Adsorption of Polyadenylic acid on graphene oxide: experiments and computer modeling.

In this work, we study the adsorption of poly(rA) on graphene oxide (GO) using AFM and UV absorption spectroscopies. A transformation of the homopolynucleotide structure on the GO surface is observed. It is found that an energetically favorable conformation of poly(rA) on GO is achieved after a considerable amount of time (days). It is revealed that GO can induce formation of self-structures of single-stranded poly(rA) including a duplex at pH 7. The phenomenon is analyzed by polymer melting measurements and observed by AFM. Details of the noncovalent interaction of poly(rA) with graphene are also investigated using molecular dynamics simulations. The adsorption of (rA)10 oligonucleotide on graphene is compared with the graphene adsorption of (rC)10. DFT calculations are used to determine equilibrium structures and the corresponding interaction energies of the adenine-GO complexes with different numbers of the oxygen-containing groups. The IR intensities and vibrational frequencies of free and adsorbed adenines on the GO surface are calculated. The obtained spectral transformations are caused by the interaction of adenine with GO.

Interaction of double-stranded polynucleotide poly(A:U) with graphene/graphene oxide.

Hybrids formed by DNA/RNA and graphene family nanomaterials are considered as potentially useful multifunctional agents in biosensing and nanomedicine. In this work, we study the noncovalent interaction between double-stranded (ds) RNA, polyadenylic:polyuridylic acids (poly(A:U)) and graphene oxide/graphene (GO/Gr) using UV absorption spectroscopy and molecular dynamics (MD) simulations. RNA melting showed that relatively long ds-RNA is adsorbed onto GO (at an ionic strength of [Formula: see text]) at that a large fraction of RNA maintains the duplex structure. It was revealed that this fraction decreases over long time (during a few days), indicating a slow adsorption process of the long polymer. MD simulations showed that the adsorption of duplex (rA)[Formula: see text]: (rU)[Formula: see text] or (rA)[Formula: see text]: (rU)[Formula: see text] on graphene starts with the interaction between [Formula: see text]-systems of graphene and base pairs located at a duplex tail. In contrast to relatively long duplex (rA)[Formula: see text]: (rU)[Formula: see text] which keeps parallel arrangement along the graphene surface, the shorter one ((rA)[Formula: see text]: (rU)[Formula: see text]) always adopts a perpendicular orientation relative to graphene even in case of the initial parallel orientation. It was found out that (rA)[Formula: see text]: (rU)[Formula: see text] forms the stable hybrid with graphene keeping essential fraction of the duplex, while (rA)[Formula: see text]: (rU)[Formula: see text] demonstrates the duplex unzipping into two single strands with time. The interaction energies between adenine/uracil stacked with graphene as well between nucleotides in water environment were determined.

Enhancement of Photoluminescence from Semiconducting Nanotubes in Aqueous Suspensions due to Cysteine and Dithiothreitol Doping: Influence of the Sonication Treatment.

The influence of tip sonication duration on the spectral characteristics of carbon single-walled nanotubes (SWNTs) in aqueous suspension with single-stranded DNA (ssDNA) has been studied by NIR luminescence, NIR absorption, and Raman spectroscopy. It was revealed that prolongation of sonication leads to weakening of the SWNT polymer coverage and appearance of additional defects on the nanotube surface. Prolongation of the tip sonication treatment of SWNT/ssDNA from 30 to 90 min leads to the increase of the number of individual nanotubes in the aqueous suspension, but it significantly decreases the photoluminescence (PL) from semiconducting SWNTs because more defects are formed on the nanotube surface. At probing the SWNT/ssDNA emission with cysteine or dithiothreitol (DTT) doping the nanotube aqueous suspension showed the different PL intensity enhancement depending on the duration of the sonication treatment and on the ability of these reducing agents to passivate emission-quenching defects on the carbon nanotube sidewall. The magnitude of the PL enhancement rises with sonication prolongation and depends on the nanotube chirality. Tight and ordered polymer coverage of (6,4) nanotubes hampers the access of the reducing agent to emission-quenching defects on the nanotube surface and provides the weaker PL intensity increasing while (7,5) nanotubes show the strongest reaction to the doping effect. The comparison of cysteine and DTT ability to passivate the emission-quenching defects showed the higher efficiency of DTT doping. This prevailing is explained by the stronger reducing activity of DTT which is determined by a lower redox potential of this molecule.

The effect of protonation of cytosine and adenine on their interactions with carbon nanotubes.

