Relevant bibliographies by topics / Degenerate Oligonucleotide Primed PCR

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  2. Dissertations / Theses
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Academic literature on the topic 'Degenerate Oligonucleotide Primed PCR'

Author: Grafiati
Published: 4 June 2021
Last updated: 12 February 2022

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Journal articles on the topic "Degenerate Oligonucleotide Primed PCR"

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Arneson, N., S. Hughes, R. Houlston, and S. Done. "Whole-Genome Amplification by Degenerate Oligonucleotide Primed PCR (DOP-PCR)." Cold Spring Harbor Protocols 2008, no. 2 (2008): pdb.prot4919. http://dx.doi.org/10.1101/pdb.prot4919.

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Telenius, Ha˚kan, Nigel P. Carter, Charlotte E. Bebb, Magnus Nordenskjo¨ld, Bruce A. J. Ponder, and Alan Tunnacliffe. "Degenerate oligonucleotide-primed PCR: General amplification of target DNA by a single degenerate primer." Genomics 13, no. 3 (1992): 718–25. http://dx.doi.org/10.1016/0888-7543(92)90147-k.

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Kiss, Csaba, Maria Kost-Alimova, George Klein, and Laszlo Szekely. "Optimisation of the degenerate oligonucleotide primed PCR (DOP-PCR) for capillary thermocycler." Biomolecular Engineering 19, no. 1 (2002): 31–34. http://dx.doi.org/10.1016/s1389-0344(02)00008-4.

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Janiak, Agnieszka, Moon Young Kim, Kyujung Van, and Suk-Ha Lee. "Application of degenerate oligonucleotide primed PCR (DOP-PCR) for SNP discovery in soybean." Euphytica 162, no. 2 (2007): 249–56. http://dx.doi.org/10.1007/s10681-007-9599-8.

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Rose, T. "CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer) PCR primer design." Nucleic Acids Research 31, no. 13 (2003): 3763–66. http://dx.doi.org/10.1093/nar/gkg524.

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He, Yu, Hongmei Li, Derek Brown, Franco Lamberti, and Maurice Moens. "Isolation and characterisation of microsatellites for Xiphinema index using degenerate oligonucleotide primed PCR." Nematology 5, no. 6 (2003): 809–19. http://dx.doi.org/10.1163/156854103773040718.

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Abstract A short insert genomic library for Xiphinema index, the natural vector of Grapevine Fanleaf Virus, was constructed from degenerate oligonucleotide primed PCR (DOP-PCR) products. The genomic library was screened for (CA)n microsatellites. Screening of 6200 colonies and comparison of the sequencing results revealed seven (CA)n containing microsatellites, coded here as XIMSL1, XIMSL2, XIMSL3, XIMSL4, XIMSL5, XIMSL6 and XIMSS1. XIMSL prefixed microsatellites were followed by the motif of the same long interspersed element. Microsatellite XIMSS1 has some similarity to the short interspersed element. Except for XIMSL1, all microsatellites were proven to be effective diagnostic tools at species level. Genetic diversity between and within populations was also evaluated for each microsatellite.
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Barbaux, Sandrine, Odette Poirier, and François Cambien. "Use of degenerate oligonucleotide primed PCR (DOP-PCR) for the genotyping of low-concentration DNA samples." Journal of Molecular Medicine 79, no. 5-6 (2001): 329–32. http://dx.doi.org/10.1007/s001090100214.

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Isagi, Y., M. Honjo, and I. Washitani. "Development of microsatellite markers for Primula sieboldii using degenerate oligonucleotide-primed PCR-amplified DNA." Molecular Ecology Notes 1, no. 1-2 (2001): 22–24. http://dx.doi.org/10.1046/j.1471-8278.2000.00009.x.

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Jamshidian-Mojaver, M., S.-E. Tabatabaeizadeh, M. Naeemipour, H. R. Farzin, and M. R. Bassami. "Use of degenerate oligonucleotide primed polymerase chain reaction for detection of chicken anaemia virus contamination in avian viral vaccines." BULGARIAN JOURNAL OF VETERINARY MEDICINE 23, no. 3 (2020): 304–9. http://dx.doi.org/10.15547/bjvm.2230.

