Abstract
Among many structures in the cells of living beings, there are proteins called transcription factors (TF) that are responsible to inhibit or promote the transcription of the DNA. To accomplish their function, the transcription factors perform aleatory searches around the cytoplasm (for prokaryotic cells) and along the DNA chain as well for specific targets located in the DNA. Its movement fits into the class of anomalous Brownian. The efficiency in TFs search has implications in the cellular copy and in protection against viruses, hence the knowledge of the mechanism is of great interest. In the present work, we study the searching process of the TFs by simulating the anomalous Brownian motion through the cytoplasm and DNA chain by means of Levy flights through a lattice model and through a free grid model. The final distribution of positions of the TF are obtained. The search efficiency is investigated in terms of the model parameters.
Highlights
Deoxyribonucleic acid (DNA) is a heteropolymer molecule present in the cells of all living beings that, among other functions, is responsible for genetic information contained in living organisms and for its transmission to the daughter-cells [5]
DNA transcription factor (TF) searches were simulated based on the theoretical model known as facilitated diffusion where there are rounds of transcription factors (TF) searches in three-dimensional movements in the bulk and in 1D movements attached to the DNA
The simulations were performed with a lattice model and in free grid model and it was assumed that the diffusion is anomalous
Summary
Deoxyribonucleic acid (DNA) is a heteropolymer molecule present in the cells of all living beings that, among other functions, is responsible for genetic information contained in living organisms and for its transmission to the daughter-cells [5]. Despite the wide variety of living creatures and the amount of genetic information, their DNA molecules carry a physically identical structure, the B-DNA. It consists of two helical-twisted supporting structures composed of phosphate and sugar with base pairs of two types, AT (adenine-thymine) and GC (guanine-cytosine), where A, T, C and G are residues present in the DNA. The enzyme responsible for the synthesis of the RNA, according to the information present in DNA is called RNA polymerase. The role of the transcription factors (TFs) is to bind to specific starting points of transcription of sequences in DNA to enable the link of the RNA polymerase and, allowing the RNA synthesis. Some TFs are able to inhibit this process, such as the lac repressor, on which the mechanism of binding and recognition of TF in DNA [2]
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