Aqueous Suspension of Carbon Nanotubes Enhances the Specificity of Long PCR

Zhang, Zhizhou; Shen, Cencao; Wang, Mingchun; Han, Han; Cao, Xiaohong

doi:10.2144/000112692

Cited by 55 publications

(55 citation statements)

References 21 publications

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“…1C and D, the filtered NH 2 -MWCNTs enhanced the PCR efficiency and the specificity at increasing concentrations while the non-filtered NH 2 -MWCNTs presented a downward trend on the gel at similar concentrations. In the recent literature, different types of CNTs have been found beneficial in the PCR enhancement of a diverse DNA sequences ranging from 76 bp to 15 kb in length (Cui et al 2004;Zhang et al 2008;Cao et al 2011;Quaglio et al 2011;Williams et al 2014). In these reports, enhancement of the amplification reactions was shown to be concentration dependent that concluded with an immediate drop in electrophoretic band intensities of DNA targets at high CNT concentrations.…”

Section: Resultsmentioning

confidence: 99%

“…in the SWCNT-assisted amplification reaction, which is an essential cofactor for DNA polymerase enzyme to maintain its activity. On the other hand, fidelity assessment of CNT-assisted PCR (SWCNTs and MWCNTs) was investigated by Zhang et al who evaluated Sanger sequencing data of CNT-free and CNT-assisted PCR (Zhang et al 2008). The results showed no significant drop in DNA replication fidelity comparing to the conventional PCR.…”

Section: Introductionmentioning

confidence: 99%

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Dispersion quality of amine functionalized multiwall carbon nanotubes plays critical roles in polymerase chain reaction enhancement

Yüce

Budak

2014

J Nanopart Res

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Impact of dispersion quality of NH 2 -MWCNTs (13-18 nm in diameter with a length between 1 and 12 lm, [99 % purity) in the amplification efficiency of a random DNA oligonucleotide library (96 bp) was investigated. Amplification yield in the presence of non-filtered NH 2 -MWCNT dispersion, filtered NH 2 -MWCNT dispersion and surfaceattached NH 2 -MWCNTs was explored, and physical interactions between NH 2 -MWCNTs and major PCR reagents including DNA template, wild type Taq DNA polymerase enzyme and primers were determined using high resolution polyacrylamide gel electrophoresis, dynamic light scattering, UV-Vis-NIR spectroscopy and scanning electron microscopy techniques. The results revealed that presence of NH 2 -MWCNT dispersion which was sonicated, centrifuged and filtered, enhanced the total PCR efficiency up to 70 % while the presence of NH 2 -MWCNT only centrifuged after sonication, inhibited the reaction significantly at similar concentrations. Furthermore, the NH 2 -MWCNTs coupled covalently onto magnetic microspheres, contributed for the specificity enhancement whilst decreasing the amplification efficiency by 30 % at the maximum concentration, which suggests a removable enhancement system for sensitive applications. On the other hand, the relative hydrodynamic size distribution measurements displayed a clear difference between the filtered NH 2 and non-filtered NH 2 -MWCNT water dispersions, which justifies the inhibition of the amplification by the non-filtered NH 2 -MWCNTs containing big agglomerates and bundles. Finally, we demonstrated that major PCR components adsorb onto the NH 2 -MWCNTs with diverse affinities, and maintain their functions after adsorption, which provides a good framework to further develop tunable NH 2 -MWCNT-carriers to be utilized in various nanobiotechnology and material science applications.Keywords Polymerase chain reaction Á Nano PCR Á Amine functionalized multiwall carbon nanotubes Á Random DNA oligonucleotide library Á Magnetic beads Guest Editors: Mustafa Culha, Rawil F. Fakhrullin, Ratnesh Lal This article is part of the topical collection on Nanobiotechnology Electronic supplementary material The online version of this article (

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Dispersion quality of amine functionalized multiwall carbon nanotubes plays critical roles in polymerase chain reaction enhancement

Yüce

Budak

2014

J Nanopart Res

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“…These outcomes show that some amount of Taq polymerase is captured by magnetic nanoparticle clusters, and consequently, the amount of Taq polymerase that should have been used in PCR is reduced in the PCR solution. There are several reports on the effect of various nanoparticles on PCR amplification [2][3][4][5][6][7][8][9][10]. However, their reports did not focus on interaction between the particle clusters and Taq polymerase.…”

