Physical properties of core promoter sequences DNA

Khodykov M.V., Il’icheva I.A., Panchenko L.A.1, Polozov R.V.2, Nechipurenko Y.D.

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia

1Faculty of Biology Moscow State University, 119991 Moscow, Russia

2Institute of Theoretical and Experimental Biophysics, 142290, Pushchino

The genes promoters transcribed by RNA polymerase II (Pol II) contain core elements that are recognized by transcription factors. The primary structure of these sites varies significantly among different organisms. The goal of our work is to determine the general properties of those regions of the DNA sequence that correspond to the binding of RNA polymerase II. We analyzed the profiles of structural, mechanical, and ultrasonic characteristics of core promoters in a large number of different species: animals, insects, plants, and unicellular fungi. Ultrasound DNA cleavage profiles were calculated in accordance with the concepts developed earlier in [1–4]. The analysis revealed a similarity in the structural organization of core promoters in the region between the TATA box and the start of the transcription initiation site (TSS) [5-8]. Profiles of structural and mechanical characteristics indicate the spatial structure and flexibility of the double helix at the sites of binding to the TATA-binding protein, and the profiles of ultrasonic indices carry information on the characteristic conformational movements in individual strands of the DNA molecule in the section from the TATA box to the transcription initiation site (TSS ) The intensity of conformational movements in complementary chains in these regions changes in antiphase. These patterns are most pronounced on the profiles of regulatory regions of DNA from mammalian cells. Similar characteristics of the structural, mechanical, and ultrasonic profiles of S. cerevisiae core promoters are shifted down the sequence by about 20 bp and are found directly in the region of the transcription initiation site (TSS), thereby indicating a different structural organization of yeast promoters. Ultrasonic cleavage profiles show a decrease in the intensity of ultrasonic cleavage around the -30 bp position, which may reflect a significant decrease in the conformational movement of the sugar phosphate backbone in the region of the TATA box. In the regulatory region, the ability of DNA to bend along a large groove increases, while stiffness decreases. These structural properties are found in the promoter regions of all studied species, despite significant variations in the nucleotide sequences (the exception is S. Cerevisiae promoters). Thus, despite the diversity of nucleotide sequences in the promoter regions of various species of animals, insects and plants, the nature of their structural organization has significant similarities. The results can be used in bioinformatics and genetic engineering.

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