Humic substances cause fluorescence inhibition in real-time PCR.

Sidstedt, MajaLund University,Lunds universitet,Teknisk mikrobiologi,Centrum för tillämpade biovetenskaper,Kemiska institutionen,Institutioner vid LTH,Lunds Tekniska Högskola,Applied Microbiology,Center for Applied Life Sciences,Department of Chemistry,Departments at LTH,Faculty of Engineering, LTH,Swedish National Forensic Center (författare)

Real-time PCR (qPCR) is the cornerstone of DNA analysis, enabling detection and quantification of minute nucleic acid amounts. However, PCR-based analysis is limited, in part, by the presence of inhibitors in the samples. PCR inhibition has been viewed solely as failure to efficiently generate amplicons, i.e. amplification inhibition. Humic substances (HS) are well known inhibitors of PCR amplification. Here we show that HS from environmental samples, specifically humic acid (HA), are very potent detection inhibitors, i.e. quench the fluorescence signal of dsDNA binding dyes. HA quenched the fluorescence of the commonly used qPCR dyes EvaGreen, ResoLight, SYBR Green I and SYTO 82, generating lowered amplification plots although amplicon production was unaffected. For EvaGreen, 500 ng HA quenched almost all fluorescence, whereas 1000 ng HA completely inhibited amplification when applying Immolase DNA polymerase with BSA. Fluorescence spectroscopy measurements showed that HA quenching was either static or collisional, and indicated that HA bound directly to the dye. Fulvic acid did not act as a qPCR detection inhibitor, but inhibited amplification similarly to HA. Hydrolysis probe fluorescence was not quenched by HA. Detection inhibition is an overlooked phenomenon that needs to be considered to allow for development of optimal qPCR assays.

Jansson, LindaLund University,Lunds universitet,Teknisk mikrobiologi,Centrum för tillämpade biovetenskaper,Kemiska institutionen,Institutioner vid LTH,Lunds Tekniska Högskola,Applied Microbiology,Center for Applied Life Sciences,Department of Chemistry,Departments at LTH,Faculty of Engineering, LTH(Swepub:lu)mpu-lja (författare)
Nilsson, Elin (författare)
Noppa, Laila (författare)
Forsman, Mats (författare)
Rådström, PeterLund University,Lunds universitet,Teknisk mikrobiologi,Centrum för tillämpade biovetenskaper,Kemiska institutionen,Institutioner vid LTH,Lunds Tekniska Högskola,Applied Microbiology,Center for Applied Life Sciences,Department of Chemistry,Departments at LTH,Faculty of Engineering, LTH(Swepub:lu)tmb-pra (författare)
Hedman, JohannesLund University,Lunds universitet,Teknisk mikrobiologi,Centrum för tillämpade biovetenskaper,Kemiska institutionen,Institutioner vid LTH,Lunds Tekniska Högskola,Applied Microbiology,Center for Applied Life Sciences,Department of Chemistry,Departments at LTH,Faculty of Engineering, LTH,Swedish National Forensic Center(Swepub:lu)tmb-jeh (författare)
Teknisk mikrobiologiCentrum för tillämpade biovetenskaper (creator_code:org_t)

Av författaren/redakt...: Sidstedt, Maja; Jansson, Linda; Nilsson, Elin; Noppa, Laila; Forsman, Mats; Rådström, Peter; visa fler...; Hedman, Johannes; visa färre...

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