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Amplification products contamination has been the main impediment to using these techniques routinely in diagnostic laboratories. Over the years, several creative pre- and post-amplification methods have been developed that prevent amplicon carryover contamination. These procedures, coupled with automated systems that employ real-time amplification and simultaneous detection in a closed system, have substantially reduced the possibility of false positive results due to amplification products carryover contamination.
The ability to amplify specific regions of microbial DNA or RNA by various amplification techniques has provided rapid and sensitive detection of infectious pathogens [ 1 ]. Amplification-based techniques are now used routinely in clinical laboratories to detect organisms that do not grow in conventional culture media. The techniques facilitate the study of epidemics and the detection of mutations associated with drug resistance in viral, bacterial, and fungal agents [ 2 ].
Unfortunately, the exquisite sensitivity of these techniques makes them vulnerable to contamination [ 3 — 8 ]. At least 2 documented cases of Lyme disease, one with fatal outcome, have been attributed to false-positive PCR findings [ 910 ]. Similarly, formal retraction of published manuscripts has occurred as a result of false-positive PCR reactions [ 6 ]. Potential sources of contamination include a the large numbers of target organisms in clinical specimens that may result in cross-contamination, b plasmid clones derived from organisms that have been previously analyzed and that may be present in large numbers in the laboratory environment [ 11 ], and c most importantly, repeated amplification of the same target sequence, which leads to accumulation of amplification products in the laboratory environment [ 26 ].
A typical PCR generates as many as 10 9 copies of target sequence and if aerosolized, even the smallest aerosol will contain as many as 10 6 amplification products [ 6 ]. If uncontrolled, within a relatively short time the buildup of aerosolized amplification products will contaminate laboratory reagents, equipment, and ventilation systems [ 6 ]. Several pre- and post-amplification amplicon sterilization techniques have been proposed in order to prevent contamination from impeding the routine use of these techniques in clinical laboratories [ 212 — 19 ].
The objectives of these measures are, first, to prevent amplicon carryover contamination of reaction tubes with previously generated amplicons and, second, to sterilize all the generated amplicons so that false cause and effect what does it mean if they contaminate a reaction tube they are either ineligible targets for amplification or are destroyed prior to the next amplification reaction. Mechanical and chemical barriers both help to prevent amplification products carryover contamination.
These barriers must be in place prior to the initiation of any amplification studies. While they are inadequate, per se, to control amplification carryover contamination, their judicious use complements additional pre- or post-amplification products sterilization protocols. Mechanical barriers to prevent amplification products carryover include the strict separation of areas of the laboratory where samples and reagents are prepared from the areas where amplification is performed and amplification products are analyzed.
All traffic must be unidirectional from the reagent preparation area to the sample preparation area, to the amplification area, and to the detection area. These sites optimally are physically separated and are preferably at a substantial distance from each other. Each area must be equipped with the necessary instruments, disposable devices, laboratory coats, gloves, aerosol-free pipettes, and ventilation systems.
All reagents and disposables used in each area must be delivered directly to that area. The technologists must be alert to the possibility of transferring amplification products on their hair, glasses, jewelry, and clothing from contaminated rooms to clean rooms. Bleach causes oxidative damage to nucleic acid and prevents it from being reamplified in subsequent PCR reactions [ 20 ].
Because bleach does not discriminate between the extracted target DNA and PCR amplicons, specimens treated with bleach are not proper targets for amplification studies. Several creative methods to prevent amplification products carryover contamination have been developed [ 212 — 19 ]. While most of these techniques are optimized for use with PCR, they may also be useful for sterilizing the products of other amplification techniques.
Generally, most PCR-based diagnostic assays consist of 3 steps: sample processing, PCR amplification, and amplification products detection. Two criteria must be met by amplification products control procedures to ensure that subsequent diagnostic assays are not compromised by a carryover event [ 2621 ]. The first is that the reaction products are not exposed to the environment until they are modified in a specific manner that distinguishes them from true sequences false cause and effect what does it mean subsequent amplification.
