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Journal articles on the topic 'PCR Design'

Author: Grafiati

Published: 4 June 2021

Last updated: 1 February 2022

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1

Apte, A., and S. Daniel. "PCR Primer Design." Cold Spring Harbor Protocols 2009, no. 3 (2009): pdb.ip65. http://dx.doi.org/10.1101/pdb.ip65.

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2

Nybo, Kristie. "DNA and General PCR Methods: PCR Primer Design." BioTechniques 46, no. 7 (2009): 505–7. http://dx.doi.org/10.2144/000113179.

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3

Wojdacz, Tomasz K., Tanni Borgbo, and Lise Lotte Hansen. "Primer design versus PCR bias in methylation independent PCR amplifications." Epigenetics 4, no. 4 (2009): 231–34. http://dx.doi.org/10.4161/epi.9020.

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4

Graf, D. "Rational primer design greatly improves differential display-PCR (DD- PCR)." Nucleic Acids Research 25, no. 11 (1997): 2239–40. http://dx.doi.org/10.1093/nar/25.11.2239.

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5

Hoegh, A. M., H. Westh, and G. Lisby. "Basics of diagnostic PCR assay design." Journal of Clinical Virology 36 (January 2006): S28—S29. http://dx.doi.org/10.1016/s1386-6532(06)80805-x.

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6

Dieffenbach, C. W., T. M. Lowe, and G. S. Dveksler. "General concepts for PCR primer design." Genome Research 3, no. 3 (1993): S30—S37. http://dx.doi.org/10.1101/gr.3.3.s30.

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7

Agee, Sara. "High-Multiplex Real-Time PCR Design." Genetic Engineering & Biotechnology News 36, no. 7 (2016): 20–21. http://dx.doi.org/10.1089/gen.36.07.12.

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8

Gahoi, Shachi, Arya L, Rai Anil, and Marla SS. "DPPrimer – A Degenerate PCR Primer Design Tool." Bioinformation 9, no. 18 (2013): 937–40. http://dx.doi.org/10.6026/97320630009937.

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9

Proudnikov, Dmitri, Vadim Yuferov, Yan Zhou, K. Steven LaForge, Ann Ho, and Mary Jeanne Kreek. "Optimizing primer–probe design for fluorescent PCR." Journal of Neuroscience Methods 123, no. 1 (2003): 31–45. http://dx.doi.org/10.1016/s0165-0270(02)00325-4.

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10

Rachlin, J., C. Ding, C. Cantor, and S. Kasif. "MuPlex: multi-objective multiplex PCR assay design." Nucleic Acids Research 33, Web Server (2005): W544—W547. http://dx.doi.org/10.1093/nar/gki377.

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11

Mann, Tobias, Richard Humbert, Michael Dorschner, John Stamatoyannopoulos, and William Stafford Noble. "A thermodynamic approach to PCR primer design." Nucleic Acids Research 37, no. 13 (2009): e95-e95. http://dx.doi.org/10.1093/nar/gkp443.

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12

San Millán, Rosario, Ilargi Martínez-Ballesteros, Aitor Rementeria, Javier Garaizar, and Joseba Bikandi. "Online exercise for the design and simulation of PCR and PCR-RFLP experiments." BMC Research Notes 6, no. 1 (2013): 513. http://dx.doi.org/10.1186/1756-0500-6-513.

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13

Lee, Wan Yeon, and Jong Dae Kim. "Design and Implementation of Firmware for Low-cost Small PCR Devices." Journal of the Korea Society of Computer and Information 18, no. 6 (2013): 1–8. http://dx.doi.org/10.9708/jksci.2013.18.6.001.

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14

Kamel, A. Abd-Elsalam. "Bioinformatic tools and guideline for PCR primer design." African Journal of Biotechnology 2, no. 5 (2003): 91–95. http://dx.doi.org/10.5897/ajb2003.000-1019.

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15

Davidović, Radoslav, Ana Božović, Vesna Mandušić, and Milena Krajnović. "Methylation-specific PCR: four steps in primer design." Open Life Sciences 9, no. 12 (2014): 1127–39. http://dx.doi.org/10.2478/s11535-014-0324-z.

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AbstractMethylation-specific PCR (MSP) is still the method of choice for a single gene methylation study. The proper design of the primer pairs is a prerequisite for obtaining reliable PCR results. Despite numerous protocols describing the rules for MSP primer design, none of them provide a comprehensive approach to the problem. Our aim was to depict a workflow for the primer design that is concise and easy to follow. In order to achieve this goal, adequate tools for promoter sequence retrieval, MSP primer design and subsequent in silico analysis are presented and discussed. Furthermore, a few instructive examples regarding a good versus a poor primer design are provided. Finally, primer design is demonstrated according to the proposed workflow. This article aims to provide researchers, interested in a single gene methylation studies, with useful information regarding successful primer design.

