |first8=G. |last9=Paolucci |first9=F. |last10=Prato |first10=M. |journal= J. Mater. Chem. B |volume=5 |issue= 32 |pages=6681–6687 |doi=10.1039/c7tb01557g|pmid=32264431 }}</ref> enzymes/ligands, nucleic acids/DNA, cellular structures/cells, or biomimetic materials.<ref name=BiosensorsandBiochips>{{Cite journal | last1 = Vo-Dinh | first1 = T. | last2 = Cullum | first2 = B. | doi = 10.1007/s002160051549 | title = Biosensors and biochips: Advances in biological and medical diagnostics | journal = Fresenius' Journal of Analytical Chemistry | volume = 366 | issue = 6–7 | pages = 540–551 | year = 2000 | pmid =  11225766| s2cid = 23807719 | url = https://zenodo.org/record/1232643 | hdl = 11603/36050 | hdl-access = free }}</ref><ref>{{cite journal |title= An electrochemiluminescencesupramolecular approach to sarcosine detection for early diagnosis of prostate cancer |year=2015 |last1=Valenti |first1=G. |last2=Rampazzo |first2=E. |last3=Biavardi |first3=E. |last4= Villani |first4=E. |last5= Fracasso |first5=G. |last6= Marcaccio |first6=M. |last7= Bertani |first7=F. |last8= Ramarli |first8=D. |last9= Dalcanale |first9=E. |last10=Paolucci |first10=F. |last11=Prodi |first11=L. |journal= Faraday Discuss|volume=185 |pages=299–309 |doi=10.1039/c5fd00096c|pmid= 26394608 |bibcode=2015FaDi..185..299V }}</ref>

===Antibody/antigen interactions===
An [[immunoassay|immunosensor]] utilizes the very specific binding affinity of [[antibodies]] for a specific compound or [[antigen]]. The specific nature of the [[antibody-antigen interaction]] is analogous to a lock and key fit in that the antigen will only bind to the antibody if it has the correct conformation. Binding events result in a physicochemical change that in combination with a tracer, such as fluorescent molecules, enzymes, or radioisotopes, can generate a signal. There are limitations with using antibodies in sensors: 1. The antibody binding capacity is strongly dependent on assay conditions (e.g. pH and temperature), and 2. the antibody-antigen interaction is generally robust, however, binding can be disrupted by [[chaotropic]] reagents, organic solvents, or even ultrasonic radiation.<ref name="High-performance graphene-based bio">{{cite journal |title=High-performance graphene-based biosensor using a metasurface of asymmetric silicon disks |journal=IEEE Sensors Journal |year=2022 |doi=10.1109/JSEN.2021.3134205|last1=Parizi |first1=Mohammad Salemizadeh |last2=Salemizadehparizi |first2=Fatemeh |last3=Zarasvand |first3=Mahdi Molaei |last4=Abdolhosseini |first4=Saeed |last5=Bahadori-Haghighi |first5=Shahram |last6=Khalilian |first6=Alireza |volume=22 |issue=3 |pages=2037–2044 |bibcode=2022ISenJ..22.2037P |s2cid=245069669 }}</ref><ref name=FiberOpticBiosensor>{{Cite journal | last1 = Marazuela | first1 = M.| last2 = Moreno-Bondi | first2 = M.| doi = 10.1007/s00216-002-1235-9 | title = Fiber-optic biosensors – an overview | journal = Analytical and Bioanalytical Chemistry | volume = 372 | issue = 5–6 | pages = 664–682 | year = 2002 | pmid =  11941437| s2cid = 36791337}}</ref>

Antibody-antigen interactions can also be used for [[Serology|serological testing]], or the detection of circulating antibodies in response to a specific disease. Importantly, serology tests have become an important part of the global response to the [[COVID-19]] pandemic.<ref>{{cite journal |last1=Stowell |first1=Sean |last2=Guarner |first2=Jeannette |title=Role of Serology in the Coronavirus Disease 2019 Pandemic |journal=Clinical Infectious Diseases |date=5 November 2020 |volume=71 |issue=8 |pages=1935–1936 |doi=10.1093/cid/ciaa510 |pmid=32357206 |pmc=7197618 }}</ref>

