Have you tried spermine? A rapid and cost-effective method to eliminate dextran sodium sulfate inhibition of PCR and RT-PCR

The Dextran Sulfate Sodium (DSS) induced colitis mouse model is commonly used to investigate human inflammatory bowel disease (IBD). Nucleic acid extracts originating from these animals are often contaminated with DSS, which is a strong inhibitor of many enzymatic based molecular biology reactions i...

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Bibliographic Details
Published in:Journal of microbiological methods 2018-01, Vol.144, p.1-7
Main Authors: Krych, Łukasz, Kot, Witold, Bendtsen, Katja M.B., Hansen, Axel K., Vogensen, Finn K., Nielsen, Dennis S.
Format: Article
Language:English
Subjects:
Animals
Dextran sodium sulfate
Dextran Sulfate - antagonists & inhibitors
Dextran Sulfate - chemistry
Disease Models, Animal
DNA - analysis
DNA - isolation & purification
DSS
DSS inhibition
Humans
Mice
Polymerase Chain Reaction - methods
Polymerase Chain Reaction - standards
Polynucleotide 5'-Hydroxyl-Kinase - drug effects
Quantitative reverse transcription PCR
Reverse Transcriptase Polymerase Chain Reaction - methods
Reverse Transcriptase Polymerase Chain Reaction - standards
RNA - analysis
RNA - isolation & purification
RNA, Ribosomal, 16S - genetics
RT-qPCR
Spermine
Spermine - chemistry
Time Factors
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Summary:The Dextran Sulfate Sodium (DSS) induced colitis mouse model is commonly used to investigate human inflammatory bowel disease (IBD). Nucleic acid extracts originating from these animals are often contaminated with DSS, which is a strong inhibitor of many enzymatic based molecular biology reactions including PCR and reverse-transcription (RT). Methods for removing DSS from nucleic acids extracts exist for RNA, but no effective protocol for DNA or cDNA is currently available. However, spermine has previously been shown to be an effective agent for counteracting DSS inhibition of polynucleotide kinase, which led to the hypothesis, that spermine could be used to counteract DSS inhibition of PCR and RT. We investigated the means of adding spermine in an adequate concentration to PCR based protocols (including qPCR, two-step RT-qPCR, and amplicon sequencing library preparation) to remove DSS inhibition. Within the range up to 0.01g/L, spermine can be added to PCR/qPCR or RT prophylactically without a significant reduction of reaction efficiency. Addition of spermine at the concentration of 0.08g/L can be used to recover qualitative PCR signal inhibited by DSS in concentrations up to 0.32g/L. For optimal quantitative analysis, the concentration of spermine requires fine adjustment. Hence, we present here a simple fluorometric based method for adjusting the concentration of spermine ensuring an optimal efficiency of the reaction exposed to an unknown concentration of DSS. In conclusion, we demonstrate a cost effective and easy method to counteract DSS inhibition in PCR and two-step RT-qPCR. Fixed or fine-tuned concentrations of spermine can be administered depending on the qualitative or quantitative character of the analysis. •A simple and cost-effective method to counteract DSS inhibition in PCR is proposed.•Fix amount of spermine can be added prophylactically to PCR to prevent low concentration DSS inhibition•Fine-tuned concentration of spermine can be added to PCR to prevent inhibition caused by relatively high concentrations of DSS
ISSN:0167-7012
1872-8359
DOI:10.1016/j.mimet.2017.10.015