Interaction of fragmented double-stranded DNA with carbon nanotubes in aqueous solution

Gladchenko, G. O.; Karachevtsev, Maksym V.; Leontiev, V. S.; Valeev, Vladimir A.; Glamazda, A. Yu.; Plokhotnichenko, A. M.; Stepanian, S. G.

doi:10.1080/00268970601061220

Cited by 37 publications

(32 citation statements)

References 36 publications

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“…Recent computer simulations showed that not all the nitrogen bases of the polymer are in a stacking arrangement with the nanotube surface. [25,32] This conclusion raises questions about the mutual position of these bases and the presence or absence of binding between them. Such a variety of the arrangement of bases close to the tube surface may be manifested in subsequent hybridization with the complementary polymeric chain.…”

Section: Introductionmentioning

confidence: 93%

“…It was demonstrated that SWNTs can readily be dispersed by long genomic doublestranded DNA (dsDNA). [25] Long ssDNA can also be synthesized by a biochemical technique known as "rolling-circle amplification". [26] A longer ssDNA strand is able to wrap around the nanotube in several layers.…”

Section: Introductionmentioning

confidence: 99%

“…Native dsDNA was also thermostabilized by 2-6 8C (depending on the ionic strength of suspension) after its adsorption to the nanotube surface. [25] The temperature independence (from 20 to 50 8C) of the circular dichroism spectrum of double-stranded 20-mer oligonucleotides with a sequence of repeating GT units, adsorbed on SWNTs, was also interpreted as a strong DNA binding to the nanotube surface. [51] In addition, Figure 6 (curve 3) presents the melting curve of the double-stranded polymer formed by free poly(rU) and poly(rA) NT .…”

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confidence: 99%

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Adsorption of Poly(rA) on the Carbon Nanotube Surface and its Hybridization with Poly(rU)

Karachevtsev¹,

Gladchenko²,

Karachevtsev³

et al. 2008

ChemPhysChem

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Adsorption of poly(rA) on a single-walled carbon nanotube surface in aqueous suspension and the subsequent hybridization of this polymer with free poly(rU) is studied. A comparison of the temperature dependence of the absorbance of free poly(rA) and poly(rA) adsorbed on the nanotube surface [poly(rA)(NT)] at nu(max)= 38,500 cm(-1) shows that the thermostability of the adsorbed polymer is higher. Molecular dynamics simulations demonstrate that more than half of the adenines are not stacked on the tube surface and some of them undergo self-stacking. After addition of a complementary poly(rU) to the poly(rA)(NT) suspension, a double-stranded polymer is formed as confirmed by the characteristic S-like form of its melting curve. However, the melting temperature of this polymer is lower than that of the free poly(rA)poly(rU) duplex. This result indicates that poly(rU) hybridization with poly(rA)(NT) occurs with defects along the whole length of the polymer because of pi-pi stacking between nitrogen bases and the nanotube surface, which hinders the usual hybridization process. Computer modeling demonstrates different possible structures of hybridized polymers on the nanotube surface.

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Section: Introductionmentioning

confidence: 93%

Section: Introductionmentioning

confidence: 99%

mentioning

confidence: 99%

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Adsorption of Poly(rA) on the Carbon Nanotube Surface and its Hybridization with Poly(rU)

Karachevtsev¹,

Gladchenko²,

Karachevtsev³

et al. 2008

ChemPhysChem

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“…Iijima et al [17] produced high-resolution TEM and STM images of dsDNA/multiwalled CNTs. Gladchenko et al [18] characterized fragmented dsDNA-wrapped SWNTs in aqueous solutions. He and Bayachou [19] described the layer-by-layer fabrication and characterization of dsDNA-wrapped SWNT particles.…”

mentioning

confidence: 99%

Regulation of the Near‐IR Spectral Properties of Individually Dissolved Single‐Walled Carbon Nanotubes in Aqueous Solutions of dsDNA

