• gene delivery;
  • transformation;
  • multiwalled carbon nanotubes;
  • modified nucleotide;
  • linearized plasmid DNA


  1. Top of page
  2. Abstract
  3. Introduction
  4. Materials and Methods
  5. Results and Discussion
  6. Conclusion
  7. Acknowledgments
  8. Literature Cited

Carbon nanotubes (CNTs) are allotropes of carbon, which have unique physical, mechanical, and electronic properties. Among various biomedical applications, CNTs also attract interest as nonviral gene delivery systems. Functionalization of CNTs with cationic groups enables delivery of negatively charged DNA into cells. In contrast to this well-known strategy for DNA delivery, our approach included the covalent attachment of linearized plasmid DNA to carboxylated multiwalled CNTs (MWCNTs). Carboxyl groups were introduced onto MWCNTs by oxidative treatment, and then the carboxyl groups were activated by 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC). The whole pQE-70 vector including the gene encoding green fluorescent protein (GFP) was subjected to polymerase chain reaction (PCR) using the modified nucleotide N6-(6-Amino)hexyl-2′-deoxyadenosine-5′-triphosphate. Hence, free amino groups were introduced onto the linearized plasmid. Covalent bonding between the amino-modified plasmid DNA and the carboxylated MWCNTs was achieved via EDC chemistry. The resulting bioconjugate was successfully transformed into chemically competent Escherichia coli cells, without necessity of a heat-shock step at 42°C. The presence of Ca2+ in transformation medium was required to neutralize the electrostatic repulsion between DNA and negatively charged outer layer of E. coli. The transformants, which were able to express GFP were inspected manually on ampicillin agar plates. Our study represents a novelty with respect to other noncovalent CNT gene delivery systems. Considering the interest for delivery of linear DNA fragments, our study could give insights into further studies. © 2013 American Institute of Chemical Engineers Biotechnol. Prog., 30:224–232, 2014


  1. Top of page
  2. Abstract
  3. Introduction
  4. Materials and Methods
  5. Results and Discussion
  6. Conclusion
  7. Acknowledgments
  8. Literature Cited

Cellular uptake of biomolecules is critical for diagnosis and therapy in clinical applications. As a direct result of the advances in molecular biology and biotechnology, nucleic acid-based therapeutics for treatment of genetic and acquired diseases are being developed rapidly. Thanks to such advances, many different biological materials such as plasmid DNA (pDNA), antisense oligonucleotides, ribozymes, peptide nucleic acids, and silencing RNAs are available for gene therapy.[1] However, introducing such therapeutic biological materials to their target, intracellular matrix in this case, still remains a field to be developed. Even though satisfactory results have been obtained from viral carriers, safety issues such as immunogenicity and host chromosomal integration limit their use in therapy.[2, 3] Numerous nonviral gene delivery systems have been developed to transfer foreign genes into cells. Nonviral carrier approaches have valuable properties, such as relatively simple preparation and unlimited cargo space. Therefore, they are seen as the answer to safety concerns introduced by viral vectors.[4] Alongside with cationic lipids[5] and cationic polymers,[6, 7] novel carrier systems based on nanomaterials have been developed. Nanomaterial-based systems have been used for localized or targeted delivery of genes, small molecular weight drugs and macromolecules, such as proteins or peptides.[8]

Carbon nanotubes (CNTs) have been first discovered in 1991.[9] Owing to their unique chemical and physical properties, they have found a valuable place in many scientific areas. Among various nanomaterials, CNTs are widely used in biomedical applications.[10] One of the purposive properties of CNTs is their ability to penetrate the plasma membrane readily,[11] which makes them great tools for drug delivery systems. However, the exact mechanism of cellular uptake of CNTs remains unknown. Two main pathways have been proposed by different groups, (1) endosomal-mediated energy dependent mechanism and (2) direct translocation through the plasma membrane.[12] The biggest disadvantage of CNTs is their solubility problem in most organic and polar solvents, which hinders their usage in biological environments. However, physicochemical features of CNTs enable them to be modified using different methods to overcome this problem.[13] These strategies mainly depend on noncovalent modification[14-16] or covalent modification[17] with various materials. Surface modifications through chemical treatments yield various scaffolds for attachment of many different drugs. However, simple procedures are favored compared to complex chemical procedures and purification steps.

In this study, we used the method of oxidative treatment in H2SO4/HNO3 to modify multiwalled carbon nanotubes (MWCNTs), and we obtained functional MWCNTs bearing carboxyl groups (fCNT). Plasmid DNA included the gene fragment encoding green fluorescent protein (GFP), and it was linearized by polymerase chain reaction (PCR) using the amino-modified nucleotide in the presence of other four deoxyribonucleotides. Then, the amino-modified plasmid DNA (mpDNA) was attached covalently to fCNT. The developed fCNT-mpDNA bioconjugate was tested for its ability to penetrate the outer membrane of Escherichia coli, without the necessity of using heat-shock for plasmid DNA uptake. We achieved transformation of chemically competent cells using fCNT-mpDNA bioconjugate. The transformed colonies could survive on antibiotic selective medium, and they were identified manually by green fluorescence on agar plates. Here, we report the development of a covalent fCNT-linearized plasmid DNA bioconjugate. This work suggests that transformation of E. coli cells can be carried out by simply incubating the cells with the prepared bioconjugate.