This requires that the distinguishing modification occur before the reaction tube is opened for the detection phase of the diagnostic assay. Second, the modification s must not interfere with the detection steps. Both pre- and post-amplification sterilization should be used. Pre-amplification sterilization techniques assume that it is possible for amplification products from previous amplifications to contaminate a new PCR mix, but provide an effective remedy to eliminate the contaminants prior to the start of the next round of amplification [ 2621 ].
Post-PCR sterilization relies on modification of the amplified products prior to exposing them to the laboratory environment. Since the modified amplification products are unsuitable as PCR targets is taking space healthy in a relationship subsequent amplification reactions, they do not cause false-positive reactions.
UV light was the first sterilization technique used to eliminate amplification products carryover contamination [ 78 ]. The technique is based on the property of UV light to induce thymidine dimers and pyramidal composition art history definition covalent modifications of DNA what is the cost function of linear regression render the contaminating nucleic acid inactive as a template for further amplification.
Briefly, a reaction tube containing all the amplification reagents except the target is exposed to UV light combination of and nm for 5 to 20 min, followed by the addition of target DNA [ 22 ]. The UV irradiation of the reaction tube sterilizes the potential contaminants in the reaction tube and prevents their subsequent amplification. The technique has been reported to yield varying degrees of success in several publications [ 23 — 25 ].
In addition, the efficacy of UV irradiation depends on the distance of the nucleic acids from the light source [ 2 ]. Nucleotides present in the PCR reaction mix may protect contaminating amplification products from the UV irradiation [ 26 ]. UV irradiation may have deleterious effects on the enzyme Taq polymerase and oligonucleotide primers [ 2127 ]. After the packages have been opened, all pipettes and other disposable devices should be stored in a UV light box. Preparation of the amplification master mix and specimen processing should also be carried out in a UV light box.
The main function of this enzyme is to recognize and remove uracil residues that are generated by spontaneous deamination of cytosine residues in double-stranded DNA as a component of excision-repair processes [ 2829 ]. The technique was subsequently evaluated by several investigators [ 30 — 32 ] and UNG is now the most widely used contamination control technique. The addition of this the red means i love you flute sheet music to the amplification mix allows selective hydrolysis and removal of the contaminating amplification products from the PCR mix.
The enzyme is most active at room temperature. Therefore, following inoculation of the reaction tube with target specimens, amplification tubes are incubated at room temperature for 10 min. During this time, the UNG hydrolyzes and removes any contaminating amplification products that may be present in the PCR reaction tube. In addition, any product generated by Taq polymerase by non-specific binding of the primers to the target DNA at this reduced temperature is hydrolyzed.
Under certain circumstances, UNG may not be completely inactivated and the residual enzymatic activity may be enough to degrade amplification products generated during the early amplification cycles [ 33 ]. To achieve optimum sterilization activity, UNG and dUTP concentrations must be optimized individually for each amplification reaction.
Furocoumarin compounds such as psoralen and isopsoralen represent a class of planar tricyclic reagent that is known to intercalate between base pairs of nucleic acids [ 36 ]. These compounds contain 2 reactive double bonds that, when excited by UV irradiation — nmcovalently bind to nucleic what is bad about love bombing polymers by forming cyclobutane adducts with pyrimidine what are compositions in art [ 36 ].
The mechanism of the amplification products sterilization protocol is based on the blockage of Taq polymerase-mediated primer extension reaction when the enzyme encounters a photochemically modified base in a target sequence [ 63738 ]. Therefore, psoralen modified amplification products, if carried over to new reaction tubes, cannot serve as targets in subsequent amplification reactions.
Although psoralen and isopsoralen compounds are both capable of sterilizing amplification products, the psoralen compounds form cross-links between the complementary strands of DNA and therefore the amplification products may not be false cause and effect what does it mean using common hybridization protocols [ 39 ]. In contrast, isopsoralen does not cross-link the complementary strands and the modified DNA is easily detected using common amplification products detection protocols.