Placing electrical charges on nanomaterials is a means to extend their functional capabilities in nanoelectronics and sensoring applications. This paper explores the effect of charging nitrogen bases cytosine (Cyt) and adenine (Ade) via protonation on their noncovalent interaction with carbon nanotubes (CNT) using quantum chemical calculations performed at the M05-2X/6-31++G** level of theory alongside with a molecular graphics method. It is shown that the protonation of the bases causes threefold increase of the interaction energy in the CNT·Cyt·H+ and СNT·Ade·H+ complexes as compared to the CNT complexes formed with neutral bases. There is also some shortening of the base-CNT distance by ca 0.13Ǻ. The visualization of the electrostatic potential distribution with the molecular graphics reveals that the positive potential due to the protonated bases extends to a cylindrical domain of the nanotube segment adjacent to the base binding site. Furthermore, subtraction of the electrostatic potential maps of the protonated bases from the maps of their complexes with CNTs reveals an area of negative potential on the CNT surface, which reflects the location of the adsorbed base. The positive charge transfer of ca 0.3 e from the protonated bases to the CNT strengthens the interaction in the CNT·Cyt·H+ and СNT·Ade·H+ complexes. The analysis of the frontier orbitals shows that the LUMOs of the complexes mainly reside on the CNT, while the HOMOs spread over both components of each complex. The observed effects may facilitate the design of nanomaterials involving nitrogen bases and CNTs.

Hybridization of poly(rI) with poly(rC) adsorbed to the carbon nanotube surface.

Hybridization of homopolynucleotide poly(rC) adsorbed to the carbon nanotube surface with poly(rI) free in solution has been studied by absorption spectroscopy and molecular dynamics method. It was found that hybridization on the nanotube surface has a slow kinetics, the behavior of which differs essentially from fast hybridization of free polymers. The duplex obtained is characterized with the reduced thermostability and a lower hyperchromic coefficient than it was observed when the duplex was formed in the absence of the nanotube. These features point to the imperfectness in the structure of the duplex hybridized on the nanotube surface. Computer simulation showed that the strong interaction of nitrogen bases with the nanotube surface weakens significantly hybridization of two complementary oligomers, as the surface prevents the necessary conformational mobility of the polymer to be hybridized.

Excitonic energy transfer in polymer wrapped carbon nanotubes in gradually grown nanoassemblies.

We investigate the exciton energy transfer (ET) in nanoassemblies (nanotube based aggregates) formed by polymer wrapped single-walled carbon nanotubes (SWNTs) using photoluminescence (PL) spectroscopy and simulation. The distinctive feature of this study is the gradual growth of such nanostructures in aqueous medium induced by increasing the concentration of porphyrin molecules stitching nanotube-polymer complexes in densely packed assemblies. Experimental dependencies of PL intensity on the porphyrin concentration for different types of semiconducting SWNTs demonstrate step-like behavior controlled by the amount of bound nanotubes and are in good agreement with the simulating model. The simulation algorithm determines the criterion of the aggregate formation depending on the number of porphyrin molecules per tube and the cascade exciton energy transfer between neighboring semiconducting nanotubes of different chiralities. Aggregates of small sizes (up to six-eight individual tubes) contain mostly semiconducting species, while aggregates of a larger size (up to several tens of tubes) incorporate metallic SWNTs, inducing strong PL quenching. From the fitting procedure, an ET rate of 0.6 × 10(10) s(-1) has been determined which is consistent with the center to center distance (∼2.3 nm) between adjacent tubes separated by polymer and porphyrin molecules. The threshold of the dimer formation corresponds to one porphyrin molecule per ∼20 nm of tube lengths that was supported by molecular dynamics simulation. These findings provide insight into the ET mechanism in SWNT nanoassemblies of variable sizes, which can be gradually controlled by the external factor (the concentration of porphyrin molecules).

Self-assemblies of tricationic porphyrin on inorganic polyphosphate.

Self-assemblies formed by the new synthesized tricationic porphyrin derivative (TMPyP(3+)) on the polyanionic inorganic polyphosphate (PPS) in aqueous solution were studied using different spectroscopic techniques and DFT calculation method. From the fluorescence quenching of the bound TMPyP(3+) molecules and their Raman spectra we conclude that porphyrin chromophores form the stable π-π stacking-assemblies onto PPS polyanions. The transformation of the Soret band in absorption spectra at different PPS/TMPyP(3+)concentration ratios evidences that the assemblies are mixtures of J- and H-aggregates. Molecular modeling performed shows that the flexibility of PPS strand allows a realization of spiral or "face-to-face" one-dimensional structures formed by porphyrin molecules arranged in parallel and antiparallel modes. The peculiarity of PPS structure allows a formation of two porphyrin stacks on opposite sides of polymer strands that result in the appearance of higher-order aggregates. Their size was estimated from the light scattering data. Distinctions between TMPyP(3+) and TMPyP4 aggregation on PPS template are discussed.

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.

Peculiarities of homooligonucleotides wrapping around carbon nanotubes: molecular dynamics modeling.