Materials and Methods

  1. Top of page
  2. Abstract
  3. Introduction
  4. Materials and Methods
  5. Results and Discussion
  6. Conclusion
  7. Acknowledgments
  8. Literature Cited


MWCNT (carbon content > 90%; Fe < 0.1% diameter × length 110−170 nm × 5−9 μm; chemical vapor deposition (CVD) method), nitric acid (69%), sulfuric acid (98%), 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC), 2-(N-morpholino)ethanesulfonic acid (MES) and deoxythymidine triphosphate (dTTP), deoxyguanosine triphosphate (dGTP), deoxycytidine triphosphate (dCTP), deoxyadenosine triphosphate (dATP) were purchased from Sigma (St. Louis, MO). DreamTaq™ polymerase, agarose gel extraction kit and plasmid miniprep kit were obtained from Thermoscientific (Rockford, IL). N6-(6-Amino)hexyl-2′-deoxyadenosine-5′-triphosphate (NH2-dATP) was obtained from Jena Bioscience (Jena, Germany).

Carboxylation and characterization of MWCNT

Nearly 20 mg MWCNT was incubated in 20 mL H2SO4/HNO3 (3:1, v:v) mixture at 70°C for 4 h, and subsequently diluted with 20 mL dH2O.[18] It was then centrifuged at low speed (4,000 rpm) to let larger MWCNTs precipitate. The supernatant, which was assumed to keep shorter MWCNTs in solution was centrifuged at higher speed (12,000 rpm). The liquid phase was removed, and the pellet washed with water until a neutral pH was obtained. The pellet was allowed to dry in a drying oven at 80°C, and resuspended with MES buffer (100 mM, pH 5.0) before use. The modified nanotubes were compared to the unmodified ones using X-ray photoelectron spectroscopy (XPS) (Middle East Technical University Central Laboratory, Turkey). Transmission electron microscopy (TEM) images were taken by JEOL (JEM-2100F) microscope, and the images were acquired using a voltage of 10 kV and a spot size of 3.0−5.0.

Linearization and modification of plasmid DNA using PCR

The gene fragment encoding green fluorescent protein (GFP) from Aequorea victoria was amplified by PCR using primer pairs 5′-ACATGCATGCGTAAAGGAGAAG-3′ and 5′-CGCGGATCCTTTGTATAGTT-3′ (introduced SphI and BamHI restriction sites are underlined). PCR conditions were as follows: 95°C for 3 min; 95°C for 45 s, 57°C for 45 s and 72°C for 45 s, 35 cycles; and 72°C for 10 min. The amplified gene fragment was cloned into pQE-70 expression vector (Qiagen, Valencia, CA) using SphI and BamHI restriction sites. pQE70/gfp plasmid vector was used as the template for preparation of linearized plasmid DNA, which was modified with NH2-dATP (Figure 1). PCR amplification of the whole plasmid was achieved using the forward primer (5′-CTCGAGAAATCATAA AAA-3′) and the reverse primer (5′-GTGAAGACGAAAGGGCC-3′). The PCR mixture contained 10 ng template, 2.5 U DreamTaq DNA polymerase, Green DreamTaq reaction buffer (including 1.5 mM MgCl2), 0.2 mM dTTP, dGTP, dCTP and 1 μM of each primer. dATP and NH2-dATP were mixed at different ratios yielding a final concentration of 0.2 mM. PCR conditions were as follows: 95°C, 3 min; 95°C, 45 s; 64°C, 45 s; 72°C, 4 min; 72°C, 5 min. Steps 2–4 were repeated 35 times. The PCR product was loaded onto 1% (w/v) agarose gel in Tris–acetate-EDTA (TAE) buffer, and electrophoresed at 100 V for 20 min. The amplified fragment was excised from agarose gel using a clean scalpel, and purified by agarose gel extraction kit. DNA concentration was quantified using the NanoDrop spectrophotometer (Nanodrop ND-1000; software ND-100).


Figure 1. Structure of N6-(6-Amino)hexyl-2′-deoxyadenosine-5′-triphosphate (NH2-dATP).

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The effect of fCNT on cell viability

The possible toxic effect of fCNTs on E. coli cells was evaluated both in solid and liquid medium. Nearly 50 ng pQE-70 plasmid DNA carrying the ampicillin resistance gene was added into 0.2 mL (OD600 = 200) chemically competent E. coli XL1 Blue cells (Stratagene, La Jolla, CA). The cells were transformed with plasmid DNA using heat-shock protocol.[19] Following heat-shock step, 0.8 mL Luria Broth (LB) medium was added, and the cells were incubated at 37°C for 1 h. Then, 0.1 mL aliquots of the cell suspension were spread on LB agar plates supplemented with 150 µg mL−1 ampicillin. The agar plates were directly covered with different amounts of fCNT (0, 25, 50, 100, 250, 500, and 1000 µg) using sterile beads, and they were incubated at 37°C overnight. Colony forming units (CFU) were counted manually to compare the effect of fCNT on cell growth. To investigate the toxic effect in liquid medium, transformation experiment was performed as described above. But in this case, different amounts of fCNT (0, 25, 50, 100, 150, 200, 250 µg) were added directly into 1 mL of the transformation mixture. Following incubation of this mixture at 37°C, 0.1-mL aliquots were spread on ampicillin plates. The toxic effect was evaluated by comparing the number of CFU.