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16

Fernandes, R. J., and S. S. Skiena. "Microarray synthesis through multiple-use PCR primer design." Bioinformatics 18, Suppl 1 (2002): S128—S135. http://dx.doi.org/10.1093/bioinformatics/18.suppl_1.s128.

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17

Yao, F., R. Zhang, Z. Zhu, K. Xia, and C. Liu. "MutScreener: primer design tool for PCR-direct sequencing." Nucleic Acids Research 34, Web Server (2006): W660—W664. http://dx.doi.org/10.1093/nar/gkl168.

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18

Yang, Cheng-Hong, Yu-Huei Cheng, Li-Yeh Chuang, and Hsueh-Wei Chang. "Specific PCR product primer design using memetic algorithm." Biotechnology Progress 25, no. 3 (2009): 745–53. http://dx.doi.org/10.1002/btpr.169.

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19

Gorelenkov, V., A. Antipov, S. Lejnine, N. Daraselia, and A. Yuryev. "Set of Novel Tools for PCR Primer Design." BioTechniques 31, no. 6 (2001): 1326–30. http://dx.doi.org/10.2144/01316bc04.

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20

Boleda, M. D., P. Briones, J. Farrés, L. Tyfield, and R. Pi. "Experimental Design: A Useful Tool for PCR Optimization." BioTechniques 21, no. 1 (1996): 134–40. http://dx.doi.org/10.2144/96211rr05.

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21

Schilz, Felix, Susanne Hummel, and Bernd Herrmann. "Design of a multiplex PCR for genotyping 16 short tandem repeats in degraded DNA samples." Anthropologischer Anzeiger 62, no. 4 (2004): 369–78. http://dx.doi.org/10.1127/anthranz/62/2004/369.

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22

Xu, Jian Dong, Xue Fei Lv, Yun Liu, Xiao Qiong Li, and Yu Lin Deng. "Design of Integrated Control System for Microfluidic PCR Analysis Instrument." Applied Mechanics and Materials 241-244 (December 2012): 1491–95. http://dx.doi.org/10.4028/www.scientific.net/amm.241-244.1491.

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In this study, the design and development of an integrated control system for microfluidic PCR analysis instrument was presented. PID temperature control algorithm is used. The micro pumps, micro valves, and micro-mixers are command controlled by PC serial port to work together for samples and reagents driving. Sequential control strategy is introduced to control micro-pumps, micro valves, mixers, high-voltage module, and PCR reaction temperature. Labview as a software development platform is utilized to achieve human-computer exchange. All these designs are aimed to achieve the PCR reaction continuously on line from DNA extraction, purification, amplification to detection. An effective design idea for the coupling of complex microfluidic chip and instrument control was providing.

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23

Garafutdinov, R. R., An Kh Baymiev, G. V. Maleev, et al. "Diversity of PCR primers and principles of their design." Biomics 11, no. 1 (2019): 23–70. http://dx.doi.org/10.31301/2221-6197.bmcs.2019-04.

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24

Feldman, K. S., A. Foord, H. G. Heine, et al. "Design and evaluation of consensus PCR assays for henipaviruses." Journal of Virological Methods 161, no. 1 (2009): 52–57. http://dx.doi.org/10.1016/j.jviromet.2009.05.014.

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25

Kitchen, Robert R., Mikael Kubista, and Ales Tichopad. "Statistical aspects of quantitative real-time PCR experiment design." Methods 50, no. 4 (2010): 231–36. http://dx.doi.org/10.1016/j.ymeth.2010.01.025.

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26

Latorra, David, Khalil Arar, and J. Michael Hurley. "Design considerations and effects of LNA in PCR primers." Molecular and Cellular Probes 17, no. 5 (2003): 253–59. http://dx.doi.org/10.1016/s0890-8508(03)00062-8.

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27

Srivastava, G. P., M. Hanumappa, G. Kushwaha, H. T. Nguyen, and D. Xu. "Homolog-specific PCR primer design for profiling splice variants." Nucleic Acids Research 39, no. 10 (2011): e69-e69. http://dx.doi.org/10.1093/nar/gkr127.

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28

van der Ploeg, Claudia A., Ariel D. Rogé, Ximena L. Bordagorría, Maria T. de Urquiza, Ana B. Celi Castillo, and Susana B. Bruno. "Design of Two Multiplex PCR Assays for SerotypingShigella flexneri." Foodborne Pathogens and Disease 15, no. 1 (2018): 33–38. http://dx.doi.org/10.1089/fpd.2017.2328.

