Bulges in left-handed G-quadruplexes

Interlocking G-Quadruplexes Using a G-Triad•G Connection: Implications for G-Wire Assembly

G-quadruplexes are noncanonical structures of nucleic acids formed mainly by G-rich sequences and play crucial roles in important cellular processes. They are also increasingly used in nanotechnology for their valuable properties. Various unexpected structures of G-quadruplexes have been solved recently, including a stable G-quadruplex lacking one guanine in the G-tetrad core, harboring a vacant site. In this study, we demonstrate the interlocking of two intramolecular G-quadruplexes: one containing a vacant site (4n - 1) and the other with an unbound guanine (4n + 1). These G-quadruplexes interact through a G-triad-G connection with unprecedented 5'-3' stacking. Using these interconnection properties, we have identified a sequence capable of self-assembling into G-wires in K+ solutions with potential nanotechnological applications.

Comprehensive analysis of intramolecular G-quadruplex structures: furthering the understanding of their formalism

G-quadruplexes (G4) are helical structures found in guanine-rich DNA or RNA sequences. Generally, their formalism is based on a few dozen structures, which can produce some inconsistencies or incompleteness. Using the website ASC-G4, we analyzed the structures of 333 intramolecular G4s, of all types, which allowed us to clarify some key concepts and present new information. To each of the eight distinguishable topologies corresponds a groove-width signature and a predominant glycosidic configuration (gc) pattern governed by the directions of the strands. The relative orientations of the stacking guanines within the strands, which we quantified and related to their vertical gc successions, determine the twist and tilt of the helices. The latter impact the minimum groove widths, which represent the space available for lateral ligand binding. The G4 four helices have similar twists, even when these twists are irregular, meaning that they have various angles along the strands. Despite its importance, the vertical gc succession has no strict one-to-one relationship with the topology, which explains the discrepancy between some topologies and their corresponding circular dichroism spectra. This study allowed us to introduce the new concept of platypus G4s, which are structures with properties corresponding to several topologies.

Why Are Left-Handed G-Quadruplexes Scarce?

G-quadruplexes (G4s) are nucleic acid structures crucial for the regulation of gene expression and genome maintenance. While they hold promise as nanodevice components, achieving desired G4 folds requires understanding the interplay between stability and structural properties, like helicity. Although right-handed G4 structures dominate the experimental data, the molecular basis for this preference over left-handed helicity is unclear. To address this, we employ all-atom molecular dynamics simulations and quantum chemical methods. Our results reveal that right-handed G4s exhibit greater thermodynamic and kinetic stability as a result of favorable sugar-phosphate backbone conformations in guanine tracts. Moreover, while hydrogen-bonding patterns influence helicity-specific G4 loop conformations, they minimally affect stability differences. We also elucidate the strong correlation between helicity and the strand progression direction, essential for G4 structures. These findings deepen our understanding of G4s, providing molecular-level insights into their structural and energetic preferences, which could inform the design of novel nanodevices.

On Water Arrangements in Right- and Left-Handed DNA Structures

DNA requires hydration to maintain its structural integrity. Crystallographic analyses have enabled patterns of water arrangements to be visualized. We survey these water motifs in this review, focusing on left- and right-handed duplex and quadruplex DNAs, together with the i-motif. Common patterns of linear spines of water organization in grooves have been identified and are widely prevalent in right-handed duplexes and quadruplexes. By contrast, a left-handed quadruplex has a distinctive wheel of hydration populating the almost completely circular single groove in this structure.

Dataset of bulged G-quadruplex forming sequences in the human genome

When several continuous guanine runs are present closely in a nucleic acid sequence, a secondary structure called G-quadruplex can form (G4s). Such structures in the genome could serve as structural and functional regulators in gene expression, DNA-protein binding, epigenetic modification, and genotoxic stress. Several types of G4-forming DNA sequences exist, including bulged G4-forming sequences (G4-BS). Such bulges occur due to the presence of non-guanine bases in specific locations (G-runs) in the G4-forming sequences. At present, search algorithms do not identify stable G4-BS conformations, making genome-wide studies of G4-like structures difficult. Data provided in this study are related to a published article "Stable bulged G-quadruplexes in the human genome: Identification, experimental validation and functionalization" published by Nucleic Acids Research [DIO.org/10.193/nar/gkad252]. Based on our studies in vitro and G4-seq and G4 CUT&Tag data analysis, we have specified and validated three pG4-BS models. In this article, a large collection of 'raw' (unfiltered) dataset is presented, which includes three subfamilies of pG4-BS. For each of pG4-BS, we provide strand-specific genomic boundaries. Data on pG4-BS might be useful in elucidating their structural, functional, and evolutionary roles. Furthermore, they may provide insight into the pathobiology of G4-like structures and their potential therapeutic applications.

