Graphene oxide enhances the specificity of the polymerase chain reaction by modifying primer-template matching

Wang, Yuanyuan; Wang, Fengbang; Wang, Hailin; Song, Maoyong

doi:10.1038/s41598-017-16836-x

Cited by 22 publications

(20 citation statements)

References 43 publications

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“…2). Although previous studies have demonstrated that GO can act as an efficient assistant additive to eliminate non-specific amplification [10,14], our study provides the quantitative data on microbial community level to prove the negative effect of GO. On the other hand, these observations are based on our mock communities.…”

Section: Effect Of Go On Pcr Amplification and Microbial Communitymentioning

confidence: 86%

“…The effect of GO on DNA may be more complicated than expected Previous studies have proved that GO can eliminate non-specific amplification effectively [14,15]. However, their conclusions and proposed mechanisms lack quantitative data at the community level.…”

Section: Effect Of Go On Pcr Amplification and Microbial Communitymentioning

confidence: 99%

“…The thermal cycle parameters were as follows: denaturation at 94°C for 1 min, 30 cycles of 94°C for 20 s, 57°C for 25 s, 68°C for 45 s, a final extension at 68°C for 10 min and finally keep at 4°C. As for exploring GO's effect on community composition and diversity, 1 μg/ mL GO has been showed with the greatest enhancement in PCR, and ddH 2 O was replaced by 1 μg/mL Go solution in our PCR system [14]. PCR products were separated by agarose gel electrophoresis and purified by Gel Extraction Kit (D2500-02, OMEGA BioTek).…”

Section: Pcr Library Preparation and High-throughput Sequencingmentioning

confidence: 99%

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Effects of graphene oxide on PCR amplification for microbial community survey

Wang

Song

et al. 2020

BMC Microbiol

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Background Graphene oxide (GO) has been suggested as an efficient assistant additive to eliminate non-specific amplification of the polymerase chain reaction (PCR). Although many studies have focused on exploring its molecular mechanism, the practice of GO on the quantitation of microbial community has not been implemented yet. In this study, GO was added in PCR system to explore the changes on removing typical amplification errors, such as chimera and mismatches on two kinds of mock communities (an evenly mixed and a staggered mock communities) and environmental samples. Results High-throughput sequencing of bacterial and fungal communities, based on 16S rRNA genes and internal transcribed spacers (ITS) respectively, showed that GO could significantly increase large segmental error (chimeric sequence) in PCR procedure while had no specific effect on point error (mismatched sequence). Besides, GO reduced the α-diversity of community, and changed the composition of fungal community more obviously than bacterial community. Conclusions Our study provides the first quantitative data on microbial community level to prove the negative effect of GO, and also indicates that there may be a more complex interaction between GO and comprehensive DNA fragments in PCR process.

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Section: Effect Of Go On Pcr Amplification and Microbial Communitymentioning

confidence: 86%

Section: Effect Of Go On Pcr Amplification and Microbial Communitymentioning

confidence: 99%

Section: Pcr Library Preparation and High-throughput Sequencingmentioning

confidence: 99%

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Effects of graphene oxide on PCR amplification for microbial community survey

Wang

Song

et al. 2020

BMC Microbiol

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“…It is important to release small RNAs bound to GO surface for further PCR/sequencing analysis. Indeed, at the critical concentration of 4 µg/ml, PCR reactions are inhibited by the GO in solution (Wang et al, 2017). The desorption of NAs from GO is indeed a complex problem (Liu et al, 2016).…”

Section: Small Mirnas Are Selectively Desorbed After the Increase Of mentioning

confidence: 99%

Graphene Oxide Nano-Concentrators Selectively Modulate RNA Trapping According to Metal Cations in Solution

Palmieri

Pietro

Perini

et al. 2020

Front. Bioeng. Biotechnol.

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With recent advances in nanotechnology, graphene nanomaterials are being translated to applications in the fields of biosensing, medicine, and diagnostics, with unprecedented power. Graphene is a carbon allotrope derived from graphite exfoliation made of an extremely thin honeycomb of sp2 hybridized carbons. In comparison with the bulk materials, graphene and its water-soluble derivative graphene oxide have a smaller size suitable for diagnostic platform miniaturization as well as high surface area and consequently loading of a large number of biological probes. In this work, we propose a nanotechnological method for concentrating total RNA solution and/or enriching small RNA molecules. To this aim, we exploited the unique trapping effects of GO nanoflakes in the presence of divalent cations (i.e., calcium and magnesium) that make it flocculate and precipitate, forming complex meshes that are positively charged. Here, we demonstrated that GO traps can concentrate nucleic acids in the presence of divalent cations and that small RNAs can be selectively released from GO-magnesium traps. GO nano-concentrators will allow better analytical performance with samples available in small amounts and will increase the sensitivity of sequencing platforms by short RNA selection.

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“…The PCR procedures are shown in Supplementary Table S1. After 25 cycles, ten microliter PCR products were subjected to 1% agarose gel electrophoresis (120 V/20 min), as described 57 .…”

Section: Identification Of P Aeruginosa By Endpoint Polymer Chain Rementioning

confidence: 99%

Amphiphilic silver nanoclusters show active nano–bio interaction with compelling antibacterial activity against multidrug-resistant bacteria

et al. 2020

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Multidrug resistance represents a growing threat to human beings, and alternative antimicrobial regimens to conventional antibiotic paradigms are being extensively searched to fight against multidrug-resistant bacteria (MDRB). Although the antimicrobial potency of silver nanomaterials (AgNMs) has been previously elaborated, their efficacy against MDRB still remains to be strengthened. Here, our data revealed that small-sized silver nanoclusters (AgNCs) are superior to conventional silver nanoparticles (AgNPs) as robust antimicrobials against multidrug-resistant (MDR) Pseudomonas aeruginosa (P. aeruginosa). The core structure and surface ligands of AgNCs are crucial for the outstanding antibacterial activity of AgNCs. On the one hand, due to the presence of amphiphilic ligands, AgNCs are relatively prone to associate with the cell membrane and partake in endocytosis with targeted bacterial cells. Molecular dynamics simulations also corroborated this finding. On the other hand, the nanocluster structure of AgNCs led to strong peroxidase-like activity associated with massive production of reactive oxygen species (ROS), which contributes to their overall bactericidal potency. These outstanding features of AgNCs result in elevated bacterial killing efficacy by impairing the cell wall/membrane, promoting oxidative stress and attenuating pivotal cellular processes, e.g., ATP synthesis. Notably, AgNCs manifested great efficacy in treating P. aeruginosa-generated pneumonia in mice and increased the survival of infected animals, as well as exhibited excellent biocompatibility. Taken together, the results of this study pinpoint the great promise of AgNCs as new alternative therapeutics against MDR P. aeruginosa.

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Graphene oxide enhances the specificity of the polymerase chain reaction by modifying primer-template matching

Cited by 22 publications

References 43 publications

Effects of graphene oxide on PCR amplification for microbial community survey

Effects of graphene oxide on PCR amplification for microbial community survey

Graphene Oxide Nano-Concentrators Selectively Modulate RNA Trapping According to Metal Cations in Solution

Amphiphilic silver nanoclusters show active nano–bio interaction with compelling antibacterial activity against multidrug-resistant bacteria

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