Menu
Home
People
Places
Arts
History
Plants & Animals
Science
Life & Culture
Technology
Reference.org
Hybridization probe
open-in-new
<h2 id="examples-of-probes">Examples of probes</h2> <ul><li>Scorpion® probes</li> <li><a href="/facts/Molecular_beacon/InEra73Y">Molecular Beacon</a> probes</li> <li><a href="/facts/TaqMan/VeWurWzx">TaqMan</a>® probes</li> <li>LNA® (<a href="/facts/Locked_nucleic_acid/2BPGJG8Q">Locked Nucleic Acid</a>) probes</li> <li><a href="/facts/Cycling_probe_technology/NM4xLT0e">Cycling Probe Technology</a> (CPT)</li> <li><a href="/facts/In_situ_hybridization/RFKJedCS"><i>In situ</i> hybridization</a></li> <li>Binary (split) probes</li> <li>Multicomponent probes</li></ul> <h2 id="uses-in-microbial-ecology">Uses in microbial ecology</h2> <p>Within the field of <a href="/facts/Microbial_ecology/LYtxfSaC">microbial ecology</a>, oligonucleotide probes are used in order to determine the presence of microbial species, genera, or microorganisms classified on a more broad level, such as <a href="/facts/Bacteria/wC8xSCsU">bacteria</a>, <a href="/facts/Archaea/Adxh0aHw">archaea</a>, and <a href="/facts/Eukaryotes/SkwyPLMA">eukaryotes</a> via <a href="/facts/Fluorescence_in_situ_hybridization/L4juqPoq">fluorescence in situ hybridization</a> (FISH).<a class="footnote-ref" id="fnref:2" href="#fn:2"><sup>2</sup></a> rRNA probes have enabled scientists to visualize microorganisms, yet to be cultured in laboratory settings, by retrieval of rRNA sequences directly from the environment.<a class="footnote-ref" id="fnref:3" href="#fn:3"><sup>3</sup></a> Examples of these types of microorganisms include: </p> <ul><li><i><a href="/facts/Nevskia_ramosa/cQBdM3IQ">Nevskia ramosa</a></i>: <i>N. ramosa</i> is a neuston bacterium that forms typical, dichotomically-branching rosettes on the surface of shallow freshwater habitats.<a class="footnote-ref" id="fnref:4" href="#fn:4"><sup>4</sup></a></li> <li><i>Achromatium oxaliferum</i>: This huge bacterium (cell length up to >100 μm, diameter up to 50 μm) contains sulfur globules and massive calcite inclusions and inhabits the upper layers of freshwater sediments. It is visible to the naked eye and has, by its resistance to cultivation, puzzled generations of microbiologists.<a class="footnote-ref" id="fnref:5" href="#fn:5"><sup>5</sup></a></li></ul> <h3>Limitations</h3> <p>In some instances, differentiation between species may be problematic when using <a href="/facts/16S_ribosomal_RNA/XCgSahoy">16S rRNA</a> sequences due to similarity. In such instances, 23S rRNA may be a better alternative.<a class="footnote-ref" id="fnref:6" href="#fn:6"><sup>6</sup></a> The global standard library of rRNA sequences is constantly becoming larger and continuously being updated, and thus the possibility of a random hybridization event between a specifically-designed probe (based on complete and current data from a range of test organisms) and an undesired/unknown target organism cannot be easily dismissed.<a class="footnote-ref" id="fnref:7" href="#fn:7"><sup>7</sup></a> On the contrary, it is plausible that there exist microorganisms, yet to be identified, which are phylogenetically members of a probe target group, but have partial or near-perfect target sites, usually applies when designing group-specific probes. </p><p>Probably the greatest practical limitation to this technique is the lack of available automation.