Covalent conjugation between fCNT and mpDNA

We achieved covalent conjugation using a reaction between the activated carboxyl groups of fCNT and the introduced amino groups of mpDNA. For this aim, MWCNTs (100 µg) were activated with EDC in MES buffer (100 mM, pH 5.0) for 15 min at room temperature. Final concentration of EDC was 0.4 M in the reaction medium. Following activation of carboxyl groups, 4.9 µg of the PCR product was introduced into the fCNT suspension. The final reaction volume was 500 µL. The mixture was incubated at 4°C overnight. The obtained bioconjugate was removed by centrifugation at 8,000 rpm, and washed with Tris-EDTA buffer (10 mM, pH 8.0) three times to remove the by-products and the adsorbed mpDNA. Aliquots from the reaction mixture, pellet, and supernatants were loaded onto agarose gel to visualize the presence of unbound mpDNA.

Competent cell preparation and transformation

Chemically competent cells were prepared as described earlier.[19] As described above, fCNT-mpDNA bioconjugate was prepared, and washed with Tris-EDTA buffer. About 100 µg of fCNT-mpDNA bioconjugate (pellet fraction) was resuspended in 10 µL Tris-EDTA buffer (100 mM, pH 8.0), and an aliquot from this suspension was loaded onto agarose gel. fCNT-mpDNA bioconjugate was not purified from agarose gel. Instead, the bioconjugate was directly introduced into 0.1 mL of chemically competent cells (OD600 = 200). Then, the cell suspension was incubated on ice for 15 min. We did not use a heat-shock step (42°C, 45 s) for uptake of the bioconjugate. Following incubation, a 0.1-mL aliquot was spread on ampicillin agar plate. The plate was incubated at 37°C overnight, and CFU were counted.

Results and Discussion

  1. Top of page
  2. Abstract
  3. Introduction
  4. Materials and Methods
  5. Results and Discussion
  6. Conclusion
  7. Acknowledgments
  8. Literature Cited

Carboxylation of MWCNT

As we discussed earlier, surface modification of CNTs are essential not only for binding them to other materials, but also to improve their solubility. In our case, MWCNTs were functionalized by oxidation through acid treatment, which enabled us to incorporate carboxyl groups as binding sites to the linearized plasmid. Among different oxidation treatments available, the H2SO4/NO3 (3:1, v:v) method has been demonstrated to yield carboxyl groups with complete oxidation of side walls.[20] We used this method with some minor modifications, as reported in our previous study.[21] The obtained fCNTs were soluble, and they did not aggregate in MES buffer (100 mM, pH 5.0) up to a concentration of 2 mg mL−1.

Additionally, characterization of the oxidized MWCNTs was carried out by comparing them with the unmodified MWCNTs using X-ray photoelectron spectroscopy. An increase in intensity was clearly observed by comparing the changes in O(1s) spectral envelope. According to the C(1s) spectrum, no significant structural damage was observed even in the presence of strong oxidizing agent (Figure 2). For further characterization and visualization of the morphologies, TEM images of the modified and unmodified MWCNTs were taken. Compared to pristine CNTs (Figure 3a), the reduced dimensions of fCNTs (Figure 3b) resulting from the acidic treatment were clearly observed.


Figure 2. The X-ray photoelectron spectra of unmodified MWCNT (A) and fCNT (B).

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Figure 3. TEM images of unmodified CNT (a) and fCNT (b).

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Effect of fCNT on cell viability

Even though carbon nanotubes are widely used for their intrinsic properties, there is a debate for their cytotoxicity in biomedical applications.[22] Their toxic properties result from surface metal residues (Fe, Co, Ni) originating from synthesis process, as well as their low solubility in unmodified form. However, it is possible exclude these disadvantages using a proper modification method.[23]

When we tested the toxic effect of fCNT in solid medium, we did not observe any significant changes in colony numbers. Even in the presence of 1 mg fCNT, E. coli cells were able to grow on agar plates (Figure 4). We also carried out the experiments using chemically competent cells in liquid medium, as described in methods. Considering that competent cells are readily open to cytotoxic effects, the effect of fCNT in transformation medium was expected to be greater. We observed a significant decrease in colony numbers, when fCNT was present in amounts >150 μg mL−1 (Table 1). Thus, we did not exceed the 100 μg fCNT limit in further experiments.


Figure 4. The effect of fCNT on cell viability was tested in solid medium.

E. coli cells were incubated in the absence of fCNT, or in the presence of 1 mg fCNT. Colony forming units (CFU) were inspected manually on agar plates.

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Table 1. The Effect of Different Concentrations of fCNT on E. coli Cell Viability was Tested in Liquid Medium (see the text for details)
  1. For each fCNT concentration, the number of observed colonies on agar plate was expressed as colony forming units (CFU).

fCNT (µg)02550100150200250

Several studies evaluated the toxicity of CNTs using different strategies.[24-26] Differentiation of the methods yielded contradictive results because of different structure, agglomeration state, and perhaps most importantly, surface functionalization parameters.[13] In a recent study, time-dependency of cytotoxic effect has been investigated at different incubation times (15 min, 1 h, 5 h and overnight). It has been shown that a 1-h incubation with CNTs results in a 50% viability loss of E. coli cells.[27] The main reason of this toxicity could be attributed to cell membrane damage. In our study, a 15-min of incubation time was sufficient for transformation experiments. Therefore, it is unlikely to see a dramatic cytotoxic effect of MWCNTs in our study.