Noguchi

Fujigaya

Niidome

et al. 2008

Chemistry A European J

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Two different single-walled carbon nanotubes (SWNTs), the so-called HiPco and CoMoCAT, have been individually dissolved in aqueous solutions of double-stranded DNA (dsDNA). Atomic force microscopy (AFM) revealed the fine structures of the dsDNA-wrapped SWNTs. The near-IR absorption and photoluminescence (PL) spectra of aqueous solutions of dsDNA-wrapped SWNTs were recorded and, in pure water, we observed only a single two-dimensional PL spot from (6,5) SWNTs for both HiPco and CoMoCAT. In sharp contrast, when Tris-EDTA (TE) buffer was used in place of pure water, the PL-mapping images of the solutions showed chirality indices of (6,5), (7,5), (7,6), (8,4), (9,4), and (10,2) for HiPco-SWNTs, and (6,5) and (7,5) for CoMoCAT-SWNTs. The first semiconducting bands in the near-IR absorption spectra of solutions of dsDNA-wrapped SWNTs are different. To explain the observed differences in the near-IR absorption and PL behavior we conducted several experiments and found that the near-IR optical properties of the SWNTs can be modulated by changing the pH of the solutions. The pH break-points for near-IR absorption bleaching and PL quenching are different and the phenomena are explained by differences in the numbers of holes generated on the SWNTs. These findings are important from both fundamental and applied viewpoints.

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“…37,[41][42][43][44][45][46] These models have been used to study SWCNTs interacting with oligomers of varying lengths (from ∼0 bases 30,47 to ∼100 bases) for both singlestranded DNA (ssDNA) [48][49] and double-stranded DNA (dsDNA), 48 as well as hybrids consisting of both alternating ssDNA and dsDNA. 41 Changing the length and sequence of the DNA, as well as the SWCNT diameter and chirality, can strongly affect the dispersion process.…”

Section: Molecular-level Interactions Of Dna-swcnt Hybridsmentioning

confidence: 99%

Review—Engineering the Selectivity of the DNA-SWCNT Sensor

Kupis-Rozmysłowicz¹,

Antonucci²,

Boghossian³

2016

ECS J. Solid State Sci. Technol.

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Single-walled carbon nanotubes (SWCNTs) demonstrate a unique combination of optical, chemical, and physical properties that render them suitable for a variety of sensing applications. Their photostable near-infrared (nIR) fluorescence emissions are highly sensitive to perturbations in the surrounding SWCNT environment, enabling optical sensors with single-molecule detection limits. Despite these immanent advantages, SWCNTs lack the inherent molecular recognition capabilities required for selective sensing applications. One approach to tuning sensor selectivity is to engineer synthetic and biological wrappings that cover the nanotube's surface in a manner that limits chemical access to the surface to specific target analytes. Among the numerous possible wrappings, deoxyribonucleic acid (DNA) has emerged as the most studied polymeric wrapping. In addition to the sequence-dependent tunability DNA offers in engineering selectivity, DNA assumes a peculiar helical wrapping conformation along the SWCNT surface that has been the focus of many experimental and computational studies. In this review, we summarize some of the major findings in the field, focusing on the underlying molecular interactions responsible for the conformational and molecular recognition elements of the wrapping. Special focus is given to characterizing the nucleotide binding affinity, DNA sequence dependency, DNA length variation, SWCNT chirality, and sugar backbone (RNA vs. DNA) contributions to the wrapping conformation and SWCNT fluorescence. This article concludes with an assessment of the latest DNA-SWCNT-based sensing platforms used for the selective, single-and multi-modal detection of target analytes. Since their introduction in the early 60s, 1 biosensors have become an indispensable part of our daily lives, finding disparate applications in a variety of analytical fields ranging from biomedical diagnostics to environmental monitoring to food technology.2 Notably, optical biosensors based on fluorescent-light emission, which exploit diverse fluorescent probes as labeling agents for the recognition units, have emerged as highly sensitive, rapid, reproducible, and simple-to-operate analytical tools capable of quantitatively monitoring specific molecular interactions in real time.3,4 However, several drawbacks limit their application in more complex chemical and biological environments. For example, typical fluorescence-based sensors conventionally employ organic fluorophores that emit fluorescence with visible wavelengths that do not penetrate well through biological tissue.5 Furthermore, such fluorophores are often subject to rapid photobleaching, thus compromising their sensor lifetimes. These limitations are unfavorable for long-term in vivo sensing 6 for diagnostic applications. Recent research is thus focused on finding new technologies and materials to engineer novel sensing platforms with increased sensitivity and selectivity over extended periods of time.Single-walled carbon nanotubes (SWCNTs) have become widely used in a new genera...

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Interaction of fragmented double-stranded DNA with carbon nanotubes in aqueous solution

Cited by 37 publications

References 36 publications

Adsorption of Poly(rA) on the Carbon Nanotube Surface and its Hybridization with Poly(rU)

Adsorption of Poly(rA) on the Carbon Nanotube Surface and its Hybridization with Poly(rU)

Regulation of the Near‐IR Spectral Properties of Individually Dissolved Single‐Walled Carbon Nanotubes in Aqueous Solutions of dsDNA

Review—Engineering the Selectivity of the DNA-SWCNT Sensor

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