===Artificial binding proteins===
The use of antibodies as the bio-recognition component of biosensors has several drawbacks. They have high molecular weights and limited stability, contain essential disulfide bonds and are expensive to produce. In one approach to overcome these limitations, recombinant binding fragments ([[Fragment antigen-binding|Fab]], [[Fragment variable|Fv]] or [[scFv]]) or domains (VH, [[VHH]]) of antibodies have been engineered.<ref>{{cite journal|last1=Crivianu-Gaita|first1=V|last2=Thompson|first2=M|title=Aptamers, antibody scFv, and antibody Fab' fragments: An overview and comparison of three of the most versatile biosensor biorecognition elements|journal=Biosens Bioelectron|date=Nov 2016|volume=85|pages=32–45|doi=10.1016/j.bios.2016.04.091|pmid=27155114}}</ref> In another approach, small protein scaffolds with favorable biophysical properties have been engineered to generate artificial families of Antigen Binding Proteins (AgBP), capable of specific binding to different target proteins while retaining the favorable properties of the parent molecule. The elements of the family that specifically bind to a given target antigen, are often selected in vitro by display techniques: [[phage display]], [[ribosome display]], [[yeast display]] or [[mRNA display]]. The artificial binding proteins are much smaller than antibodies (usually less than 100 amino-acid residues), have a strong stability, lack disulfide bonds and can be expressed in high yield in reducing cellular environments like the bacterial cytoplasm, contrary to antibodies and their derivatives.<ref>{{cite journal|last1=Skrlec|first1=K|last2=Strukelj|first2=B|last3=Berlec|first3=A|title=Non-immunoglobulin scaffolds: a focus on their targets|journal=Trends Biotechnol|date=Jul 2015|volume=33|issue=7|pages=408–418|doi=10.1016/j.tibtech.2015.03.012|pmid=25931178}}</ref><ref>{{cite journal|last1=Jost|first1=C|last2=Plückthun|first2=A|title=Engineered proteins with desired specificity: DARPins, other alternative scaffolds and bispecific IgGs|journal=Curr Opin Struct Biol|date=Aug 2014|volume=27|pages=102–112|doi=10.1016/j.sbi.2014.05.011|pmid=25033247}}</ref> They are thus especially suitable to create biosensors.<ref name="pmid19945965">{{cite journal|last1=Brient-Litzler|first1=E|last2=Plückthun|first2=A|last3=Bedouelle|first3=H|title=Knowledge-based design of reagentless fluorescent biosensors from a designed ankyrin repeat protein|journal=Protein Eng Des Sel|date=Apr 2010|volume=23|issue=4|pages=229–241|doi=10.1093/protein/gzp074|pmid=19945965|url=http://doc.rero.ch/record/298976/files/gzp074.pdf|doi-access=free}}</ref><ref name="pmid21565483">{{cite journal|last1=Miranda|first1=FF|last2=Brient-Litzler|first2=E|last3=Zidane|first3=N|last4=Pecorari|first4=F|last5=Bedouelle|first5=Hugues|title=Reagentless fluorescent biosensors from artificial families of antigen binding proteins|journal=Biosens Bioelectron|date=Jun 2011|volume=26|issue=10|pages=4184–4190|doi=10.1016/j.bios.2011.04.030|pmid=21565483}}</ref>

===Enzymatic interactions===
The specific binding capabilities and catalytic activity of [[enzyme]]s make them popular bioreceptors. Analyte recognition is enabled through several possible mechanisms: 1) the enzyme converting the analyte into a product that is sensor-detectable, 2) detecting enzyme inhibition or activation by the analyte, or 3) monitoring modification of enzyme properties resulting from interaction with the analyte.<ref name=FiberOpticBiosensor/> The main reasons for the common use of enzymes in biosensors are: 1) ability to catalyze a large number of reactions; 2) potential to detect a group of analytes (substrates, products, inhibitors, and modulators of the catalytic activity); and 3) suitability with several different transduction methods for detecting the analyte. Notably, since enzymes are not consumed in reactions, the biosensor can easily be used continuously. The catalytic activity of enzymes also allows lower limits of detection compared to common binding techniques. However, the sensor's lifetime is limited by the stability of the enzyme.

