Improvement of fidelity of molecular DNA computing using laser spectroscopy

Abstract

This work is devoted to application of laser Raman spectroscopy to improve the fidelity of molecular computing by DNA strands. The developed method provides determination of concentrations of specific nitrogenous bases not lower than 0.03 g l −1 and the accuracy of determining the total concentration of DNA in solutions 0.02-0.04 g l −1 by the Raman spectra of DNA solutions. The method allows us to control the temperature of DNA solutions in the process of molecular computing with an accuracy better than 0.2 °C. The obtained results provide required control of the parameters of DNA solutions to increase the speed and accuracy of solving the problems in the results of molecular computing.

Improvement of reliability of molecular DNA computing: solution of inverse problem of Raman spectroscopy using artificial neural networks

“…In addition, for a DNA concentration range of 0-9 g l −1 [30], the calibration dependence of the intensity of the nitrogenous base markers on its concentration could be approximated really well by a straight line. However, according to the literature, for a concrete problem the maximal concentration of DNA can vary within rather wide limits-from 3.32 g l −1 [33] up to 32.5 g l −1 [34].…”

“…The authors of this publication have demonstrated that Raman spectroscopy allowed us to determine (in non-contact real-time mode) both the total concentration of DNA molecules in the solution and the concentration of individual nitrogenous bases in their single-component solutions, using the calibration dependencies of Raman marker bands of nitrogenous bases (figure 1) on their concentration in the range of 0 to 9 g l −1 [30,31]. Also it was shown that the use of laser Raman spectroscopy for monitoring biochemical reactions provided for the detection and control of the processes of renaturation and denaturation of DNA strands, determination of the state of the strands, and the control of possible mutations in DNA molecules [32].…”

Hydrogen bond network relaxation resolved by alcohol hydration (methanol, ethanol, and glycerol)

“…To minimize the effect of elastic scattering and extract useful Raman signal of water in the spectral region of 50–300 cm −1 , we used the so‐called R‐representation method proposed by Brooker et al The measured Raman intensity I ( ω ) can be expressed by where C is a constant, ω 0 is the absolute wavenumber (in wavenumber units) of the excitation laser line, ω i is the Raman shift, S i is the intrinsic molar scattering activity at ω i for a Raman process, h is the Plank constant, k is the Boltzman constant, c is the speed of light, and T is the absolute temperature. To eliminate the dependence on temperature and wavenumber, a reduced Raman spectrum R ( ω ) is defined as …”

“…where C is a constant, ω 0 is the absolute wavenumber (in wavenumber units) of the excitation laser line, ω i is the Raman shift, S i is the intrinsic molar scattering activity at ω i for a Raman process, h is the Plank constant, k is the Boltzman constant, c is the speed of light, and T is the absolute temperature. To eliminate the dependence on temperature and wavenumber, a reduced Raman spectrum R(ω) is defined as [56,57] R ω ð Þ ¼…”

Adsorption of DNA Nitrogenous Bases on Nanodiamond Particles: Theory and Experiment

“…Then, the dependencies of the intensity of each of the specified markers of A, T, C, and G on their concentration in water in the range from 0 to 5 g/L with the concentration increment of 0.5 g/L were obtained. As in the other studies of the authors of this article, it turned out that these dependencies are well-approximated by straight lines (Figures and S1–S3). Moreover, the dependences of the intensities of the markers on the concentration of the corresponding NBs in water with/without the addition of NaOH coincided in the relevant concentration ranges of DNA NBs.…”