Optical Absorption of DNA−Carbon Nanotube Structures

Abstract

We measured the UV optical absorption of single-stranded DNA bound to single-walled carbon nanotubes (DNA/SWNT). The nucleotide absorbance from DNA/SWNT provides the first experimental confirmation that DNA binds to nanotubes through π-stacking. Because the hypochromic absorbance typical of π-stacked structures are expected to occur primarily for DNA dipole transitions that lie along the axis of the optically anisotropic SWNTs, the absorbance changes following binding of DNA to nanotubes reveal the preferred orientation assumed by each of the four bound nucleotides with respect to the nanotube's long axis.Zheng et al. reported that bundles of SWNTs in water can be effectively dispersed by sonication in the presence of single-stranded DNA (ssDNA). 1,2 Molecular modeling by that group suggested that DNA molecules hybridize with individual nanotubes by wrapping around them, with the interaction strength being provided by π-stacking, with the plane of the aromatic nucleotide bases oriented parallel to the surface of the nanotube. 1 The novel properties of this hybrid structure make it possible to separate a motley collection of nanotubes by electronic type, 1 an essential step toward nanotube electronic devices. The electrical properties of the hybrid may also be of special interest in the development of molecular-based electronic devices. Finally, nanotubes offer the potential of providing a scaffold on which DNA molecules can be oriented, manipulated, and studied without the need for chemical functionalization.Although DNA/SWNT structures have been studied using optical absorption spectroscopy in the past, 1-7 little attention has been paid to the range of wavelengths of most interest for examining DNA, namely the UV region. DNA's UV absorbance has been studied extensively and has been central in understanding conformational changes of nucleic acids, such as the transition from double-stranded to single-stranded DNA. 8 Absorbance studies of DNA/SWNT samples have largely ignored the UV because, until not long ago, there was very little known about the absorbance properties of SWNT in this region. Some authors argue that the UV absorbance is entirely due to amorphous carbon material, 7 while others find the two absorbance peaks in the UV to be intrinsic to the nanotubes and, furthermore, to display a strong polarization dependence. 9 By the methods described here, we have found the UV absorbance peak locations and intensities to be repeatable under a variety of SWNT sample preparation conditions, and we demonstrate that the UV region provides important information about DNA/SWNT structure.We used optical absorption spectroscopy from λ) 190900 nm to explore the DNA-SWNT interaction of SWNT dispersed with DNA homopolymers of poly d(A30), poly d(C30), poly

Near‐Infrared Fluorescent Sensors based on Single‐Walled Carbon Nanotubes for Life Sciences Applications

“…Under direct sonication in the presence of SWCNTs, the ssDNA self-assembles along the nanotube in a manner such that its nucleobases directly interact with the nanotube surface and its charged backbone faces outward towards its aqueous surroundings. This is consistent to previous experimental evidence including atomic force microscopy (AFM) [26c, 41] and optical absorption data, [42] as well as molecular dynamics simulationsreported to date. [43] To examine the sequence-dependency of this dispersion in chirality separation, SWCNTs were dispersed using different sequences of ssDNA and subsequently subjected to anion-exchange chromatography, wherein electrostatic interactions between the negatively charged DNA and the positively charged column govern the nanotube elution times.…”

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

“…SDS is known to have no influence on SWNT properties upon dispersion and no noticeable absorption in the range of wavenumbers studied. [35] Nevertheless, upon UV absorption measurement, we excluded SDS absorption by placing an aqueous solution of SDS at an appropriate concentration into the comparative cuvette of the spectrometer. Spectrum b (Figure 2) was obtained for a nanotube suspension content which is the same as in the poly(rA):SWNT aqueous suspension (spectrum a) that was determined from identical absorption at n % 14 000 cm…”

“…Adsorption of poly(rA) on the nanotube surface induces a red shift of the UV part of the spectrum, which results from p-p stacking interactions of the poly(rA) nitrogen base with the SWNT. [35] At the same time, the intensity values of both spectra at n = 38 500 cm À1 (the wavenumber at which melting curves are registered) coincide. When employing differential absorption spectroscopy (see Experimental Section), we could easily exclude the intrinsic absorption of the nanotubes and record changes in optical absorption of only a nucleic acid.…”

Translocation of biomolecules through solid‐state nanopores: Theory meets experiments

“…Embedding the ss-DNA-CNT structure into a nanopore and measuring the transverse conductance from the CNT to the nanopore wall could be an equally promising approach as the proposed device. In a similar manner, the optical absorption of the bases-CNT system is also distinguishable for each base, 62 possibly allowing for an optical detection of the nucleotides. The use of CNTs as nonpolar pores through which nucleic acids are being translocated has also been demonstrated through MD calculations.…”