===Affinity binding receptors===
Antibodies have a high [[binding constant]] in excess of 10^8 L/mol, which stands for a nearly irreversible association once the antigen-antibody couple has formed. For certain analyte molecules like [[glucose]] affinity binding proteins exist that bind their ligand with a high [[sensitivity and specificity|specificity]] like an antibody, but with a much smaller binding constant on the order of 10^2 to 10^4 L/mol. The association between analyte and receptor then is of [[reversible process (thermodynamics)|reversible]] nature and next to the couple between both also their free molecules occur in a measurable concentration. In case of glucose, for instance, [[concanavalin A]] may function as affinity receptor exhibiting a binding constant of 4x10^2 L/mol.<ref name= SMG1982>{{cite journal | author = J. S. Schultz | author2 = S. Mansouri | author3 = I. J. Goldstein | title = Affinity sensor: A New Technique for Developing Implantable Sensors for Glucose and Other Metabolites | journal = Diabetes Care| volume = 5 | issue = 3 | pages = 245–253 | year = 1982 | doi=10.2337/diacare.5.3.245| pmid = 6184210 | s2cid = 20186661 }}</ref> The use of affinity binding receptors for purposes of biosensing has been proposed by Schultz and Sims in 1979 <ref name= SSi1979>{{cite journal | author = J. S. Schultz | author2 =  G. Sims | title = Affinity sensors for individual metabolites | journal = Biotechnol. Bioeng. Symp. | volume = 9 | pages = 65–71 | year = 1979 | issue = 9 | pmid = 94999 }}</ref> and was subsequently configured into a fluorescent assay for measuring glucose in the relevant [[blood sugar|physiological range]] between 4.4 and 6.1&nbsp;mmol/L.<ref name= BS2000>{{cite journal | author = R. Ballerstadt | author2 = J. S. Schultz | title = A Fluorescence Affinity Hollow Fiber Sensor for Continuous Transdermal Glucose Monitoring| journal = Anal. Chem. | volume = 72 | issue = 17 | pages = 4185–4192 | year = 2000 | doi = 10.1021/ac000215r | pmid = 10994982 }}</ref> The sensor principle has the advantage that it does not consume the analyte in a chemical reaction as occurs in enzymatic assays.

===Nucleic acid interactions===
Biosensors employing nucleic acid based receptors can be either based on complementary base pairing interactions referred to as genosensors or specific nucleic acid based antibody mimics (aptamers) as aptasensors.<ref>{{cite journal |last1=Kaur |first1=Harmanjit |last2=Shorie |first2=Munish |title=Nanomaterial based aptasensors for clinical and environmental diagnostic applications |journal=Nanoscale Advances |date=29 Apr 2019 |volume=1 |issue=6 |pages=2123–2138 |doi=10.1039/C9NA00153K |pmid=36131986 |pmc=9418768 |bibcode=2019NanoA...1.2123K |doi-access=free }}</ref> In the former, the recognition process is based on the principle of complementary [[base pair]]ing, adenine:thymine and cytosine:guanine in [[DNA]]. If the target nucleic acid sequence is known, complementary sequences can be synthesized, labeled, and then immobilized on the sensor. The hybridization event can be optically detected and presence of target DNA/RNA ascertained. In the latter, aptamers generated against the target recognise it via interplay of specific non-covalent interactions and induced fitting. These aptamers can be labelled with a fluorophore/metal nanoparticles easily for optical detection or may be employed for label-free electrochemical or cantilever based detection platforms for a wide range of target molecules or complex targets like cells and viruses.<ref>{{cite journal |last1=Sefah |first1=Kwame |title=Development of DNA aptamers using Cell-SELEX |url=https://www.nature.com/articles/nprot.2010.66 |doi=10.1038/nprot.2010.66 |volume=5 |year=2010 |journal=Nature Protocols |issue=6 |pages=1169–1185|pmid=20539292 |s2cid=4953042 |url-access=subscription }}</ref><ref>{{cite journal |title= Microtitre Plate Based Cell-SELEX Method|date=20 October 2018 |volume=8 |issue=20 |pages=e3051 |url=https://bio-protocol.org/e3051 |doi=10.21769/BioProtoc.3051|last1=Shorie |first1=Munish |last2=Kaur |first2=Harmanjit |journal=Bio-Protocol |pmid=34532522 |pmc=8342047 }}</ref> Additionally, aptamers can be combined with nucleic acid enzymes, such as RNA-cleaving DNAzymes, providing both target recognition and signal generation in a single molecule, which shows potential applications in the development of multiplex biosensors.<ref>{{cite journal |last1=Montserrat Pagès| first1=Aida | title=DNA-only bioassay for simultaneous detection of proteins and nucleic acids | journal=Analytical and Bioanalytical Chemistry | year=2021 | volume=413 | issue=20 | pages=4925–4937 | doi=10.1007/s00216-021-03458-6| pmid=34184101 | pmc=8238030 }}</ref>

