ArticleNucleic acids research2003
Mechanisms underlying the impact of humic acids on DNA quantification by SYBR Green I and consequences for the analysis of soils and aquatic sediments.
Article in Nucleic acids research, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 101 citations in OpenAlex.
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- First shotgun metagenomics study of Juan de Fuca deep-sea sediments reveals distinct microbial communities above, within, between, and below sulfate methane transition zones.Frontiers in microbiology · 2023Article
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- The Antibacterial and Anti-biofilm Activity of Metal Complexes Incorporating 3,6,9-Trioxaundecanedioate and 1,10-Phenanthroline Ligands in Clinical Isolates ofAntibiotics (Basel, Switzerland) · 2020Article
- Robust DNA protocols for tropical soils.Heliyon · 2020Article
- PCR inhibition in qPCR, dPCR and MPS-mechanisms and solutions.Analytical and bioanalytical chemistry · 2020Review
- The Response of Microbial Communities to Peatland Drainage and Rewetting. A Review.Frontiers in microbiology · 2020Review
- Library Construction from Subnanogram DNA for Pelagic Sea Water and Deep-Sea Sediments.Microbes and environments · 2017Article
- A novel label-free fluorescence assay for one-step sensitive detection of HgScientific reports · 2017Article
- Transparent DNA/RNA Co-extraction Workflow Protocol Suitable for Inhibitor-Rich Environmental Samples That Focuses on Complete DNA Removal for Transcriptomic Analyses.Frontiers in microbiology · 2016Article
- Development of a nucleic Acid extraction procedure for simultaneous recovery of DNA and RNA from diverse microbes in water.Pathogens (Basel, Switzerland) · 2015Article
- Effects of humic acid on DNA quantification with Quantifiler® Human DNA Quantification kit and short tandem repeat amplification efficiency.International journal of legal medicine · 2012Article
- Extraction of bacterial RNA from soil: challenges and solutions.Microbes and environments · 2012Review
- Mutants of Taq DNA polymerase resistant to PCR inhibitors allow DNA amplification from whole blood and crude soil samples.Nucleic acids research · 2009Article
- Abundance and activity of methanotrophic bacteria in littoral and profundal sediments of lake constance (Germany).Applied and environmental microbiology · 2009Article
- Lipopolyamine-mediated single nanoparticle formation of calf thymus DNA analyzed by fluorescence correlation spectroscopy.Pharmaceutical research · 2006Article
- Sensitive determination of microbial growth by nucleic acid staining in aqueous suspension.Applied and environmental microbiology · 2006Article
- Simultaneous recovery of extracellular and intracellular DNA suitable for molecular studies from marine sediments.Applied and environmental microbiology · 2005Article
Corrections and comments
- Erratum issued
Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA quantification of soils and sediments is useful for the investigation of microbial communities and for the acquisition of their genomes that are exploited for the production of natural products. However, in such samples DNA quantification is impaired by humic acids (HA). Due to its lack of specificity and sensitivity, UV spectrophotometry cannot be applied. Consequently, fluorimetric assays applying Hoechst (H) 33258 or PicoGreen (PG) are used. Here, we investigated the SYBR Green I (SG) assay, which was also affected by HA, but was found to be 25- and 1.7-fold more sensitive compared to the H 33258 and PG assays, respectively. Spectrophotometric, fluorimetric and quenching studies as well as gel mobility shift assays suggested that the effect of HA on the SG assay was based on an inner filter effect, collisional quenching and binding of SG to HA. As to the latter finding, the standard 6250-fold dilution of the SG reagent was optimised to a 2000-fold dilution. Although the sensitivity of the optimised SG assay was reduced by a factor of 1.3, the interfering effect of HA could be reduced up to 22-fold. A significant reduction of HA interferences by lowering the pH of the assay was not observed. Finally, the performance of the modified SG assay and the corresponding evaluation methods were verified by the determination of DNA recoveries and concentrations of standards and environmental samples in comparison to the PG assay.
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