METHODS IN ENZYMOLOGY - PROTEIN - DNA INTERACTIONS
CHAPTER ONE EXPLANATORY CHAPTER: PCR PRIMER DESIGN 1 THEORY THERMODYNAMICS GENERAL GUIDELINES FOR PRIMER DESIGN MELTING TEMPERATURE (TM) AND GC CONTENT PRIMER LENGTH PRIMER SEQUENCE AND SECONDARY STRUCTURES PCR PRODUCT LENGTH AND PLACEMENT WITHIN THE TARGET SEQUENCE STEP-BY-STEP GUIDE FOR PRIMER DESIGN TROUBLESHOOTING AND GENERAL RULE SPECIFIC APPLICATIONS 110 TARGET CLONING 111 REVERSE-TRANSCRIPTION PCR (RT-PCR) 112 REAL-TIME PCR (QUANTITATIVE PCR, QPCR) 113 MULTIPLEX PCR 114 SEQUENCING 115 DEGENERATE PRIMERS 116 MODIFIED PRIMERS 117 RECOMBINEERING 118 PRIMERS FOR HOMOLOGOUS RECOMBINATION 119 SOFTWARE TOOLS LIST ACKNOWLEDGMENTS REFERENCES ABSTRACT THIS CHAPTER IS INTENDED AS A GUIDE ON POLYMERASE CHAIN REACTION (PCR) PRIMER DESIGN (FOR INFORMATION ON PCR, SEE GENERAL PCR AND EXPLANATORY CHAPTER: TROUBLESHOOTING PCR) IN THE NEXT SECTION, GENERAL GUIDELINES WILL BE PROVIDED, FOLLOWED BY A DISCUSSION ON PRIMER DESIGN FOR SPECIFIC APPLICATIONS A LIST OF RECOMMENDED SOFTWARE TOOLS IS SHOWN AT THE END