Effect of the modified nucleotide ratio on PCR yield

Intrinsic properties of DNA molecules make them ideal scaffolds for preparation of nanoparticles and immobilization onto nanomaterials.[28] As reviewed elsewhere,[29] DNA oligonucleotides have been modified with various groups that have affinity for proteins of interest, and noncovalent conjugates have been prepared. Covalent conjugation is mostly based on thiol chemistry, which has been used for conjugation of a 500-bp DNA fragment with cytochrome c protein.[30] In that study, the DNA fragment has been PCR-amplified using 2-aminoallyl-dUTP, and then a second reaction has been performed to introduce free thiol groups. In a similar approach, we introduced primary amino groups into pQE-70/gfp plasmid using commercially available N6-(6-Amino)hexyl-2′-deoxyadenosine-5′-triphosphate (NH2-dATP). The circular plasmid DNA was linearized, and modified with amino groups in a semirandom manner. The length of the PCR product was ∼4100 bp, which was then covalently conjugated with fCNT.

To optimize the PCR conditions, two parameters were investigated. Molar ratio of the modified nucleotide (NH2-dATP), and primer annealing temperatures were tested. Three PCR mixtures were prepared as follows: (a) without NH2-dATP, (b) NH2-dATP:dATP at 1:9 molar ratio, and (c) NH2-dATP:dATP at 1:3 molar ratio. For each reaction mixture, PCRs were performed at six different annealing temperatures ranging between 50 and 64°C. The intensities of the amplified fragments were examined under UV light, which revealed that adding NH2-dATP at 1:9 molar ratio had only a slight effect on PCR efficiency. As shown in Figure 5, increasing the concentration of NH2-dATP resulted in relatively weak DNA bands, which indicated a lower yield in case of the 1:3 molar ratio. It has been reported that PCR yield is strongly dependent on chemical nature of the modified nucleotide and DNA polymerase used.[31] Therefore, the PCR conditions were determined experimentally. As shown in Figure 5, the annealing temperatures of 62 and 64°C were found to be optimum for primer binding.


Figure 5. Gradient PCR with annealing temperatures of 50, 55, 58, 60, 62, and 64°C was performed in the absence of NH2-dATP (lanes a1-a6).

For comparision of the PCR yield, gradient PCR was also performed using NH2-dATP at molar ratios of 1:9 (lanes b1-b6) or 1:3 (lanes c1-c6). The amplification products were visualized on agarose gel under UV light. DNA marker (NanoHelix, South Korea) is indicated by M.

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EDC reaction and agarose gel analysis of the reaction products

The well established EDC chemistry was used to bind fCNT and mpDNA covalently. The binding reaction was continued at 4°C overnight. Before removal of the pellet by centrifugation, an aliquot from the reaction mixture was taken. Then, the reaction mixture was centrifuged, and another aliquot was taken from the supernatant fraction. The free mpDNA was used as a control, which gave a bright DNA band with an expected size of ∼4100 bp (Figure 6). Staining of the agarose gels with ethidium bromide (EtBr) enabled detection of DNA bands under UV light. Interestingly, the samples taken before (R) and after centrifugation (Rs) were retarded, and moved slower on agarose gel. These samples yielded DNA bands of approximately equal intensity. As it has been reported,[32] MWCNTs show different water dispersion properties depending on surface chemistry and length. We assumed that a certain amount of fCNTs were highly dispersed in the reaction medium, and they could not be removed by centrifugation at 8,000 rpm. We concluded that the unbound mpDNA might have interacted with the highly dispersed fCNTs. The pellet obtained by centrifugation was also examined on agarose gel under UV light, which yielded no DNA bands. It has been reported that non-covalent NH2-MWCNT-DNA complex with a tendency to aggregate could not move through the agarose gel, and it is not visible on agarose gel.[33] Similarly, we could not observe the presence of bound DNA. Nevertheless, the brightness of samples taken from the soluble fraction of the reaction mixture (Figure 6, lanes R and Rs) were weaker than that of free mpDNA (Figure 6, lane C). Therefore, it was deduced that a significant amount of mpDNA was bound by fCNT. Using Tris-EDTA buffer in washing steps enabled a net negative charge on mpDNA. Thus, we assumed that the non-covalently adsorbed mpDNA could be eliminated by electrostatic repulsion forces between the negatively charged DNA and the carboxylate groups of fCNT. The supernatants obtained from washing with Tris-EDTA buffer were subjected to agarose gel electrophoresis (Figure 6, lanes 1′, 2′, and 3′), but no DNA bands were observed. This could be attributed to the absence of unbound mpDNA, or that the samples were below detection limit. EtBr has a detection limit of 2–10 ng,[33] and we introduced 4.9 µg mpDNA into the reaction. Thus, regarding the binding yield of mpDNA, the presence of DNA at ng levels could be negligible compared to µg level.


