Untangling or further entangling? Revelation of the complicated world of nucleic acid quadruplex folds

Abstract

Quadruplexes are four-stranded nucleic acid secondary structures playing diverse biological roles. A recent meticulous analysis of known quadruplex structures formed from synthetic oligonucleotides shows that quadruplexes can take 33 distinct structural motifs (pair of stacked quartets) that act as scaffolds for simple (multi-layered quartets) and complex (multi-motifs) quadruplex folds. These motifs differ from one another in terms of interstrand connectivity and orientation. The connectivity is primarily governed by diagonal loops that connect alternate strands, and lateral and propeller loops that connect adjacent strands. These loops are absent in the tetramer, wherein interstrand orientation alone dictates the motif type. Nevertheless, a key question that remains unresolved is the complete structural landscape of quadruplex motifs, limiting our understanding of the fold-dependency in various biological functions and diseases. To address this, a total of 156 unique theoretically possible quadruplex motifs are mathematically devised here. A tool named 3D-NuS-Qplex (https://project.iith.ac.in/3d-nus-qplex/) has also been developed to model all the theoretically possible energy-minimized quadruplex folds with the options to incorporate overhangs and non-G-quartets (in addition to G-quartets) in both DNA and RNA contexts. The diversity of quadruplex motifs reported here provides new insight into their structural complexity, which appears greater than previously anticipated. HighlightsO_LIQuadruplex folds can be segmented into two-layered structural motifs that act as their scaffold C_LIO_LI156 unique theoretically possible quadruplex motifs are mathematically devised, and an option to model them is discussed C_LIO_LIThis reveals the complexity of quadruplex structures and offers new perspectives on quadruplex biology and disease C_LI