===Epigenetics===
It has been proposed that properly optimized integrated optical resonators can be exploited for detecting epigenetic modifications (e.g. DNA methylation, histone post-translational modifications) in body fluids from patients affected by cancer or other diseases.<ref>{{cite journal | last1 = Donzella | first1 = V | last2 = Crea | first2 = F | date = June 2011 | title = Optical biosensors to analyze novel biomarkers in oncology | journal = J Biophotonics | volume = 4 | issue = 6| pages = 442–52 | doi = 10.1002/jbio.201000123 | pmid = 21567973 | s2cid = 5190250 }}</ref> Photonic biosensors with ultra-sensitivity are nowadays being developed at a research level to easily detect cancerous cells within the patient's urine.<ref>{{cite journal | last1 = Vollmer| first1 = F | last2 = Yang | first2 = Lang | date = October 2012 | title = Label-free detection with high-Q microcavities: a review of biosensing mechanisms for integrated devices | url = http://www.degruyter.com/dg/viewarticle.fullcontentlink:pdfeventlink/$002fj$002fnanoph.2012.1.issue-3-4$002fnanoph-2012-0021$002fnanoph-2012-0021.xml?t:ac=j$002fnanoph.2012.1.issue-3-4$002fnanoph-2012-0021$002fnanoph-2012-0021.xml | journal = Nanophotonics | volume = 1 | issue = 3–4| pages = 267–291 | doi = 10.1515/nanoph-2012-0021 | pmid = 26918228 |bibcode = 2012Nanop...1..267V | pmc = 4764104 }}</ref> Different research projects aim to develop new portable devices that use cheap, environmentally friendly, disposable cartridges that require only simple handling with no need of further processing, washing, or manipulation by expert technicians.<ref>{{cite web|url=http://www.glam-project.eu|title=Home - GLAM Project - Glass-Laser Multiplexed Biosensor|website=GLAM Project - Glass-Laser Multiplexed Biosensor}}</ref>

===Organelles===
Organelles form separate compartments inside cells and usually perform functions independently. Different kinds of organelles have various metabolic pathways and contain enzymes to fulfill its function. Commonly used organelles include lysosome, chloroplast and mitochondria. The spatial-temporal distribution pattern of calcium is closely related to ubiquitous signaling pathway. Mitochondria actively participate in the metabolism of calcium ions to control the function and also modulate the calcium related signaling pathways. Experiments have proved that mitochondria have the ability to respond to high calcium concentrations generated in their proximity by opening the calcium channels.<ref>{{Cite journal | last1 = Rizzuto | first1 = R. | last2 = Pinton | first2 = P. | last3 = Brini | first3 = M. | last4 = Chiesa | first4 = A. | last5 = Filippin | first5 = L. | last6 = Pozzan | first6 = T. | doi = 10.1054/ceca.1999.0076 | title = Mitochondria as biosensors of calcium microdomains | journal = Cell Calcium | volume = 26 | issue = 5 | pages = 193–199 | year = 1999 | pmid =  10643557}}</ref> In this way, mitochondria can be used to detect the calcium concentration in medium and the detection is very sensitive due to high spatial resolution. Another application of mitochondria is used for detection of water pollution. Detergent compounds' toxicity will damage the cell and subcellular structure including mitochondria. The detergents will cause a swelling effect which could be measured by an absorbance change. Experiment data shows the change rate is proportional to the detergent concentration, providing a high standard for detection accuracy.<ref>{{Cite journal | last1 = Bragadin | first1 = M. | last2 = Manente | first2 = S. | last3 = Piazza | first3 = R. | last4 = Scutari | first4 = G. | title = The Mitochondria as Biosensors for the Monitoring of Detergent Compounds in Solution | doi = 10.1006/abio.2001.5097 | journal = Analytical Biochemistry | volume = 292 | issue = 2 | pages = 305–307 | year = 2001 | pmid =  11355867| hdl = 10278/16452 | hdl-access = free }}</ref>

