Modeling intermolecular interaction of DNA nucleotides, carbon nanostructure of the sequencer sensor and the buffer solution components in the process of single molecular DNA sequencing
Yuri Gagarin State Technical Univercity of Saratov email@example.com firstname.lastname@example.org
The aim of this work is to analyze by numerically simulating the level of interaction of DNA nucleotides with elements of a buffer solution and with a sequencer sensor (the surface of which is enriched with maleimide) during single-molecule DNA sequencing.
Molecular modeling was performed using the Gaussian 09 and DFTB + software packages based on the density functional theory (DFT).
In the process of sequencing, it is possible to establish the sequence of nucleotides in a DNA molecule using various techniques, in particular, the procedure of single-molecular sequencing in real time is investigated. The idea of the method is to determine the DNA sequence by monitoring the operation of a single DNA polymerase molecule in real time.
In this technique, DNA nucleotides are deposited on a special substrate coated with an alkane enriched with maleimide.
In the course of the work, charge distribution maps, spectra and structures of interacting elements during sequencing were calculated and analyzed.
As a result of the analysis, recommendations were made on the selection of optimal conditions for increasing the quality of single-molecular sequencing.