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For quality control of biologicals of veterinary use, the absence of extraneous agents needs to be certified. One of the requirements for quality control of avian viral vaccines is to demonstrate freedom from extraneous and adventitious pathogenic agents, like chicken anaemia virus (CAV). In this study, a degenerate oligonucleotide primed PCR (DOP-PCR) for the detection of CAV was developed. Degenerate oligonucleotide primers were selected based on sequences corresponding to conserved regions of VP1 gene. After spiking of CAV genomic DNA to an infectious laryngotracheitis virus (ILTV) vaccine, detection limit for the test was 3.056×10-9 ng/µl. To evaluate the performance of the test, 11 avian viral vaccines including infectious bronchitis virus (IBV), newcastle disease virus (NDV), infectious bursal disease virus (IBDV) and ILTV vaccines from 5 manufacturers were screened for CAV and no contamination was detected. The test described here may provide a rapid, sensitive and specific method for contamination detection of avian viral vaccines with CAV, and may be applied for quality control of live and killed commercial vaccines.
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Larsen, Jacob, Anne Marie Ottesen, Maria Kirchhoff, Claes Lundsteen, and Jørgen K. Larsen. "High Resolution Comparative Genomic Hybridization Detects 7–8 Megabasepair Deletion in PCR Amplified DNA1." Analytical Cellular Pathology 23, no. 2 (2001): 61–64. http://dx.doi.org/10.1155/2001/301570.

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We investigated if any change in spatial resolution of comparative genomic hybridization analysis could be detected when using DNA amplified by degenerate oligonucleotide primed PCR (DOP‐PCR) as opposed to the use of unamplified DNA. Five DNA samples from B‐cell leukemias with small 11q deletions were amplified by DOP‐PCR and analysed by means of high resolution comparative genomic hybridization (HR‐CGH) for the evaluation of aberration size detection limit. By means of HR‐CGH, we found the detection limit of DOP‐PCR CGH for deletions to be between 3 Mbp and 7–8 Mbp.
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Dissertations / Theses on the topic "Degenerate Oligonucleotide Primed PCR"

1

Rodier, Denise N. "Degenerate Oligonucleotide Primed-PCR: Thermalcycling Modifications and Comparison Studies." VCU Scholars Compass, 2006. http://scholarscompass.vcu.edu/etd/1496.

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Degenerate Oligonucleotide Primed-PCR (DOP-PCR) can potentially enhance analysis of low copy number DNA samples. Theoretically, this procedure replicates fragments of the genome that can then be used for downstream multiplex STR analysis. The objective of this study is to optimize DOP-PCR by examining ramplelongation times and cycle numbers in the non-specific amplification portion of DOP-PCR, and by modifying the degenerate primer. Additionally, other methods such as Multiple Displacement Amplification (MDA) and Low Copy Number PCR (LCN PCR) were examined for their ability to create accurate DNA profiles from low DNA input amounts. Increasing the ramplelongation times showed no effect on downstream STR amplification success. An increase of cycle number increased DNA yield, but STR amplification success was undetermined. Although modifying the degenerate primer to one with a higher degeneracy decreased DNA yield, it ultimately improved STR amplification success. In comparison studies, LCN PCR produced higher STR amplification success than MDA.
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Freedman, Benjamin Gordon. "Degenerate oligonucleotide primed amplification of genomic DNA for combinatorial screening libraries and strain enrichment." Diss., Virginia Tech, 2014. http://hdl.handle.net/10919/71346.

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Combinatorial approaches in metabolic engineering can make use of randomized mutations and/or overexpression of randomized DNA fragments. When DNA fragments are obtained from a common genome or metagenome and packaged into the same expression vector, this is referred to as a DNA library. Generating quality DNA libraries that incorporate broad genetic diversity is challenging, despite the availability of published protocols. In response, a novel, efficient, and reproducible technique for creating DNA libraries was created in this research based on whole genome amplification using degenerate oligonucleotide primed PCR (DOP-PCR). The approach can produce DNA libraries from nanograms of a template genome or the metagenome of multiple microbial populations. The DOP-PCR primers contain random bases, and thermodynamics of hairpin formation was used to design primers capable of binding randomly to template DNA for amplification with minimal bias. Next-generation high-throughput sequencing was used to determine the design is capable of amplifying up to 98% of template genomic DNA and consistently out-performed other DOP-PCR primers. Application of these new DOP-PCR amplified DNA libraries was demonstrated in multiple strain enrichments to isolate genetic library fragments capable of (i) increasing tolerance of E. coli ER2256 to toxic levels of 1-butanol by doubling the growth rate of the culture, (ii) redirecting metabolism to ethanol and pyruvate production (over 250% increase in yield) in Clostridium cellulolyticum when consuming cellobiose, and (iii) enhancing L-arginine production when used in conjunction with a new synthetic gene circuit.<br>Ph. D.
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Thompson, Lindsay Paige. "Degenerate Oligonucleotide Primed - Polymerase Chain Reaction Evaluation And Optimization To Improve Downstream Forensic STR Analysis Of Low Quality/Low Quantity DNA." VCU Scholars Compass, 2006. http://scholarscompass.vcu.edu/etd/1299.