Stable bulged G-quadruplexes in the human genome: identification, experimental validation and functionalization

DNA sequence composition determines the topology and stability of G-quadruplexes (G4s). Bulged G-quadruplex structures (G4-Bs) are a subset of G4s characterized by 3D conformations with bulges. Current search algorithms fail to capture stable G4-B, making their genome-wide study infeasible. Here, we introduced a large family of computationally defined and experimentally verified potential G4-B forming sequences (pG4-BS). We found 478 263 pG4-BS regions that do not overlap 'canonical' G4-forming sequences in the human genome and are preferentially localized in transcription regulatory regions including R-loops and open chromatin. Over 90% of protein-coding genes contain pG4-BS in their promoter or gene body. We observed generally higher pG4-BS content in R-loops and their flanks, longer genes that are associated with brain tissue, immune and developmental processes. Also, the presence of pG4-BS on both template and non-template strands in promoters is associated with oncogenesis, cardiovascular disease and stemness. Our G4-BS models predicted G4-forming ability in vitro with 91.5% accuracy. Analysis of G4-seq and CUT&Tag data strongly supports the existence of G4-BS conformations genome-wide. We reconstructed a novel G4-B 3D structure located in the E2F8 promoter. This study defines a large family of G4-like sequences, offering new insights into the essential biological functions and potential future therapeutic uses of G4-B.

G-QINDER Tool: Bioinformatically Predicted Formation of Different Four-Stranded DNA Motifs from (GT)n and (GA)n Repeats

The recently introduced semi-orthogonal system of nucleic acid imaging offers a greatly improved method of identifying DNA sequences that are capable of adopting noncanonical structures. This paper uses our newly developed G-QINDER tool to identify specific repeat sequences that adopt unique structural motifs in DNA: TG and AG repeats. The structures were found to adopt a left-handed G-quadruplex form under extreme crowding conditions and a unique tetrahelical motif under certain other conditions. The tetrahelical structure likely consists of stacked AGAG-tetrads but, unlike G-quadruplexes, their stability does not appear to be dependent on the type of monovalent cation present. The occurrence of TG and AG repeats in genomes is not rare, and they are also found frequently in the regulatory regions of nucleic acids, so it is reasonable to assume that putative structural motifs, like other noncanonical forms, could play an important regulatory role in cells. This hypothesis is supported by the structural stability of the AGAG motif; its unfolding can occur even at physiological temperatures since the melting temperature is primarily dependent on the number of AG repeats in the sequence.

ASC-G4, an algorithm to calculate advanced structural characteristics of G-quadruplexes

ASC-G4 is an algorithm for the calculation of the advanced structural characteristics of G-quadruplexes (G4). It allows the unambiguous determination of the intramolecular G4 topology, based on the oriented strand numbering. It also resolves the ambiguity in the determination of the guanine glycosidic configuration. With this algorithm, we showed that the use of the C3' or C5' atoms to calculate the groove width in G4 is more appropriate than the P atoms and that the groove width does not always reflect the space available within the groove. For the latter, the minimum groove width is more appropriate. The application of ASC-G4 to 207 G4 structures guided the choices made for the calculations. A website based on ASC-G4 (http://tiny.cc/ASC-G4) was created, where the user uploads his G4 structure and gets its topology, the types of its loops and their lengths, the presence of snapbacks and bulges, the distribution of guanines in the tetrads and strands, the glycosidic configuration of these guanines, their rise, the groove widths, the minimum groove widths, the tilt and twist angles, the backbone dihedral angles, etc. It also provides a large number of atom-atom and atom-plane distances that are relevant to evaluating the quality of the structure.

Machine learning shows torsion angle preferences in left-handed and right-handed quadruplex DNAs

Left-handed G quadruplexes (LHG4) have been recently discovered as a new class of G quadruplexes. The biological functions of LHG4s are still unknown, but they share a striking resemblance to Z-DNA in their helicity and jagged phosphate backbone. To further understand structural features of the LHG4s that define their left handedness, we have employed human-interpretable machine-learning methods to classify right- and left-handed G4s purely based on torsional angle analysis. Our results reveal the importance of the α, β, δ, and χ angles in left-handed structuring across both Z-DNAs and LHG4s. Our analysis may serve as the first step to understanding the conditions of formation for LHG4s and their potential biological relevance.

Tetrad-binding ligands do not bind specifically to left-handed G-quadruplexes

G-quadruplexes (G4s) are attractive anticancer targets. While right-handed G4s have been extensively investigated with many specific ligands reported, left-handed G4s formed by natural DNA have been recently discovered. Here we show that ligands specific for right-handed G4s, such as Phen-DC₃ and RHAU peptide, do not bind specifically to left-handed G4s. In right-handed G4s, these ligands can displace capping overhangs and/or loops to stack on the exposed terminal tetrads. In contrast, the presence of tight T-capping in left-handed G4s hinders access to the tetrads.

Folding dynamics of polymorphic G-quadruplex structures

G-quadruplexes (G4), found in numerous places within the human genome, are involved in essential processes of cell regulation. Chromosomal DNA G4s are involved for example, in replication and transcription as first steps of gene expression. Hence, they influence a plethora of downstream processes. G4s possess an intricate structure that differs from canonical B-form DNA. Identical DNA G4 sequences can adopt multiple long-lived conformations, a phenomenon known as G4 polymorphism. A detailed understanding of the molecular mechanisms that drive G4 folding is essential to understand their ambivalent regulatory roles. Disentangling the inherent dynamic and polymorphic nature of G4 structures thus is key to unravel their biological functions and make them amenable as molecular targets in novel therapeutic approaches. We here review recent experimental approaches to monitor G4 folding and discuss structural aspects for possible folding pathways. Substantial progress in the understanding of G4 folding within the recent years now allows drawing comprehensive models of the complex folding energy landscape of G4s that we herein evaluate based on computational and experimental evidence.