Figure 6. Agarose gel visualization of free mpDNA and samples taken from the reaction mixture.

Lane 1, DNA marker (Thermoscientific, Rockford, IL); lane 2, free mpDNA that was introduced into the reaction; lane 3, the pellet fraction obtained by centrifugation (Rp); lane 4, an aliquot taken from the reaction mixture before centrifugation (R); lane 5, an aliquot taken from the reaction mixture after centrifugation (Rs). Lanes 6, 7 and 8 indicate samples taken from first, second and third washing steps, respectively. The weak DNA bands in lanes 4 and 5 are indicated by white arrows.

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Transformation of chemically competent E. coli cells

The negatively charged lipopolysaccharide layer of E. coli prevents the entry of foreign DNA. Thus, E. coli cells are artificially made “competent” for uptake of DNA.[19] Chemical transformation includes treatment of the cells with chloride salts of calcium, magnesium, or rubidium, which is followed by a brief heat-shock at 42°C. Addition of CaCl2 is required to neutralize the unfavorable interactions between DNA and the negatively charged outer layer. When we used non-competent cells for transformation of fCNT-mpDNA bioconjugate, we could not observe any transformants. For this reason, we treated the cells with CaCl2, and we aimed to reduce the electrostatic repulsion between fCNT-mpDNA and lipopolysaccharide layer. Computational studies revealed the cell penetration mechanism of single walled carbon nanotubes (SWCNTs).[34] Therefore, we hypothesized that fCNT-mpDNA including the surrounding Ca2+ ions would be able to penetrate into the cells, and the heat-shock step at 42°C would not be required. In our approach, we excluded the heat-shock step for transformation of fCNT-mpDNA bioconjugate into E. coli cells. It has been reported that heat-pulse and cold-shock steps are responsible for formation of pores on cell surface and lowering of membrane potential, which facilitate DNA to cross inner membrane of E. coli.[35]

As a control, we performed transformation of chemically competent cells with the purified pQE-70/gfp plasmid DNA using heat-shock step at 42°C. When we used NH2-dATP:dATP at 1:9 molar ratio, we could not observe any transformants. We assumed that wide distribution of NH2-dATP on the plasmid DNA resulted in a high degree of fCNT conjugation, and that steric hindrance interfered with gene expression in E. coli cell. Thus, we decided to reduce the number of binding points by decreasing the molar ratio of NH2-dATP. Cell transformation experiments were achieved using the 1:19 ratio, which corresponded to 5% substitution by NH2-dATP. E. coli cells, which were transformed with either control plasmid or with the bioconjugate were spread on agar plates supplemented with ampicillin. Because pQE-70 carries the ampicillin resistance gene, only the cells that acquired the plasmid were able to survive. As shown in Figure 7, the number of CFU was roughly same for both control and bioconjugate transformations. Presence of a cloned gfp gene on the plasmid enabled us to detect GFP fluorescence manually. When the agar plates were inspected under UV light, the cells that expressed GFP were identified manually. Compared with the control, GFP fluorescence of the cells transformed with the bioconjugate was slightly weaker. This could be attributed to the behavior of the linearized plasmid DNA in E. coli cell. When the linearized pBR322 plasmid DNA has been transformed into Ca2+-treated E. coli cells, deletions or rearrangements have been observed.[36] Because of intracellular DNA ligase activity, linearized DNA could recircularize and form the functional plasmid in the cell. In our case, we assumed that recircularization occurred depending on the steric hindrance of the covalently bound fCNT. Therefore, rearrangement of the linearized plasmid, or steric effects could be responsible for the hindered expression of GFP.


Figure 7. Chemically competent E. coli cells were transformed with pQE-70/gfp (as control) and fCNT-mpDNA bioconjugate.

The green fluorescence expressed by E. coli cells was visualized under UV light.

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We achieved transformation of the linearized plasmid DNA using covalently bound fCNT. Although plasmids are widely used for gene transfection, the use of linear DNA fragments avoids the need for plasmid propagation in bacterial cells and antibiotic resistance genes. Thus, linear DNA transfection is preferred for medical purposes. However, nuclease attack on the foreign DNA fragment and low transfection efficiency are limiting factors. Besides its cell penetrating properties, single walled carbon nanotubes (SWCNTs) have been shown to protect nucleic acid strands from nuclease digestion.[37] To accomplish this, the SWCNT has been wrapped non-covalently with a 30-base-paired single-stranded oligonucleotide. This study differs in two ways from our strategy. First, we used a double stranded plasmid DNA, which was linearized by PCR. Second, our strategy was based on a covalent chemical reaction between the carboxylated fCNT and the amino-modified plasmid DNA. The linearized plasmid DNA with a cloned β-galactosidase gene has been transfected into Vero cells using a cationic lipid, albeit with a 10–15% β-galactosidase expression yield.[38] In a more recent study, micro-linear vector has been developed for gene transfection, and GFP expression has been achieved.[39] Considering the need for linear gene delivery systems, the developed fCNT-mpDNA bioconjugate could give insights into the use of CNTs for this aim. CNT-based gene delivery systems have been described in the literature,[40-42] which involve functionalization of CNTs with positively charged groups and electrostatic interactions with DNA. In contrast to these noncovalent conjugates, we developed a covalent conjugate between the linearized plasmid DNA and fCNT.

