title: Humic substances cause fluorescence inhibition in real-time polymerase chain reaction.
abstract: Real-time polymerase chain reaction (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, that is, 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, that is, quench the fluorescence signal of double-stranded DNA (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 of HA quenched nearly all fluorescence, whereas 1000 ng of HA completely inhibited amplification when applying Immolase DNA polymerase with bovine serum albumin (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.
authors.affiliation: Applied Microbiology, Department of Chemistry, Lund University, SE-221 00 Lund, Sweden; National Forensic Centre, SE-581 94 Linköping, Sweden.
authors.forename: Maja
authors.initials: M
authors.lastname: Sidstedt
authors.affiliation: Applied Microbiology, Department of Chemistry, Lund University, SE-221 00 Lund, Sweden.
authors.forename: Linda
authors.initials: L
authors.lastname: Jansson
authors.affiliation: CBRN Defence and Security, Swedish Defence Research Agency, SE-901 82 Umeå, Sweden.
authors.forename: Elin
authors.initials: E
authors.lastname: Nilsson
authors.affiliation: CBRN Defence and Security, Swedish Defence Research Agency, SE-901 82 Umeå, Sweden.
authors.forename: Laila
authors.initials: L
authors.lastname: Noppa
authors.affiliation: CBRN Defence and Security, Swedish Defence Research Agency, SE-901 82 Umeå, Sweden.
authors.forename: Mats
authors.initials: M
authors.lastname: Forsman
authors.affiliation: Applied Microbiology, Department of Chemistry, Lund University, SE-221 00 Lund, Sweden.
authors.forename: Peter
authors.initials: P
authors.lastname: Rådström
authors.affiliation: Applied Microbiology, Department of Chemistry, Lund University, SE-221 00 Lund, Sweden; National Forensic Centre, SE-581 94 Linköping, Sweden. Electronic address: johannes.hedman@tmb.lth.se.
authors.forename: Johannes
authors.initials: J
authors.lastname: Hedman
mesh_terms: D004396:Coloring Agents / Q000737:chemistry; D004247:DNA / Q000037:antagonists & inhibitors* / Q000737:chemistry / Q000235:genetics; D005453:Fluorescence; D006812:Humic Substances; D060888:Real-Time Polymerase Chain Reaction; D013050:Spectrometry, Fluorescence
chemical_list: D004396:Coloring Agents; D006812:Humic Substances; D004247:DNA
keywords: Fluorescence quenching; Fulvic acid; Humic acid; PCR inhibition; Soil; qPCR