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29

Rieu, Ivo, and Stephen J. Powers. "Real-Time Quantitative RT-PCR: Design, Calculations, and Statistics." Plant Cell 21, no. 4 (2009): 1031–33. http://dx.doi.org/10.1105/tpc.109.066001.

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30

Fislage, R., M. Berceanu, Y. Humboldt, M. Wendt, and H. Oberender. "Primer design for a prokaryotic differential display RT-PCR." Nucleic Acids Research 25, no. 9 (1997): 1830–35. http://dx.doi.org/10.1093/nar/25.9.1830.

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31

Shen, Zhiyong, Wubin Qu, Wen Wang, et al. "MPprimer: a program for reliable multiplex PCR primer design." BMC Bioinformatics 11, no. 1 (2010): 143. http://dx.doi.org/10.1186/1471-2105-11-143.

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32

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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33

Lane, Courtney E., Daniel Hulgan, Kelly O’Quinn, and Michael G. Benton. "CEMAsuite: open source degenerate PCR primer design: Fig. 1." Bioinformatics 31, no. 22 (2015): 3688–90. http://dx.doi.org/10.1093/bioinformatics/btv420.

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34

Sharrocks, Andrew D., and Peter E. Shaw. "Improved primer design for PCR-based, site-directed mutagenesis." Nucleic Acids Research 20, no. 5 (1992): 1147. http://dx.doi.org/10.1093/nar/20.5.1147.

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35

Thomas, Susan, Ryan Luis Orozco, and Tim Ameel. "Thermal gradient continuous-flow PCR: a guide to design." Microfluidics and Nanofluidics 17, no. 6 (2014): 1039–51. http://dx.doi.org/10.1007/s10404-014-1401-3.

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36

Wu, Li-Cheng, Jorng-Tzong Horng, Hsi-Yuan Huang, Feng-Mao Lin, Hsien-Da Huang, and Meng-Feng Tsai. "Primer design for multiplex PCR using a genetic algorithm." Soft Computing 11, no. 9 (2006): 855–63. http://dx.doi.org/10.1007/s00500-006-0137-8.

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37

Martin, Gerald, and Robert J. Mairs. "Design of Clone-Specific Quantitation Standards for Competitive PCR." BioTechniques 21, no. 4 (1996): 594–602. http://dx.doi.org/10.2144/96214bm06.

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38

Tichopad, Ales, Rob Kitchen, Irmgard Riedmaier, Christiane Becker, Anders Ståhlberg, and Mikael Kubista. "Design and Optimization of Reverse-Transcription Quantitative PCR Experiments." Clinical Chemistry 55, no. 10 (2009): 1816–23. http://dx.doi.org/10.1373/clinchem.2009.126201.

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Abstract Background: Quantitative PCR (qPCR) is a valuable technique for accurately and reliably profiling and quantifying gene expression. Typically, samples obtained from the organism of study have to be processed via several preparative steps before qPCR. Method: We estimated the errors of sample withdrawal and extraction, reverse transcription (RT), and qPCR that are introduced into measurements of mRNA concentrations. We performed hierarchically arranged experiments with 3 animals, 3 samples, 3 RT reactions, and 3 qPCRs and quantified the expression of several genes in solid tissue, blood, cell culture, and single cells. Results: A nested ANOVA design was used to model the experiments, and relative and absolute errors were calculated with this model for each processing level in the hierarchical design. We found that intersubject differences became easily confounded by sample heterogeneity for single cells and solid tissue. In cell cultures and blood, the noise from the RT and qPCR steps contributed substantially to the overall error because the sampling noise was less pronounced. Conclusions: We recommend the use of sample replicates preferentially to any other replicates when working with solid tissue, cell cultures, and single cells, and we recommend the use of RT replicates when working with blood. We show how an optimal sampling plan can be calculated for a limited budget. .

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39

Robertson, Amber L., and Allison R. Phillips. "Integrating PCR Theory and Bioinformatics into a Research-oriented Primer Design Exercise." CBE—Life Sciences Education 7, no. 1 (2008): 89–95. http://dx.doi.org/10.1187/cbe.07-07-0051.

