Maksym V. Karachevtsev

Raman Spectroscopy Study and First-Principles Calculations of the Interaction between Nucleic Acid Bases and Carbon Nanotubes

In this work, we have used Raman spectroscopy and quantum chemical methods (MP2 and DFT) to study the interactions between nucleic acid bases (NABs) and single-walled carbon nanotubes (SWCNT). We found that the appearance of the interaction between the nanotubes and the NABs is accompanied by a spectral shift of the high-frequency component of the SWCNT G band in the Raman spectrum to a lower frequency region. The value of this shift varies from 0.7 to 1.3 cm(-1) for the metallic nanotubes and from 2.1 to 3.2 cm(-1) for the semiconducting nanotubes. Calculations of the interaction energies between the NABs and a fragment of the zigzag(10,0) carbon nanotube performed at the MP2/6-31++G(d,p)[NABs atoms]|6-31G(d)[nanotube atoms] level of theory while accounting for the basis set superposition error during geometry optimization allowed us to order the NABs according to the increasing interaction energy value. The order is: guanine (-67.1 kJ mol(-1)) > adenine (-59.0 kJ mol(-1)) > cytosine (-50.3 kJ mol(-1)) approximately = thymine (-50.2 kJ mol(-1)) > uracil (-44.2 kJ mol(-1)). The MP2 equilibrium structures and the interaction energies were used as reference points in the evaluation of the ability of various functionals in the DFT method to predict those structures and energies. We showed that the M05, MPWB1K, and MPW1B95 density functionals are capable of correctly predicting the SWCNT-NAB geometries but not the interaction energies, while the M05-2X functional is capable of correctly predicting both the geometries and the interaction energies.

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

Aqueous suspensions of ultrasonically fragmented double-stranded (fds-) DNA and single-walled carbon nanotubes (SWNTs) have been investigated by UV- and IR-absorption, NIR-emission and Raman spectroscopy. According to gel-electrophoresis, the lengths of the polymer fragments were 100–500 base pairs. Analysis of IR and UV data indicates the presence of both double-stranded (ds) and single-stranded (ss)-regions in the fragments. SWNT complex with DNA was revealed by NIR-emission and Raman spectroscopy. It turned out that fds-DNA is less efficient in holding nanotubes in the aqueous solution than ss-DNA. From the UV-data, the character of the helix-coil transition is seen to be like that for fds-DNA off and on nanotube, however, DNA thermostability increased in this latter case. The effective charge density on the DNA sugar-phosphate backbone of the fds-DNA:SWNT hybrid was less than that of DNA alone. Spectroscopic data can be explained by a model in which the formation of hybrids starts due to the interaction between untwisted ss-regions of DNA and the nanotube: the strands wrap on the tube and thus create an ‘anchor’ for the whole polymer. The ds-part of the polymer is located close to the nanotube.

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

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.

Adsorption of biopolymers on SWCNT: ordered poly(rC) and disordered poly(rI).

Polymer adsorption onto single-walled carbon nanotubes (SWCNTs) depends on its rigidity/flexibility. The adsorption properties of two related homopolynucleotides poly(rI) and poly(rC) but of different rigidities were compared, employing absorption spectroscopy and molecular dynamics simulation. It was shown that adsorption of the poor base stacked poly(rI) onto the nanotube is less effective than that of the strong base stacked poly(rC), the chain of which is of higher rigidity. Analysis of UV absorption spectra of polymer:nanotube suspension at heating until 90 °C, which leads to partial nanotube aggregation because of the weakly bound polymer sliding from the tube surface, revealed that the percent of precipitated nanotubes in suspension with poly(rI) is larger than that in suspension with poly(rC) (16% vs 7%). This fact indicates the higher stability of SWCNT:poly(rC) hybrid in comparison with SWCNT:poly(rI). Less effective adsorption of poly(rI) is confirmed with a weaker hypochromic effect of nanotubes covered with poly(rI) than with poly(rC), which originates from π-π stacking of nitrogen bases with the nanotube surface. Spontaneous adsorption of oligomers on the nanotube simulated by the molecular dynamics showed that oligomer r(I)25 has a weaker energy of binding to the carbon nanotube surface than r(C)25. The oligomer with ordered bases has a tendency to form the stretched conformation along the nanotube, which provides a higher binding energy, while more flexible r(I)25 forms the stable loop spaced away from the nanotube surface, the stability of which is strengthened with H-bonding between bases.

RNA-Wrapped Carbon Nanotubes Aggregation Induced by Polymer Hybridization

The aggregation of poly(rA)-wrapped single-walled carbon nanotubes (SWNTs) induced by hybridization of the adsorbed polymer with free poly(rU) has been studied by differential UV absorption spectroscopy, NIR luminescence, and AFM. After the addition of poly(rU) into a poly(rA):SWNTs suspension, the double-stranded poly(rA)·poly(rU) was formed, which is evident from the characteristic S-like form of the melting curve for the polymer created. Hybridization of free poly(rU) with two complementary poly(rA), one of which was adsorbed to different individual nanotubes, links them together and causes the appearance of aggregates. The aggregation of nanotubes is accompanied with light scattering and can be monitored in an AFM image after the deposition of the suspension on a mica substrate. Molecular dynamic simulation demonstrates a possible structure of the SWNTs aggregate.

Emission of carbon nanotube-DNA-GOX bionanohybrid for glucose detection

Emission of individual single-walled carbon nanotubes (SWNTs) in aqueous suspension with single-stranded DNA (ss-DNA) wrapped around the tube with and without glucose oxidase (GOX) has been studied in the spectral range (9-13)•103 cm-1. GOX was added into the aqueous suspension of SWNTs with wrapped ss-DNA, which was prepared before using ultrasonication/ultracentrifugation treatment. AFM images of the nanotube with the adsorbed enzyme show that GOX retains its native globular structure. Computer simulation of SWNT:DNA:GOX bionanohybrid formation in water demonstrates effective coupling of the enzyme with DNA wrapped around the nanotube. GOX adding was not accompanied by a change of Raman spectrum of nanotubes. However, in the spectrum of nanotubes emission a small spectral blue shift was observed after GOX immobilization. Small glucose injections (1 mM in portion) into the prepared aqueous suspension lead to the quenching of the intensity of nanotube luminescence due to the appearance of H2O2 in the solution as a result of glucose oxidizing. The DNA interlayer between the GOX and nanotube keeps the enzyme activity which usually decreases when the enzyme is bound directly to the nanotube.