Optical Properties of DNA in Aqueous Solution

Abstract

In the study of DNA electric birefringence, it is usual to use theories that consider that molecules in solution are small in relation to the light wavelength. In this work, we study the DNA electric birefringence using a broken-rod macroion (BRM) model composed of two cylindrical arms which does not restrict the size of the molecules. To achieve this, we include the inhomogeneity effect of the light electric field through the molecule and the interaction between its different parts. To analyze the interaction between a molecule and the incident beam of light, we apply the discrete dipole approximation (DDA), according to which each molecule is described as a finite array of electronic coupled oscillators. The electric birefringence is calculated from the oscillator polarizability. This is obtained from experimental data of electric birefringence saturation and from the increment of the solution refraction index in relation to that of the solvent. Furthermore, the oscillator polarizability is also estimated from DNA absorption spectrum using the KronigKramers relations. This allows us to analyze the contributions of the different absorption bands of DNA to the electric birefringence. We analyze the influence of the inhomogeneity of the light electric field and of the intramolecular interactions in the characterization of DNA optical properties using electric birefringence measurements.

Plasmonic Manipulation of DNA using a Combination of Optical and Thermophoretic Forces: Separation of Different-Sized DNA from Mixture Solution

“…However, it is very difficult to precisely evaluate α for flexible DNA chains taking random coil structures in water. Umazano and Bertolotto theoretically calculated values of α (polarizability) for DNA at visible light frequencies 48 . They adopted the broken-rod macroion (BRM) model and applied the discrete dipole approximation (DDA), according to which each molecule is described as a finite array of electronic coupled oscillators.…”

Probing the dynamical behavior of surface dipoles through energy-absorption interferometry

“…The α m are proportional to the levels of excitation of each of the incident modes, whereas the β n correspond to the relative responsivities with which the system absorbs energy in each of its modes. According to (25), the response matrix L contains two effects: the intrinsic ability of the dipoles to absorb energy, Σ r , and the appearance of collective behaviour due to scattering, [M] −1 . The electromagnetic Green's dyadic induces a wide variety of coherent behaviour, but additionally an elastic Green's dyadic could have been included in (2) to describe acoustic coupling through the excitation of surface waves.…”

“…According to (25) jφ2 corresponded to point sources at the positions of the dipoles, the response matrix L could be found directly, but in reality only distributed fields are possible.…”

“…where Σ is the matrix equivalent of (11), and Σ r is the real part. Taking the trace of each side of the last line of (25), noting that the trace is invariant to cyclic permutation, and calculating the expectation value gives…”

“…The SUT is modeled by using the Discrete Dipole Approximation (DDA) [16][17][18], to-gether with a polarizability that allows for bound states and damping to the substrate. DDA was originally devised [19] to model light extinction by astrophysical particles, but has since been developed in areas as diverse as modeling the aggregation of irregular particles from colloids [20], the scattering of light by particles on surfaces [21,22], the scattering of light by periodic targets [23], and the optical properties of viruses, proteins, DNA, and blood cells [24][25][26]. Formulating our measurement procedure in terms of DDA opens the way to predicting the interferometric response of a wide variety of complex objects such as biomolecules, droplets, and nanoparticles, and thereby creating representative dynamical models of measured interferometric data.…”