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Polymerase chain reaction (PCR) is a conceptually difficult technique that embodies many fundamental biological processes. Traditionally, students have struggled to analyze PCR results due to an incomplete understanding of the biological concepts (theory) of DNA replication and strand complementarity. Here we describe the design of a novel research-oriented exercise that prepares students to design DNA primers for PCR. Our exercise design includes broad and specific learning goals and assessments of student performance and perceptions. We developed this interactive Primer Design Exercise using the principles of scientific teaching to enhance student understanding of the theory behind PCR and provide practice in designing PCR primers to amplify DNA. In the end, the students were more poised to troubleshoot problems that arose in real experiments using PCR. In addition, students had the opportunity to utilize several bioinformatics tools to gain an increased understanding of primer quality, directionality, and specificity. In the course of this study many misconceptions about DNA replication during PCR and the need for primer specificity were identified and addressed. Students were receptive to the new materials and the majority achieved the learning goals.

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40

Wang, Li, Hui Xue Song, Tan Chen, and Zhan Hui Wang. "A Design of DSPIC Based Microfluidic PCR Chip Temperature Controlling System." Applied Mechanics and Materials 108 (October 2011): 206–11. http://dx.doi.org/10.4028/www.scientific.net/amm.108.206.

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In this paper a dsPIC microcontroller based temperature control system is developed for polymerase chain reaction (PCR) on-chip. PCR is one of the most important techniques in molecular biology and temperature control is the key technique of PCR. Yet, most of the works are based on PC, through an RS 232 interface to set and control the temperature. Here we design a temperature control system based on DSPIC Microcontroller. It can be much portable and cheaper than PC based systems. The system configuration mainly consists of a high precision, stable performance sensor PT1000, a signal amplification circuit, a PID algorithm. And then, we use MAX1978 to improve the accuracy of temperature control. After that we choose thermoelectric cooler (TEC) modules as actuator to improve system heating and cooling rate. It is believe that the portable PCR temperature control system will play an important role in the development of the Microfluidic PCR.

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41

Hui, Kwokyin, and Zhong-Ping Feng. "Efficient experimental design and analysis of real-time PCR assays." Channels 7, no. 3 (2013): 160–70. http://dx.doi.org/10.4161/chan.24024.

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42

Gervais, Alain L., Maud Marques, and Luc Gaudreau. "PCRTiler: automated design of tiled and specific PCR primer pairs." Nucleic Acids Research 38, suppl_2 (2010): W308—W312. http://dx.doi.org/10.1093/nar/gkq485.

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43

Collins, Andrew, and Xiayi Ke. "Primer1: Primer Design Web Service for Tetra-Primer ARMS-PCR." Open Bioinformatics Journal 6, no. 1 (2012): 55–58. http://dx.doi.org/10.2174/1875036201206010055.

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44

Thornton, Brenda, and Chhandak Basu. "Real-time PCR (qPCR) primer design using free online software." Biochemistry and Molecular Biology Education 39, no. 2 (2011): 145–54. http://dx.doi.org/10.1002/bmb.20461.

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45

van Seters, Janneke R., Joan Wellink, Johannes Tramper, Martin J. Goedhart, and Miriam A. Ossevoort. "A web-based adaptive tutor to teach PCR primer design." Biochemistry and Molecular Biology Education 40, no. 1 (2011): 8–13. http://dx.doi.org/10.1002/bmb.20563.

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46

GRYZINSKA, MAGDALENA, JACEK RECHULICZ, JUSTYNA BATKOWSKA, GRAZYNA JEZEWSKA-WITKOWSKA, and ANETA STRACHECKA. "Comparison of programs to design primers for Methylation-Specific PCR." Romanian Biotechnological Letters 24, no. 3 (2019): 479–84. http://dx.doi.org/10.25083/rbl/24.3/479.484.

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47

Dopazo, J., A. Rodriguez, J. C. Sáiz, and F. Sobrino. "Design of primers for PCR ampiification of highly variable genomes." Bioinformatics 9, no. 2 (1993): 123–25. http://dx.doi.org/10.1093/bioinformatics/9.2.123.

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48

McKay, S. J., and S. J. M. Jones. "AcePrimer: automation of PCR primer design based on gene structure." Bioinformatics 18, no. 11 (2002): 1538–39. http://dx.doi.org/10.1093/bioinformatics/18.11.1538.

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49

Hou, J. "Design of endonuclease restriction sites into primers for PCR cloning." Bioinformatics 18, no. 12 (2002): 1690–91. http://dx.doi.org/10.1093/bioinformatics/18.12.1690.

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50

Dinca, Mihai P., Marin Gheorghe, and Paul Galvin. "Design of a PID Controller for a PCR Micro Reactor." IEEE Transactions on Education 52, no. 1 (2009): 116–25. http://dx.doi.org/10.1109/te.2008.919811.

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