As previously reported, transformation yield depends on number of the cells, especially when a carrier or auxiliary molecule is present.[43] We performed the transformation experiments using E. coli XL1 Blue cells at OD600 = 200, which required a high cell density. E. coli XL1 Blue is one of the most widely used strains for cloning and transformation.

In another study, transformation has been achieved by microwave exposure to a non-covalent mixture consisting of MWCNT, E. coli DH5α cells and pUC19 plasmid DNA.[44] Compared with this study, our approach relied on a covalent fCNT-mpDNA bioconjugate instead of a noncovalent interaction. Moreover, we did not require additional steps, such as microwave activation or heat-shock step. In the previous study,[44] E. coli cells have been used following washing with phosphate buffered saline buffer. In our study, we washed E. coli cells with CaCl2 in order to make the cells chemically competent.

Plasmid DNA can be delivered into competent E. coli cells using electroporation. Compared to chemical transformation, this method enables a higher transformation efficiency (108−1011 CFU µg−1 DNA). However, it is limited by high rate of cellular mortality, and electroporation conditions should be carefully optimized. As mentioned above, the method of microwave activation of MWCNTs has been developed as an alternative to electroporation, which has resulted in a transformation efficiency ranging between 9 and 32 CFU µg−1 circular pUC19 plasmid DNA.[44] MWCNT-aided plasmid delivery is not as efficient as electroporation, but it eliminates some disadvantages of electroporation, such as cell damage and the need for instrumentation. It should also be considered that electroporation of linear plasmid DNA results in a 1,000-fold drop in transformation efficiency.[45] In our approach, we used fCNT for delivery of PCR-linearized plasmid DNA. Following transformation of the bioconjugate, we investigated GFP expression rather than evaluation of transformation efficiency. Nevertheless, based on the cell growth on the plates, we estimated that transformation efficiency of linear DNA was comparable with that of circular plasmid DNA. We assume that our approach could be particularly useful for delivery of linear DNA, albeit with a lower transformation efficiency than that of electroporation.

Cellular uptake mechanism of CNTs has been discussed in a recent study,[46] which concludes that several internalization pathways might simultaneously operate. To our knowledge, there is no study that could reveal possible interactions between CNT and cellular components inside the cell. However, it has been reported that MWCNTs could induce pro-inflammatory responses depending on their length and cell type.[47] Further experiments are necessary to characterize the effects of E. coli cell type and DNA length on transformation. Moreover, the uptake mechanism of the developed covalent bioconjugate needs to be revealed. EDC chemistry has been used for functionalization of CNTs with single-stranded short DNA oligonucleotides[48-50] and proteins.[51] However, in those studies, delivery of DNA-functionalized CNT into cells has not been attempted. We employed a similar EDC chemistry, but in order to attach the double-stranded plasmid DNA. We also achieved the transformation of E. coli cells with the developed covalent bioconjugate, which allowed the expression of GFP in E. coli cells.


  1. Top of page
  2. Abstract
  3. Introduction
  4. Materials and Methods
  5. Results and Discussion
  6. Conclusion
  7. Acknowledgments
  8. Literature Cited

We developed a covalent bioconjugate between PCR-linearized plasmid DNA and fCNT. E. coli XL1 Blue cells were transformed with the bioconjugate, and the transformed cells were identified by ampicillin resistance and green fluorescence. We provide here a model approach that could be further improved using various modified nucleotides and nanomaterials for intracellular delivery of linear expression cassettes.


  1. Top of page
  2. Abstract
  3. Introduction
  4. Materials and Methods
  5. Results and Discussion
  6. Conclusion
  7. Acknowledgments
  8. Literature Cited

The authors acknowledge financial support from the Research Foundation of Ege University (project number: 10-FEN-052). There is no conflict of interest associated with this manuscript.