In Cimino et al [ 37 ] explored the possibility of using the unique chemical property of these compounds to control amplification products carryover contamination. They added these compounds to the PCR reaction mix that amplified either a mer sequence unique to HIV-1 or a mer sequence unique to bacteriphage lambda [ 3740 ]. Following amplification, isopsoralen was activated by irradiating the reaction tubes with UV light for 15 min.
Then a known concentration of false cause and effect what does it mean isopsoralen modified amplification products was reamplified in subsequent PCR reactions. Isopsoralen did not appear to have an inhibitory effect on PCR and successfully sterilized up to 10 4 of mer HIV specific amplification products and 10 8 of mer bacteriophage-specific amplification products. They concluded that the level of sterilization depended on the length and sequence of the amplification products [ 37 false cause and effect what does it mean, 40 ].
The sterilization efficiency improved with increasing isoposralen concentration [ 41 ]. The inhibitory effects of psoralen may persist in some PCR reactions, even in the presence of glycerol. It is recommended that the psoralen concentrations be optimized for each primer and PCR assay. In one study, an inhibitory concentration of IP was successfully utilized to sterilize amplification products by addition of this compound to the reaction tubes after completion of PCR reactions [ 42 ]. PCR was performed without IP; the compound was added to the tube after completion of PCR and activated to sterilize all the amplification products.
The tubes were placed at room temperature for a few min to allow the Ampliwax to solidify. The solidified wax formed a barrier between the PCR products and the laboratory environment. The tubes were then opened without aerosolizing the amplification products and the desired concentration of IP was layered on top of the wax. Finally, the tube was exposed to UV light for 15 min to sterilize the amplification products.
While this modification requires post-amplification addition of IP to the reaction mix, the modification virtually eliminates the inhibitory effects of IP on PCR. These compounds are carcinogenic and must be used with care [ 36 ]. The generated amplification products containing ribose residue s are susceptible to alkaline hydrolysis at the site of the ribose molecule s.
PCR products are usually exposed to 1M NaOH and incubated for 30 min to hydrolyze the amplification products at the site s of ribose. Once the amplification products have been hydrolyzed, the truncated amplicons lack the primer binding sites. Even if they are aerosolized and introduced into the subsequent amplification reaction mix, they will not be recognized as targets during the next amplification cycles.
Opening of the tubes at the time that NaOH is false cause and effect what does it mean, however, may provide an opportunity for contamination by the aerosolized amplification products. The sterilization efficiency of this protocol may range from 10 4 to 10 9 amplification products [ 32 ]. The compound preferentially reacts with the oxygen atoms of the cytosine residue [ 4344 ] and creates covalent adducts that prevent base-pairing with guanine residues in subsequent reactions.
Thus, modified amplification products are how to interpret scatter plot in excel recognized as amplification targets in subsequent PCR reactions. Hydroxylamine binds to these products in a dose-dependent manner as determined by their migration in agarose gel. The compound, must be added to the reaction tubes following the amplification, which may result in amplification products aerosolization.
Therefore, the implementation of one or more of these methods does not replace good laboratory practice. In fact, the sterilizing limit of these techniques may be saturated with few uncontrolled PCR assays. Espy et al [ 30 ] compared the efficacy of UNG and IP to sterilize amplification products generated from human herpes simplex virus, cytomegalovirus, Epstein-Barre virus false cause and effect what does it mean human papilomavirus Both techniques effectively controlled amplification products that were bp in length.
Comparison of amplification products sterilization techniques to control PCR carryover contamination. Rys and colleagues [ 32 ] compared UNG, isopsoralen, and primer hydrolysis to sterilize bp amplification products unique to the B. The 3 protocols were equally reliable in controlling amplification carry-over contamination.
IP and UNG consistently sterilized as many as 10 9 amplification products. The sterilization efficiency of this technique ranged from 10 4 to 10 9 amplification products. The authors recommend the use of a combined approach to control PCR carry-over contamination. This approach allows them to use isopsoralen as the first-line control measure.
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