ElTetrado: a tool for identification and classification of tetrads and quadruplexes

Tomasz Zok,Marta Szachniuk,Mariusz Popenda

doi:10.1186/s12859-020-3385-1

Abstract

BackgroundQuadruplexes are specific structure motifs occurring, e.g., in telomeres and transcriptional regulatory regions. Recent discoveries confirmed their importance in biomedicine and led to an intensified examination of their properties. So far, the study of these motifs has focused mainly on the sequence and the tertiary structure, and concerned canonical structures only. Whereas, more and more non-canonical quadruplex motifs are being discovered.ResultsHere, we present ElTetrado, a software that identifies quadruplexes (composed of guanine- and other nucleobase-containing tetrads) in nucleic acid structures and classifies them according to the recently introduced ONZ taxonomy. The categorization is based on the secondary structure topology of quadruplexes and their component tetrads. It supports the analysis of canonical and non-canonical motifs. Besides the class recognition, ElTetrado prepares a dot-bracket and graphical representations of the secondary structure, which reflect the specificity of the quadruplex’s structure topology. It is implemented as a freely available, standalone application, available at https://github.com/tzok/eltetrado.ConclusionsThe proposed software tool allows to identify and classify tetrads and quadruplexes based on the topology of their secondary structures. It complements existing approaches focusing on the sequence and 3D structure.

Highlights

Quadruplexes are specific structure motifs occurring, e.g., in telomeres and transcriptional regulatory regions
We focused on unimolecular motifs, as the classification is based on the order of nucleotides in the chain, which is unambiguously determined only in the case of singlestranded structures
Strand reordering can be switched off by calling ElTetrado with --no-reorder parameter. In such a program call, biand tetramolecular motifs are not classified according to the ONZ taxonomy

Summary

Introduction

Quadruplexes are specific structure motifs occurring, e.g., in telomeres and transcriptional regulatory regions. Recent discoveries confirmed their importance in biomedicine and led to an intensified examination of their properties. These structures were first found in DNA, in two tetrads are stacked upon one another at a distance the late 1960s. Only after their association with of about 3.3 Å, the quadruplex is created [12]. The 3D structure analysis encompasses the properties of tetrads, stems and

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