Extraction of DNA from soil using nanoparticles by magnetic bioseparation

Sebastianelli, Antonio; Sen, Tapas; Bruce, Ian J.

doi:10.1111/j.1472-765x.2008.02343.x

Cited by 40 publications

(15 citation statements)

References 19 publications

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“…In the context of bioseparation and purification, magnetic carrier technology has become an increasingly popular tool for the separation of biomolecules: DNA, RNA and proteins . Silica–magnetite nanoparticles are employed in the isolation of DNA from environmental samples . In recent years application of magnetizable solid‐phase supports has been found to be advantageous over common methods in numerous biological fields .…”

Section: Introductionmentioning

confidence: 99%

Potential application of superparamagnetic nanoparticles for extraction of bacterial genomic DNA from contaminated food and environmental samples

et al. 2012

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BACKGROUND: Isolation of high‐molecular‐weight DNA is essential for many molecular biology applications. Owing to the presence of polymerase chain reaction (PCR) inhibitors, there is a scarcity of suitable protocols for PCR‐ready DNA extraction from food and natural environments. The conventional chemical methods of DNA extraction are time consuming and laborious and the yield is very low. Thus the aim of this research was to develop a simple, rapid, cost‐effective method of genomic DNA extraction from food (milk and fruit juice) and environmental (pond water) samples and to detect bacterial contaminants present in those samples. RESULTS: This approach is efficient for both Gram‐positive and Gram‐negative bacteria from all the studied samples. Herein super paramagnetic bare iron oxide nanoparticles were implemented for bacterial genomic DNA isolation. The method was also compared to the conventional phenol–chloroform method in the context of quality, quantity and timing process. This method took only half an hour or less to obtain high‐molecular‐weight purified DNA from minimum bacterial contamination. Additionally, the method was directly compatible to PCR amplification. CONCLUSION: The problem of availability of suitable generalized methods for DNA isolation from various samples including food and environmental has been solved by a nanobiotechnological approach that may prove to be extremely useful in biotechnological applications. © 2012 Society of Chemical Industry

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Section: Introductionmentioning

confidence: 99%

Potential application of superparamagnetic nanoparticles for extraction of bacterial genomic DNA from contaminated food and environmental samples

et al. 2012

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“…Soft lysis method is based on the disruption of micro‐organism solely by enzymatic and chemical means, whereas harsh lysis approach involves the mechanical cell disruption by bead beating, sonication, freeze‐thawing and grinding. The indirect DNA extraction protocols involved blending, cation‐exchange method (Desai and Madamwar 2007) or other new approaches, such as the use of super paramagnetic silica–magnetite nanoparticles for the isolation and purification of DNA from soil samples (Sebastianelli and Bruce 2008).…”

Section: Introductionmentioning

confidence: 99%

Assessment of various methods for extraction of metagenomic DNA from saline habitats of coastal Gujarat (India) to explore molecular diversity

Purohit

Singh

2009

Letters in Applied Microbiology

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Aims: To develop total DNA extraction protocol from saline soil for further metagenomic applications. Methods and Results: The protocols combine the application of mechanical (Beads and Sonicator) and Soft Lysis (SDS and enzymes) method for the isolation of total DNA from saline soil of coastal Gujarat followed by its quantification and purity assessment. The quality and purity of metagenomic DNA was quite consistent and reliable, although it contained residual concentartions of humic acid. The extracted DNA was used to successfully amplify 16S rRNA region. The amplicons were suitable for further applications such as diversity‐based analysis by denaturing gradient gel electrophoresis (DGGE). Conclusions: The methods appear to have wide applicability in investigating molecular diversity and exploring functional genes from the total DNA. Significance and Impact of the Study: The protocol is simple, short and facilitates rapid isolation of PCR amplifiable total genomic DNA from saline soil. The method yielded good quality of the DNA suitable for metagenomic studies. The results are also significant as only few extreme environments, particularly saline habitats, are explored for their metagenomic potential.

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“…Therefore, much research has been directed toward the development of optimized DNA extraction protocols for difficult environmental samples (1,2,8,18,21,23,24,27,31,32). Nevertheless, coextraction of PCR-inhibiting compounds often cannot be completely prevented, thereby potentially leading to false-negative results (4,5,7,13).…”

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confidence: 99%

Accurate Quantification of Microorganisms in PCR-Inhibiting Environmental DNA Extracts by a Novel Internal Amplification Control Approach Using Biotrove OpenArrays

Doorn

Klerks

Gent-Pelzer

et al. 2009

Appl Environ Microbiol

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PCR-based detection assays are prone to inhibition by substances present in environmental samples, thereby potentially leading to inaccurate target quantification or false-negative results. Internal amplification controls (IACs) have been developed to help alleviate this problem but are generally applied in a single concentration, thereby yielding less-than-optimal results across the wide range of microbial gene target concentrations possible in environmental samples (J. Hoorfar, B. Malorny, A. Abdulmawjood, N. Cook, M. Wagner, and P. Fach, J. Clin. Microbiol. 42:1863-1868, 2004). Increasing the number of IACs for each quantitative PCR (qPCR) sample individually, however, typically reduces sensitivity and, more importantly, the reliability of quantification. Fortunately, current advances in high-throughput qPCR platforms offer the possibility of multiple reactions for a single sample simultaneously, thereby allowing the implementation of more than one IAC concentration per sample. Here, we describe the development of a novel IAC approach that is specifically designed for the state-of-the-art Biotrove OpenArray platform. Different IAC targets were applied at a range of concentrations, yielding a calibration IAC curve for each individual DNA sample. The developed IACs were optimized, tested, and validated by using more than 5,000 unique qPCR amplifications, allowing accurate quantification of microorganisms when applied to soil DNA extracts containing various levels of PCR-inhibiting compounds. To our knowledge, this is the first study using a suite of IACs at different target concentrations to monitor PCR inhibition across a wide target range, thereby allowing reliable and accurate quantification of microorganisms in PCR-inhibiting DNA extracts. The developed IAC is ideally suited for high-throughput screenings of, for example, ecological and agricultural samples on next-generation qPCR platforms.

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Extraction of DNA from soil using nanoparticles by magnetic bioseparation

Cited by 40 publications

References 19 publications

Potential application of superparamagnetic nanoparticles for extraction of bacterial genomic DNA from contaminated food and environmental samples

Potential application of superparamagnetic nanoparticles for extraction of bacterial genomic DNA from contaminated food and environmental samples

Assessment of various methods for extraction of metagenomic DNA from saline habitats of coastal Gujarat (India) to explore molecular diversity

Accurate Quantification of Microorganisms in PCR-Inhibiting Environmental DNA Extracts by a Novel Internal Amplification Control Approach Using Biotrove OpenArrays

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