<a class="footnote-ref" id="fnref:8" href="#fn:8"><sup>8</sup></a> </p> <h2 id="use-in-forensic-science">Use in forensic science</h2> <p>In forensic science, hybridization probes are used, for example, for detection of short tandem repeats (<a href="/facts/Microsatellite_(genetics)/SwfHbeXG">microsatellite</a>) regions<a class="footnote-ref" id="fnref:9" href="#fn:9"><sup>9</sup></a> and in restriction fragment length polymorphism (<a href="/facts/RFLP/tJutAmFv">RFLP</a>) methods, all of which are widely used as part of <a href="/facts/DNA_profiling/NhYPDDH4">DNA profiling</a> analysis. </p> <h2 id="see-also">See also</h2> <ul><li><a href="/facts/Molecular_probe/YnSfHQdh">Molecular probe</a></li></ul> <h2 id="references">References</h2> <ol> <li id="fn:1"><p>"Nucleic Acid Hybridizations". www.ndsu.edu. Retrieved 2017-05-26. <a href="https://www.ndsu.edu/pubweb/~mcclean/plsc731/dna/dna6.htm" target="_blank">https://www.ndsu.edu/pubweb/~mcclean/plsc731/dna/dna6.htm</a> <a href="#fnref:1" class="footnote-back-ref">↩</a></p></li> <li id="fn:2"><p>Amann R, Ludwig W (2000). "Ribosomal RNA-targeted nucleic acid probes for studies in microbial ecology". FEMS Microbiology Reviews. 24 (5): 555–565. doi:10.1111/j.1574-6976.2000.tb00557.x. PMID 11077149. <a href="https://doi.org/10.1111%2Fj.1574-6976.2000.tb00557.x" target="_blank">https://doi.org/10.1111%2Fj.1574-6976.2000.tb00557.x</a> <a href="#fnref:2" class="footnote-back-ref">↩</a></p></li> <li id="fn:3"><p>Amann, R.; Ludwig, W.; Schleifer, K.-H. (1995). "Phylogenetic identification and in situ detection of individual microbial cells without cultivation". Microbiological Reviews. 59 (1): 143–169. doi:10.1128/MMBR.59.1.143-169.1995. PMC 239358. PMID 7535888. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC239358" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC239358</a> <a href="#fnref:3" class="footnote-back-ref">↩</a></p></li> <li id="fn:4"><p>Glöckner, F.O.; Babenzien H.D.; Amann R. (1998). "Phylogeny and identification in situ of Nevskia ramosa". Appl. Environ. Microbiol. 64 (5): 1895–1901. Bibcode:1998ApEnM..64.1895G. doi:10.1128/AEM.64.5.1895-1901.1998. PMC 106248. PMID 9572969. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC106248" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC106248</a> <a href="#fnref:4" class="footnote-back-ref">↩</a></p></li> <li id="fn:5"><p>Glöckner, F.O.; Babenzien H.D.; Amann R. (1999). "Phylogeny and diversity of Achromatium oxaliferum". Syst. Appl. Microbiol. 22 (1): 28–38. doi:10.1016/s0723-2020(99)80025-3. PMID 10188276. <a href="/wiki/Doi_(identifier)" target="_blank">/wiki/Doi_(identifier)</a> <a href="#fnref:5" class="footnote-back-ref">↩</a></p></li> <li id="fn:6"><p>Fox, G.E.; Wisotzkey, J.D.; Jurtshuk Jr., P. (1992). "How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity". Int. J. Syst. Bacteriol. 42 (1): 166–170. doi:10.1099/00207713-42-1-166. PMID 1371061. <a href="https://doi.org/10.1099%2F00207713-42-1-166" target="_blank">https://doi.org/10.1099%2F00207713-42-1-166</a> <a href="#fnref:6" class="footnote-back-ref">↩</a></p></li> <li id="fn:7"><p>Olsen, G.J.; Lane, D.J.; Giovannoni, S.J.; Pace, N.R.; Stahl, D.A. (1986). "Microbial ecology and evolution: a ribosomal RNA approach". Annu. Rev. Microbiol. 40: 337–365. doi:10.1146/annurev.mi.40.100186.002005. PMID 2430518. <a href="/wiki/Doi_(identifier)" target="_blank">/wiki/Doi_(identifier)</a> <a href="#fnref:7" class="footnote-back-ref">↩</a></p></li> <li id="fn:8"><p>Amann R, Ludwig W (2000). "Ribosomal RNA-targeted nucleic acid probes for studies in microbial ecology". FEMS Microbiology Reviews. 24 (5): 555–565. doi:10.1111/j.1574-6976.2000.tb00557.x. PMID 11077149. <a href="https://doi.org/10.1111%2Fj.1574-6976.2000.tb00557.x" target="_blank">https://doi.org/10.1111%2Fj.1574-6976.2000.tb00557.x</a> <a href="#fnref:8" class="footnote-back-ref">↩</a></p></li> <li id="fn:9"><p>Tytgat, Olivier (2021). "STRide probes: Single-labeled short tandem repeat identification probes" (PDF). Biosensors and Bioelectronics. 180: 113135. doi:10.1016/j.bios.2021.113135. PMID 33690100. <a href="https://biblio.ugent.be/publication/8717666/file/8717669.pdf" target="_blank">https://biblio.ugent.be/publication/8717666/file/8717669.pdf</a> <a href="#fnref:9" class="footnote-back-ref">↩</a></p></li> </ol>