Literature Cited

  1. Top of page
  2. Abstract
  3. Introduction
  4. Materials and Methods
  5. Results and Discussion
  6. Conclusion
  7. Acknowledgments
  8. Literature Cited
  • 1
    Mahato RI, Kim SW. Pharmaceutical perspectives of nucleic acid-based therapeutics. London: Taylor & Francis; 2002.
  • 2
    Baum C, Kustikova O, Modlich U, Li ZX, Fehse B. Mutagenesis and oncogenesis by chromosomal insertion of gene transfer vectors. Hum Gene Ther. 2006;17:253263.
  • 3
    Gansbacher B, Danos O, Dickson G, Thielemans K, Cosset FL, Deglon N, Dilber MS, Galun E, Klatzmann D, Mavilio F, Taylor N. French gene therapy group reports on the adverse event in a clinical trial of gene therapy for X-linked severe combined immune deficiency (X-SCID)—position statement from the European Society of Gene Therapy (ESGT). J Gene Med. 2003;5:8284.
  • 4
    Hung MC, Huang L, Wagner E. Nonviral vectors for gene therapy. New York: Academic Press; 1999.
  • 5
    Felgner PL, Tsai YJ, Sukhu L, Wheeler CJ, Manthorpe M, Marshall J, Cheng SH. Improved cationic lipid formulations for in vivo gene therapy. Ann NY Acad Sci. 1995;772:126139.
  • 6
    Boussif O, Lezoualch F, Zanta MA, Mergny MD, Scherman D, Demeneix B, Behr JP. A versatile vector for gene and oligonucleotide transfer into cells in culture and in-vivo—polyethylenimine. Proc Natl Acad Sci USA 1995;92:72977301.
  • 7
    Midoux P, Monsigny M. Efficient gene transfer by histidylated polylysine pDNA complexes. Bioconjug Chem. 1999;10:406411.
  • 8
    Moghimi SM, Hunter AC, Murray JC. Long-circulating and target-specific nanoparticles: theory to practice. Pharmacol Rev. 2001;53:283318.
  • 9
    Iijima S. Helical microtubules of graphitic carbon. Nature 1991;354:5658.
  • 10
    Zhang Y, Bai YH, Yan B. Functionalized carbon nanotubes for potential medicinal applications. Drug Discov Today. 2010;15:428435.
  • 11
    Pantarotto D, Singh R, McCarthy D, Erhardt M, Briand JP, Prato M, Kostarelos K, Bianco A. Functionalized carbon nanotubes for plasmid DNA gene delivery. Angew Chem Int Edit. 2004;43:52425246.
  • 12
    Lacerda L, Russier J, Pastorin G, Herrero MA, Venturelli E, Dumortier H, Al-Jamal KT, Prato M, Kostarelos K, Bianco A. Translocation mechanisms of chemically functionalised carbon nanotubes across plasma membranes. Biomaterials. 2012;33:33343343.
  • 13
    Tasis D, Tagmatarchis N, Bianco A, Prato M. Chemistry of carbon nanotubes. Chem Rev. 2006;106:11051136.
  • 14
    Islam MF, Rojas E, Bergey DM, Johnson AT, Yodh AG. High weight fraction surfactant solubilization of single-wall carbon nanotubes in water. Nano Lett. 2003;3:269273.
  • 15
    Richard C, Balavoine F, Schultz P, Ebbesen TW, Mioskowski C. Supramolecular self-assembly of lipid derivatives on carbon nanotubes. Science. 2003;300:775778.
  • 16
    Zheng M, Jagota A, Semke ED, Diner BA, Mclean RS, Lustig SR, Richardson RE, Tassi NG. DNA-assisted dispersion and separation of carbon nanotubes. Nat Mater. 2003;2:338342.
  • 17
    Tagmatarchis N, Prato M. Functionalization of carbon nanotubes via 1,3-dipolar cycloadditions. J Mater Chem. 2004;14:437439.
  • 18
    Jain AK, Dubey V, Mehra NK, Lodhi N, Nahar M, Mishra DK, Jain NK. Carbohydrate-conjugated multiwalled carbon nanotubes: development and characterization. Nanomedicine. 2009;5:432442.
  • 19
    Ausubel FM. Short protocols in molecular biology: a compendium of methods from current protocols in molecular biology, 5th ed. New York: Wiley; 2002.
  • 20
    Wepasnick KA, Smith BA, Schrote KE, Wilson HK, Diegelmann SR, Fairbrother DH. Surface and structural characterization of multi-walled carbon nanotubes following different oxidative treatments. Carbon. 2011;49:2436.
  • 21
    Yuksel M, Colak DG, Akin M, Cianga I, Kukut M, Medine EI, Can M, Sakarya S, Unak P, Timur S, Yagci Y. Nonionic, water self-dispersible “hairy-rod” poly(p-phenylene)-g-poly(ethylene glycol) copolymer/carbon nanotube conjugates for targeted cell imaging. Biomacromolecules. 2012;13:26802691.
  • 22
    Ji SR, Liu C, Zhang B, Yang F, Xu J, Long JA, Jin C, Fu DL, Ni QX, Yu XJ. Carbon nanotubes in cancer diagnosis and therapy. Biochim Biophys Acta. 2010;1806:2935.
  • 23
    Firme CP III, Bandaru PR. Toxicity issues in the application of carbon nanotubes to biological systems. Nanomedicine. 2010;6:245256.
  • 24
    Cherukuri P, Bachilo SM, Litovsky SH, Weisman RB. Near-infrared fluorescence microscopy of single-walled carbon nanotubes in phagocytic cells. J Am Chem Soc. 2004;126:1563815639.
  • 25
    Davoren M, Herzog E, Casey A, Cottineau B, Chambers G, Byrne HJ, Lyng FM. In vitro toxicity evaluation of single walled carbon nanotubes on human A549 lung cells. Toxicol in Vitro. 2007;21:438448.
  • 26
    Sayes CM, Liang F, Hudson JL, Mendez J, Guo W, Beach JM, Moore VC, Doyle CD, West JL, Billups WE, Ausman KD, Colvin VL. Functionalization density dependence of single-walled carbon nanotubes cytotoxicity in vitro. Toxicol Lett. 2006;161:135142.