Section: Resultsmentioning

confidence: 99%

“…Currently, the PCR method is widely used in genetic technology, bioscience, diagnosis therapy, medicine development and personal identification. Recently, it has been reported that PCR efficiency is improved by nanoparticles such as single-walled carbon nanotubes (SWCNTs), multi-walled carbon nanotubes (MWCNTs), carbon nanopowder, metallic nanoparticles and nonmetallic nanoparticles [2][3][4][5]. Among the variety of nanoparticles used, gold nanoparticles have been reported to have an outstanding effect on PCR efficiency.…”

Section: Introductionmentioning

confidence: 99%

Effects of Superparamagnetic Nanoparticle Clusters on the Polymerase Chain Reaction

et al. 2012

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Abstract:The polymerase chain reaction (PCR) method is widely used for the reproduction and amplification of specific DNA segments, and a novel PCR method using nanomaterials such as gold nanoparticles has recently been reported. This paper reports on the effects of superparamagnetic nanoparticles on PCR amplification without an external magnetic field, and clarifies the mechanism behind the effects of superparamagnetic particle clusters on PCR efficiency by estimating the structures of such clusters in PCR. It was found that superparamagnetic nanoparticles tend to inhibit PCR amplification depending on the structure of the magnetic nanoparticle clusters. The paper also clarifies that Taq polymerase is captured in the spaces formed among magnetic nanoparticle clusters, and that it is captured more efficiently as a result of their motion from heat treatment in PCR thermal cycles. Consequently, Taq polymerase that should be used in PCR is reduced in the PCR solution. These outcomes will be applied to novel PCR techniques using magnetic particles in an external magnetic field.

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“…Besides the conventionally used small molecular additives, such as formamide, 11 tetramethylammonium chloride 12 and its derivatives, 13 and betaine, 14 nanoparticles (NPs) have received considerable attention due to their unique physicochemical properties, which are significantly different from those of their bulk counterparts. Various NP systems, including nanogold, [15][16][17][18] carbon nanotubes (CNTs), 19 carbon nanopowder, 20 magnetic NPs, 21 semiconducting NPs, 22,23 and dendrimers 24 have been used as additives to improve the PCR specificity and efficiency. Nonspecific amplification problems can be overcome in the presence of NPs.…”

Section: Introductionmentioning

confidence: 99%

Enhancing the specificity and efficiency of polymerase chain reaction using polyethyleneimine-based derivatives and hybrid nanocomposites

Tong¹,

Cao²,

Wen³

et al. 2012

IJN

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Abstract:There is a general necessity to improve the specificity and efficiency of the polymerase chain reaction (PCR), and exploring the PCR-enhancing mechanism still remains a great challenge. In this paper we report the use of branched polyethyleneimine (PEI)-based derivatives and hybrid nanocomposites as a novel class of enhancers to improve the specificity and efficiency of a nonspecific PCR system. We show that the surface-charge polarity of PEI and PEI derivatives plays a major role in their effectiveness to enhance the PCR. Positively charged amine-terminated pristine PEI, partially (50%) acetylated PEI (PEI-Ac 50 ), and completely acetylated PEI (PEIAc) are able to improve PCR efficiency and specificity with an optimum concentration order of PEI , PEI-Ac 50 , PEI-Ac, whereas negatively charged carboxyl-terminated PEI (PEI-SAH; SAH denotes succinamic acid groups) and neutralized PEI modified with both polyethylene glycol (PEG) and acetyl (Ac) groups (PEI-PEG-Ac) are unable to improve PCR specificity and efficiency even at concentrations three orders of magnitude higher than that of PEI. Our data clearly suggests that the PCR-enhancing effect is primarily based on the interaction between the PCR components and the PEI derivatives, where electrostatic interaction plays a major role in concentrating the PCR components locally on the backbones of the branched PEI. In addition, multiwalled carbon nanotubes modified with PEI and PEI-stabilized gold nanoparticles are also able to improve the PCR specificity and efficiency with an optimum PEI concentration less than that of the PEI alone, indicating that the inorganic component of the nanocomposites may help improve the interaction between PEI and the PCR components. The developed PEIbased derivatives or nanocomposites may be used as efficient additives to enhance other PCR systems for different biomedical applications.

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Aqueous Suspension of Carbon Nanotubes Enhances the Specificity of Long PCR

Cited by 55 publications

References 21 publications

Dispersion quality of amine functionalized multiwall carbon nanotubes plays critical roles in polymerase chain reaction enhancement

Dispersion quality of amine functionalized multiwall carbon nanotubes plays critical roles in polymerase chain reaction enhancement

Effects of Superparamagnetic Nanoparticle Clusters on the Polymerase Chain Reaction

Enhancing the specificity and efficiency of polymerase chain reaction using polyethyleneimine-based derivatives and hybrid nanocomposites

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