===Cells===
Cells are often used in bioreceptors because they are sensitive to surrounding environment and they can respond to all kinds of stimulants. Cells tend to attach to the surface so they can be easily immobilized. Compared to organelles they remain active for longer period and the reproducibility makes them reusable. They are commonly used to detect global parameter like stress condition, toxicity and organic derivatives. They can also be used to monitor the treatment effect of drugs. One application is to use cells to determine herbicides which are main aquatic contaminant.<ref>{{cite journal | last1 = Védrine | first1 = C. | last2 = Leclerc | first2 = J.-C. | last3 = Durrieu | first3 = C. | last4 = Tran-Minh | first4 = C. | year = 2003 | title = Optical whole-cell biosensor using Chlorella vulgaris designed for monitoring herbicides | journal = Biosensors & Bioelectronics | volume = 18 | issue = 4| pages = 457–63 | doi=10.1016/s0956-5663(02)00157-4| pmid = 12604263 | citeseerx = 10.1.1.1031.5904 }}</ref> Microalgae are entrapped on a quartz [[microfiber]] and the chlorophyll fluorescence modified by herbicides is collected at the tip of an optical fiber bundle and transmitted to a fluorimeter. The algae are continuously cultured to get optimized measurement. Results show that detection limit of certain herbicide can reach sub-ppb concentration level. Some cells can also be used to monitor the microbial corrosion.<ref>{{cite journal | last1 = Dubey | first1 = R. S. | last2 = Upadhyay | first2 = S. N. | year = 2001 | title = Microbial corrosion monitoring by an amperometric microbial biosensor developed using whole cell of Pseudomonas sp. | journal = Biosensors & Bioelectronics | volume = 16 | issue = 9–12| pages = 995–1000 | doi=10.1016/s0956-5663(01)00203-2| pmid = 11679280 }}</ref> Pseudomonas sp. is isolated from corroded material surface and immobilized on acetylcellulose membrane. The respiration activity is determined by measuring oxygen consumption. There is linear relationship between the current generated and the concentration of [[sulfuric acid]]. The response time is related to the loading of cells and surrounding environments and can be controlled to no more than 5min.

===Tissue===
Tissues are used for biosensor for the abundance of enzymes existing. Advantages of tissues as biosensors include the following:<ref name=planttissue>{{Cite journal | last1 = Campàs | first1 = M. | last2 = Carpentier | first2 = R. | last3 = Rouillon | first3 = R. | doi = 10.1016/j.biotechadv.2008.04.001 | title = Plant tissue-and photosynthesis-based biosensors | journal = Biotechnology Advances | volume = 26 | issue = 4 | pages = 370–378 | year = 2008 | pmid =  18495408| url = https://zenodo.org/record/896022 }}</ref>

* easier to immobilize compared to cells and organelles
* the higher activity and stability from maintaining enzymes in the natural environment
* the availability and low price
* the avoidance of tedious work of extraction, centrifuge, and purification of enzymes
* necessary cofactors for an enzyme to function exists
* the diversity providing a wide range of choices concerning different objectives.

There also exist some disadvantages of tissues, like the lack of specificity due to the interference of other enzymes and longer response time due to the transport barrier.

===Microbial biosensors===
Microbial biosensors exploit the response of bacteria to a given substance. For example, [[arsenic]] can be detected using the [[ars operon]] found in several bacterial taxon.<ref>{{cite journal|title=Construction and use of broad host range mercury and arsenite sensor plasmids in the soil bacterium ''Pseudomonas fluorescens'' OS8 |first1=T.|last1=Petänen|first2=M.|last2=Virta|first3=M.|last3=Karp|first4=M.|last4=Romantschuk|journal=Microbial Ecology|volume=41|issue=4|pages=360–368|doi=10.1007/s002480000095|pmid=12032610|year=2001 |bibcode=2001MicEc..41..360P |s2cid=21147572}}</ref>