Enhancing the specificity of polymerase chain reaction by graphene oxide through surface modification: zwitterionic polymer is superior to other polymers with different charges

Zhong, Yong; Huang, Lihong; Zhang, Zhisen; Xiong, Yunjing; Sun, Liping; Weng, Jian

doi:10.2147/ijn.s120659

Cited by 23 publications

(13 citation statements)

References 50 publications

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“…Recently, Huang et al . reported the interaction between GO surface and Pfu DNA polymerase could affect the specificity of PCR 27 . Here the interaction of the polymerase and GO was investigated by the fluorescence quenching experiments (Figure S1 ).…”

Section: Resultsmentioning

confidence: 99%

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

Wang

et al. 2017

Sci Rep

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Aiming at improved specificity, nanoparticle assisted polymerase chain reaction (PCR) has been widely studied and shown to improve PCR. However, the reliability and mechanism of this method are still controversial. Here, we demonstrated that 1 μg/mL of graphene oxide (GO) effectively enhances the specificity of the error-prone multi-round PCR. Mismatched primers were designed as interference to produce nonspecific products when the same amounts of matched and mismatched primers were added into semi-multiplex PCR. It was found that GO can enhance specificity by suppressing the amplification of mismatched primers. We monitored the primer-template-polymerase-GO interactions involved in the PCR using a capillary electrophoresis/laser-induced fluorescence polarization (CE-LIFP) assay. The results showed that the addition of GO promoted the formation of a matched primer-template complex, but suppressed the formation of a mismatched primer-template complex during PCR, suggesting that interactions between the primers and GO play an essential role. Furthermore, we successfully amplified the FOXL2 gene from PEGFP-N1 vectors using GO to eliminate the nonspecific products in PCR. Taken together, these results suggest that the GO can be used as an efficient additive for improving the conventional PCR system.

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Section: Resultsmentioning

confidence: 99%

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

Wang

et al. 2017

Sci Rep

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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%

“…Till now, many factors have been found to affect the specificity of PCR, such as chimeric reads, primer mismatches or amplification mismatches and sequencing errors, which are frequently included in the PCR mixture [5][6][7][8][9]. Usually, when the concentration of template DNA is very low, or the structure of DNA template is very complicated, such as GC-rich gene or mammalian genomic DNA, the specificity of PCR might be very low [10].…”

Section: Introductionmentioning

confidence: 99%

“…Reaction components aggregated around GO increase the efficient of dynamical contact among reaction components, hence it may result in heat equilibrium in the reaction and enhance PCR efficiency. (2) Interaction of DNA polymerase with GO [10,17]. As GO surface is negatively charged, the adsorbed amount of positively charged Pfu polymerase and Mg 2+ is relatively high at low GO concentration.…”

Section: Introductionmentioning

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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“…More recently, researchers have identified numerous nanomaterials that can enhance the yield of PCR, such as silver nanoparticles 9 , gold nanoparticles 9 , 10 , magnetic nanoparticles 9 , TiO 2 nanoparticles 10 , carbon-coated silica nanoparticles 11 , and graphene-ZnO nanocomposites 12 . Nanomaterials can also improve the specificity of PCR, including gold nanoparticles 13 , poly(diallyldimethylammonium chloride)-protected gold nanoparticles 14 , dendrimers 15 , amino-modified magnetic nanoparticles 16 , and graphene oxide 17 . Furthermore, some researchers have also identified nanomaterials that can improve the efficiency 18 and fidelity 19 of PCR.…”

Section: Introductionmentioning

confidence: 99%

Enhancement of PCR Sensitivity and Yield Using Thiol-modified Primers

Bai

Xiao

Suo

et al. 2018

Sci Rep

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Various additives can enhance the quality of PCR amplification, but these generally require considerable optimization to achieve peak performance. Here, we demonstrate that the use of thiol-modified primers can enhance both PCR sensitivity and yield. In experiments with V. parahaemolyticus genomic DNA, this primer modification enhances PCR sensitivity by more than 100-fold, with accompanying improvements in amplicon yield. Then, an artificial plasmid with the same primer binding regions and different internal amplification sequence was designed. The result showed that the amplification also be improved by using the same thiol-modified primers. It indicated the enhancement was not caused by the effect of the thiol-modified primers on the second structure of amplification sequence. Subsequent experiments demonstrate that the effects of this modification are potentially due to altered interaction between the primers and proteins in the reaction mixture. Amplification with thiol-modified primers was strongly inhibited by the presence of extraneous proteins relative to standard DNA primers, which indicates that thiol-modified primers may be inhibited due to interaction with these proteins. In contaminant-free reactions, however, the thiol-modified primers might interact more strongly with DNA polymerase, which could in turn improve PCR amplification.

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Enhancing the specificity of polymerase chain reaction by graphene oxide through surface modification: zwitterionic polymer is superior to other polymers with different charges

Cited by 23 publications

References 50 publications

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

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

Effects of graphene oxide on PCR amplification for microbial community survey

Enhancement of PCR Sensitivity and Yield Using Thiol-modified Primers

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