Volume 79, Issue 6
  • ISSN: 0002-9637
  • E-ISSN: 1476-1645


Although SYBR Green is used to estimate copy number, its fluorescence varies with amplicon length and adenine/thymine (AT) content. As a result, threshold cycle (C) values obtained using real-time polymerase chain reaction (PCR) are lower for longer amplicons ( < 0.001) and amplicons with greater AT content ( < 0.001). In contrast, neither amplicon length nor AT content affects the C with TaqMan probes or LUX-labeled primers. Because SYBR Green yields lower Cs with AT-rich templates and longer templates, it overestimates copy number for those templates. Therefore, sequence-specific methods such as TaqMan probes or LUX-labeled primers should be considered when using real-time PCR to estimate copy number if the amplicons generated are AT-rich or vary in length.


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  • Received : 27 Feb 2008
  • Accepted : 26 Aug 2008

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