PCR Primer Design

This third edition provides new and updated chapters on design PCR primers for successful DNA amplification. Chapters are divided into seven parts, including primer design strategies for quantitative PCR, genotyping, multiplex PCR, in silico PCR primer design, and primer design to identify plant and animal viruses. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Authoritative and easily accessible, PCR Primer Design, Third Edition aims to be useful for various fields of molecular biology, including biotechnology, molecular genetics, and recombinant DNA technology.

SECTION I. Primer design for genotyping

M. Delghandi, M.P. Delghandi, S. Goddard

2.              Enhancing cohort PASA efficiency from lessons assimilated by mutant genotyping in C. elegans. 

Amita Pandey, Binu Bhat, Madan L. Aggarwal,  Girdhar K. Pandey 

3.              Design of oligonucleotides for allele-specific amplification based on PCR and isothermal techniques

4.              Detection of rubella virus by tri-primer RT-PCR assay and genotyping by fragment RT-PCR.

Suji George 

5.              Design of mismatch primers to identify and differentiate closely related (sub)species – application to the authentication of meat products

Maria Kaltenbrunner, Rupert Hochegger, Margit Cichna-Markl

6.              Primer design for the analysis of closely related species – application of non-coding mtDNA and cpDNA sequences 

7.              Designing PCR primers for the amplification-refractory mutation system 

Majid Komijani, Khashayar Shahin,  Esam Ibraheem Azhar, Mohammad Bahram

SECTION II. Primer design for genome-wide identification of specific regions 

8.              Validation of circular RNAs by PCR

Aniruddha Das, Debojyoti Das, and Amaresh C. Panda

9.               Primer Designing for Amplifying an AT-Rich Promoter from Arabidopsis thaliana

SECTION III. Primer design for multiplex PCR. Multiplex 

10.           PLASmid TAXonomic PCR (PlasTax-PCR), a multiplex relaxase MOB typing to assort plasmids into taxonomic units

Raquel Cuartas, Teresa M. Coque, Fernando de la Cruz, M. Pilar Garcillán-Barcia

11.           Multiplex PCR Design for Scalable Resequencing

Darren Korbie, Matt Trau

SECTION IV. Primer design for qPCR

12.           Identification of gene copy number in the transgenic plants by quantitative polymerase chain reaction (qPCR)

Poonam Kanwar, Soma Ghosh, Sibaji K. Sanyal, Girdhar K. Pandey

13.            qPrimerDB: A powerful and user-friendly database for qPCR primer design

Wei Chang, Yue Niu, Mengna Yu, Tian Li, Jiana Li, Kun Lu

14.           PCR primer design for the rapidly evolving SARS-CoV-2 genome

Jiangyu Li, Dongsheng Zhao, Haoyang Cai and Wubin Qu

15.           Universal primers for detection of novel plant capsid-less viruses: Papaya umbra-like viruses as example

Jorge H. Ramirez-Prado and Luisa A. Lopez-Ochoa

SECTION VI. Use of software for primer design

16.           A guide to using FASTPCR software for PCR, in silico PCR, and oligonucleotide analysis

Ruslan Kalendar

SECTION VII. Primer design for newer PCR approaches

17.           Pyrosequencing Primer Design for Forensic Biology Applications

Kelly M. Elkins 

18.           Phosphate methylated oligonucleotides as a novel primer for PCR and RT-PCR

Yu-Hsuan Chang, Meng-Wei Wu, Yi-Ju Chen, Cao-An Vu, Ching-Ya Hong, Wen-Yih Chen