Effects of graphene oxide on PCR amplification for microbial community survey

Abstract

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.

Multifunctional carbon nanomaterials for diagnostic applications in infectious diseases and tumors

“…The oxygen-containing groups on the GO surface can serve as attachment points for electrochemically active additives [ 34 ]. GO is currently applied in several biomedical fields, such as biosensors [ 54 , 55 ], bioimaging [ 56 , 57 ] and nucleic acid amplification [ 58 , 59 ]. In addition, graphitic carbon nitride (gC 3 N 4 ), often considered as sp 2 -hybridized nitrogen-substituted graphene, has also found increasing applications in biomedical fields in recent years due to its high specific surface area and a rich variety of nanoscale multilevel structures.…”

Accurate, rapid and highly sensitive detection of African swine fever virus via graphene oxide-based accelerated strand exchange amplification

“…19 GO has the ability to specifically bind single-stranded DNA (ssDNA) through π–π stacking interactions and hydrogen bonds, while dsDNA has a weaker affinity for the graphene surface due to complementary pairing of bases. 20,21 Therefore, GO is expected to serve as an effective auxiliary additive to reduce primer self-complementation and non-specific amplification of NAT methods.…”