A model of an optical biosensor detecting environment

Heller et. Al. (Science 311, 508 (2006)) demonstrated the first DNA-CN optical sensor by wrapping a piece of double-stranded DNA around the surface of single-walled carbon nanotubes (CN). This new type of optical device can be placed inside living cells and detect trace amounts of harmful contaminants by means of near infrared light. Using a simple exciton theory in nanostructures and the phenomena of B-Z structural phase transition of DNA, we investigate the working principle of this new class of optical biosensor from DNA by using the nanostructure surface as a sensor to detect the property change of DNA as it responds to the presence of target ions. We also propose some new design models by replacing carbon nanotubes with graphene ribbon semiconductors.Comment: 4 pages, 4 figures, Accepte

Optical Tweezers as an Effective Tool for Spermatozoa Isolation from Mixed Forensic Samples

A single focus optical tweezer is formed when a laser beam is launched through a high numerical aperture immersion objective. This objective focuses the beam down to a diffraction-limited spot, which creates an optical trap where cells suspended in aqueous solutions can be held fixed. Spermatozoa, an often probative cell type in forensic investigations, can be captured inside this optical trap and dragged one by one across millimeter-length distances in order to create a cluster of cells which can be subsequently drawn up into a capillary for collection. Sperm cells are then ejected onto a sterile cover slip, counted, and transferred to a tube for DNA analysis workflow. The objective of this research was to optimize sperm cell collection for maximum DNA yield, and to determine the number of trapped sperm cells necessary to produce a full STR profile. A varying number of sperm cells from both a single-source semen sample and a mock sexual assault sample were isolated utilizing optical tweezers and processed using conventional STR analysis methods. Results demonstrated that approximately 50 trapped spermatozoa were required to obtain a consistently full DNA profile. A complete, single-source DNA profile was also achieved by isolating sperm cells via optical trapping from a mixture of sperm and vaginal epithelial cells. Based on these results, optical tweezers are a viable option for forensic applications such as separation of mixed populations of cells in forensic evidence

Optical conductivity of wet DNA

Motivated by recent experiments we have studied the optical conductivity of DNA in its natural environment containing water molecules and counter ions. Our density functional theory calculations (using SIESTA) for four base pair B-DNA with order 250 surrounding water molecules suggest a thermally activated doping of the DNA by water states which generically leads to an electronic contribution to low-frequency absorption. The main contributions to the doping result from water near DNA ends, breaks, or nicks and are thus potentially associated with temporal or structural defects in the DNA.Comment: 4 pages, 4 figures included, final version, accepted for publication in Phys. Rev. Let

Theory of the Optical Properties of a DNA-Modified Gold Nanoparticle System

We describe a simple model for the melting and optical properties of a DNA/gold nanoparticle aggregate. The aggregate is modeled as a cluster of gold nanoparticles on a periodic lattice connected by DNA bonds, and the extinction coefficient is computed using the discrete dipole approximation. The optical properties at fixed wavelength change dramatically at the melting transition, which is found to be higher and narrower in temperature for larger particles, and much sharper than that of an isolated DNA link. All these features are in agreement with available experiments.Comment: 4 pages, 3 figures. To be published in Physica

Phase Transition of DNA-Linked Gold Nanoparticle

Melting and hybridization of DNA-capped gold nanoparticle networks are investigated with optical absorption spectroscopy. Single-stranded, 12-base DNA-capped gold nanoparticles are linked with complementary, single-stranded, 24-base linker DNA to form particle networks. Compared to free DNA, a sharp melting transition is seen in these networked DNA-nanoparticle systems. The sharpness is explained by percolation transition phenomena.Comment: 9 pages, 4 figures, submitte

Optical Identification of a DNA-Wrapped Carbon Nanotube: Signs of Helically Broken Symmetry

High intrinsic mobility and small, biologically-compatible size make single-walled carbon nanotubes (SWNTs) in demand for the next generation of electronic devices. Further, the wide range of available bandgaps due to changes in diameter and symmetry give SWNTs greater versatility than traditional semiconductors. Single-stranded DNA has been employed to make these desirable properties accessible for large scale fabrication of devices. Because single-stranded DNA can helically wrap a SWNT, forming a stable hybrid structure, DNA/polymer wrapping has been used to disperse bundles of intrinsically hydrophobic SWNTs into individual tubes in aqueous solution. The ability to isolate individual tubes, make them soluble, and separate them according to symmetry would enable fabrication of SWNT optoelectronic devices that benefit from the unique electronic properties of specific nanotube structures. Envisioning optoelectronic applications of nanotubes, we investigate whether the optical properties of DNA-wrapped SWNT materials are different than those of pristine SWNTs. Our previous work found that bandstructures of DNA-SWNTs were indeed affected by the charged wrap. That is, the direct optical bandgap, $E_{11}$, decreases, but changes are fairly small. This is consistent with the available experimental data in standard experimental geometry in which incident light is polarized along the SWNT axis. Here we consider optical absorption of light with perpendicular (or circular) polarization with respect to the tube axis, which has been measured experimentally for SWNTs dispersed using a surfactant. In this geometry we find qualitative changes in the absorption spectra of SWNTs upon hybridization with DNA, including strong optical circular dichroism in non-chiral SWNTs.Comment: 3 color figures, 4 pages, accepted for Small journa

Flat-top TIRF illumination boosts DNA-PAINT imaging and quantification

Super-resolution (SR) techniques have extended the optical resolution down to a few nanometers. However, quantitative treatment of SR data remains challenging due to its complex dependence on a manifold of experimental parameters. Among the different SR variants, DNA-PAINT is relatively straightforward to implement, since it achieves the necessary 'blinking' without the use of rather complex optical or chemical activation schemes. However, it still suffers from image and quantification artifacts caused by inhomogeneous optical excitation. Here we demonstrate that several experimental challenges can be alleviated by introducing a segment-wise analysis approach and ultimately overcome by implementing a flat-top illumination profile for TIRF microscopy using a commercially-available beam-shaping device. The improvements with regards to homogeneous spatial resolution and precise kinetic information over the whole field-of-view were quantitatively assayed using DNA origami and cell samples. Our findings open the door to high-throughput DNA-PAINT studies with thus far unprecedented accuracy for quantitative data interpretation

Theory of Melting and the Optical Properties of Gold/DNA Nanocomposites

We describe a simple model for the melting and optical properties of a DNA/gold nanoparticle aggregate. The optical properties at fixed wavelength change dramatically at the melting transition, which is found to be higher and narrower in temperature for larger particles, and much sharper than that of an isolated DNA link. All these features are in agreement with available experiments. The aggregate is modeled as a cluster of gold nanoparticles on a periodic lattice connected by DNA bonds, and the extinction coefficient is computed using the discrete dipole approximation. Melting takes place as an increasing number of these bonds break with increasing temperature. The melting temperature corresponds approximately to the bond percolation threshold.Comment: 5 pages, 4 figure. To be published in Phys. Rev.