Spontaneous adsorption of homooligonucleotides dC(25), dT(25), dG(25), and dA(25) on the surface of the carbon nanotube (16,0) has been simulated by the molecular dynamics method. It was demonstrated that the rate of pyrimidine oligonucleotide wrapping around the nanotube is higher than that of purine ones which do not form a complete pitch even after the maximum simulation time (50 ns). This behavior can be explained by a stronger self-stacking between the purines than pyrimidines, which prevents the reorientation of the polymer required for the acquisition of a more energetically favored conformation on the nanotube. Estimations obtained from modeling allowed to establish the oligonucleotide row which demonstrates decreasing interaction energies between oligonucleotides and the carbon nanotube: d(T)(25) > d(C)(25) > d(A)(25) ≈ d(G)(25). It was shown that the temperature growth increases the rate of oligonucleotides to reach the maximum binding energy mainly due to the destruction of nitrogen base self-stacking. Ribonucleic oligonucleotides r(C)(25), r(A)(25), and r(G)(25) do not make a pitch around the nanotube for 50 ns. The presence of the additional hydroxyl group in ribose restricts the conformational flexibility of ribonucleic oligonucleotides in comparison with their deoxy analogues and this reduces the possibility of rapid occupation of the stable conformation on the nanotube surface.

Spectroscopic detection of tetracationic porphyrin H-aggregation on polyanionic matrix of inorganic polyphosphate.

Self-assembly of tetracationic porphyrin TMPyP(4+) onto polyanionic matrix of inorganic polyphosphate (PPS) in aqueous solutions has been studied in a wide range of molar phosphate-to-dye ratios using techniques of polarized fluorescence, absorption, resonance Raman spectroscopy and static light scattering. The binding of TMPyP(4+) to PPS is characterized by the binding constant of 3 x 10(5) M(-1) and the cooperativity parameter of about 150. The fluorescence quenching of the bound TMPyP(4+) evidences the stacking of the porphyrine chromophores. Under the stoichiometric binding ratio TMPyP(4+) forms extended continuous face-to-face aggregates (so-called H-aggregates) which manifest themselves by a blue shift (12 nm) and a large hypochromisity (51%) of the Soret absorption band. Each face-to-face TMPyP(4+) stack is formed with participation of four PPS chains. Formation of such columnar aggregates is promoted by the ability of PPS chains to take a helix conformation where negative charges are arranged along two oppositely situated rows with intercharge distance of 0.36 nm which corresponds to the thickness of the porphyrin pi-electronic system. The ability of each PPS strand to be template for formation of two porphyrin stacks results in the integration of the adjacent stacks into higher-order aggregates which dimension was estimated from the fluorescence polarization data.

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.

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.

IR spectra of photopolymerized C60 films. Experimental and density functional theory study.

IR spectra of photopolymerized fullerene films obtained by simultaneous deposition and UV irradiation were measured in the range of 1500-450 cm(-1). The degree of the polymerization of the C60 films was estimated to be about 95%. To assist the assignment of the experimental IR spectra of the films, quantum chemical calculations of the equilibrium structures of the C60 dimers and trimers were performed at the DFT(B3LYP)/3-21G level of theory. Next, IR frequencies and intensities for those structures were calculated. For the five-trimer structures found in the calculations, the relative stabilities were determined at the B3LYP/4-31G and B3LYP/6-31G levels and used to select the lowest-energy trimers, which are Trimer A (angle between monomer centers is 90 degrees ) and Trimer B (angle between monomer centers is 120 degrees). Next, the IR spectra of the polymerized fullerene films were compared with the calculated frequencies of the lowest-energy dimer and the two lowest-energy trimers. On the basis of this analysis and on the comparison of the film spectra with the IR spectra of the C60 dimer and trimer spectra obtained by other methods, it was shown that the main components of the films are C60 dimers and the orthorhombic (O) polymer phase. The tetragonal (T) and rhombohedral (R) polymers, as well as small amounts of monomers, were also found. Although vibrational frequencies of different C60 phases are similar in most cases, we found several unique spectral features of the C60 dimer and other polymers that may be used to determine the composition of the polymerized C60 film.

Mg2+ ion effect on conformational equilibrium of poly A . 2 poly U and poly A poly U in aqueous solutions.

Differential UV spectroscopy and thermal denaturation were used to study the Mg(2+) ion effect on the conformational equilibrium in poly A.2 poly U (A2U) and poly A . poly U (AU) solutions at low (0.01 M Na(+)) and high (0.1 M Na(+)) ionic strengths. Four complete phase diagrams were obtained for Mg(2+)-polynucleotide complexes in ranges of temperatures 20-96 degrees C and concentrations (10(-5)-10(-2)) M Mg(2+). Three of them have a 'critical' point at which the type of the conformational transition changes. The value of the 'critical' concentration ([Mg(t)(2+)](cr)=(4.5+/-1.0) x 10(-5) M) is nearly independent of the initial conformation of polynucleotides (AU, A2U) and of Na(+) contents in the solution. Such a value is observed for Ni(2+) ions too. The phase diagram of the (A2U+Mg(2+)) complex with 0.01 M Na(+) has no 'critical' point: temperatures of (3-->2) and (2-->1) transitions increase in the whole Mg(2+) range. In (AU+Mg(2+)) phase diagram at 0.01 M Na(+) the temperature interval in which triple helices are formed and destroyed is several times larger than at 0.1 M Na(+). Using the ligand theory, a qualitative thermodynamic analysis of the phase diagrams was performed.