  • 27
    Amarnath S, Hussain MA, Nanjundiah V, Sood A. β-galactosidase leakage from Escherichia coli points to mechanical damageas likely cause of carbon nanotube toxicity. Soft Nanosci Lett. 2012;2:4145.
  • 28
    Matczyszyn K, Olesiak-Banska J. DNA as scaffolding for nanophotonic structures. J Nanophoton. 2012;6:064505.
  • 29
    Sacca B, Niemeyer CM. Functionalization of DNA nanostructures with proteins. Chem Soc Rev. 2011;40:59105921.
  • 30
    Berti L, Medintz, IL, Alessandrini A, Facci P. A one-pot functionalization strategy for immobilizing proteins onto linear dsDNA scaffolds. Nanotechnology. 2009;20:235101.
  • 31
    Paul N, Yee J. PCR incorporation of modified dNTPs: the substrate properties of biotinylated dNTPs. Biotechniques. 2010;48:333334.
  • 32
    Cheng XL, Zhong J, Meng J, Yang M, Jia FM, Xu Z, Kong H, Xu HY. Characterization of multiwalled carbon nanotubes dispersing in water and association with biological effects. J Nanomater. 2011;2011:Article ID 938491.
  • 33
    Mahon AR, MacDonald JH, Ott RJ, Mainwood A. A CCD-based system for the detection of DNA in electrophoresis gels by UV absorption. Phys Med Biol. 1999;44:15291541.
  • 34
    Kraszewski S, Bianco A, Tarek M, Ramseyer C. Insertion of short amino-functionalized single-walled carbon nanotubes into phospholipid bilayer occurs by passive diffusion. PLoS One. 2012;7:e40703.
  • 35
    Panja S, Aich P, Jana B, Basu T. How does plasmid DNA penetrate cell membranes in artificial transformation process of Escherichia coli? Mol Membr Biol. 2008;25:411422.
  • 36
    Conley EC, Saunders JR. Recombination-dependent recircularization of linearized pBR322 plasmid DNA following transformation of Escherichia coli. Mol Gen Genet. 1984;194:211218.
  • 37
    Wu Y, Phillips JA, Liu H, Yang R, Tan W. Carbon nanotubes protect DNA strands during cellular delivery. ACS Nano. 2008;2:20232028.
  • 38
    von Groll A, Levin Y, Barbosa MC, Ravazzolo AP. Linear DNA low efficiency transfection by liposome can be improved by the use of cationic lipid as charge neutralizer. Biotechnol Prog. 2006;22:12201224.
  • 39
    Wang HS, Chen ZJ, Zhang G, Ou XL, Yang XL, Wong CK, Giesy JP, Du J, Chen SY. A novel micro-linear vector for in vitro and in vivo gene delivery and its application for EBV positive tumors. PLoS One. 2012;7:e47159.
  • 40
    Singh R, Pantarotto D, McCarthy D, Chaloin O, Hoebeke J, Partidos CD, Briand JP, Prato M, Bianco A, Kostarelos K. Binding and condensation of plasmid DNA onto functionalized carbon nanotubes: toward the construction of nanotube-based gene delivery vectors. J Am Chem Soc. 2005;127:43884396.
  • 41
    Gao LZ, Nie L, Wang TH, Qin YJ, Guo ZX, Yang DL, Yan XY. Carbon nanotube delivery of the GFP gene into mammalian cells. Chembiochem. 2006;7:239242.
  • 42
    Yang K, Qin W, Tang H, Tan L, Xie Q, Ma M, Zhang Y, Yao S. Polyamidoamine dendrimer-functionalized carbon nanotubes-mediated GFP gene transfection for HeLa cells: effects of different types of carbon nanotubes. J Biomed Mater Res A. 201;99:231239.
  • 43
    Ito H, Fukuda Y, Murata K, Kimura A. Transformation of intact yeast-cells treated with alkali cations. J Bacteriol. 1983;153:163168.
  • 44
    Rojas-Chapana J, Troszczynska J, Firkowska I, Morsczeck C, Giersig M. Multi-walled carbon nanotubes for plasmid delivery into Escherichia coli cells. Lab Chip. 2005;5:536539.
  • 45
    Shigekawa K, Dower WJ. Electroporation of eukaryotes and prokaryotes: a general approach to the introduction of macromolecules into cells. Biotechniques. 1988;6:742751.
  • 46
    Lacerda L, Russier J, Pastorin G, Herrero MA, Venturelli E, Dumortier H, Al-Jamal KT, Prato M, Kostarelos K, Bianco A. Translocation mechanisms of chemically functionalised carbon nanotubes across plasma membranes. Biomaterials. 2012;33:33343343.
  • 47
    Liu D, Wang L, Wang Z, Cuschieri A. Different cellular response mechanisms contribute to the length-dependent cytotoxicity of multi-walled carbon nanotubes. Nanoscale Res Lett. 2012;7:361.
  • 48
    Dwyer C, Guthold M, Falvo M, Washburn S, Superfine R, Dorothy E. DNA-functionalized single-walled carbon nanotubes. Nanotechnology. 2002;13:601604.
  • 49
    Jung DH, Kim BH, Ko YK, Jung MS, Jung S, Lee SY, Jung HT. Covalent attachment and hybridization of DNA oligonucleotides on patterned single-walled carbon nanotube films. Langmuir. 2004;20:88868891.
  • 50
    Hirabayashi M. DNA attachment to carbon electrodes for binanoelectronics platforms. PhD Thesis. San Diego State University, USA; 2012.
  • 51
    Gao Y, Kyratzis I. Covalent immobilization of proteins on carbon nanotubes using the cross-linker 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide—a critical assessment. Bioconjug Chem. 2008;19:19451950.