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When forensic biological samples yield low quality/low quantity DNA, thecurrent STR analysis methods do not generate acceptable profiles. Whole genomeamplification can be used to pre-amplify the entire genome for downstream analyses. A commercially available kit for DOP-PCR, a form of WGA, is currently being used in the clinical for downstream single locus targets. Forensic analyses utilize a multiplex amplification. This study determined that the "home brew" created by our lab performs the same as the commercially available kit. Future optimization studies of DOP-PCR can utilize this "home brew". Additionally, this research determined that a 10 second increase in electrokinetic injection time onto the Capillary Electrophoresis (CE) in combination with a post-STR amplification purification and elution into formamide produces a slightly higher percent STR allele success over the standard protocol. After future optimization studies, this may be a useful method to obtain more accurate and complete STR profiles from low quality/low quantity biological samples.
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Rodier, Denise Nicole. "Degenerate Oligonucleotide Primed--PCR : thermalcycling modifications and comparison studies /." 2006. http://hdl.handle.net/10156/2156.

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Thompson, Lindsay P. "Degenerate oligonucleotide primed - polymerase chain reaction evaluation and optimization to improve downstream forensic STR analysis of low quality/low quantity DNA /." 2006. http://hdl.handle.net/10156/1959.

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Book chapters on the topic "Degenerate Oligonucleotide Primed PCR"

1

Aubele, Michaela, and Jan Smida. "Degenerate Oligonucleotide-Primed PCR." In PCR Protocols. Humana Press, 2003. http://dx.doi.org/10.1007/978-1-4612-0055-0_45.

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Preston, Gregory M. "Cloning Gene Family Members Using PCR with Degenerate Oligonucleotide Primers." In PCR Protocols. Humana Press, 2003. http://dx.doi.org/10.1007/978-1-4612-0055-0_67.

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Graham, Anthony. "RT-PCR on Embryos Using Degenerate Oligonucleotide Primers." In METHODS IN MOLECULAR BIOLOGY™. Humana Press, 2008. http://dx.doi.org/10.1007/978-1-60327-483-8_43.

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De Bault, Lawrence E., and Bao-Le Wang. "Oligonucleotide-Primed In Situ Transcription and Immunogold-Silver Staining Systems: Localization of mRNA in Tissues and Cells." In In Situ PCR and Related Technology. Birkhäuser Boston, 1995. http://dx.doi.org/10.1007/978-1-4684-6843-4_6.

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Dalva, Klara, and Meral Beksac. "HLA Typing with Sequence-Specific Oligonucleotide Primed PCR (PCR-SSO) and Use of the Luminex™ Technology." In Methods in Molecular Biology. Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4614-9437-9_6.

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Dalva, Klara, and Meral Beksac. "HLA Typing with Sequence-Specific Oligonucleotide Primed PCR (PCR-SSO) and Use of the Luminex™ Technology." In Bone Marrow and Stem Cell Transplantation. Humana Press, 2007. http://dx.doi.org/10.1007/978-1-59745-223-6_5.

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"DOP-PCR (degenerate oligonucleotide-primed polymerase chain reaction)." In Encyclopedia of Genetics, Genomics, Proteomics and Informatics. Springer Netherlands, 2008. http://dx.doi.org/10.1007/978-1-4020-6754-9_4793.

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"PCR, DOC (degenerate oligonucleotide-primed polymerase chain reaction and capillary electrophoresis of DNA)." In Encyclopedia of Genetics, Genomics, Proteomics and Informatics. Springer Netherlands, 2008. http://dx.doi.org/10.1007/978-1-4020-6754-9_12439.

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"Degenerate oligonucleotide primed-polymerase chain reaction." In Springer Reference Medizin. Springer Berlin Heidelberg, 2019. http://dx.doi.org/10.1007/978-3-662-48986-4_310975.

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