Conformations of Human Telomeric G-Quadruplex Studied Using a Nucleotide-Independent Nitroxide Label

Pulsed Dipolar EPR for Self-Limited Complexes of Oligonucleotides Studies

Pulsed electron-electron double resonance (PELDOR) spectroscopy is a powerful method for determining nucleic acid (NA) structure and conformational dynamics. PELDOR with molecular dynamics (MD) simulations opens up unique possibilities for defining the conformational ensembles of flexible, three-dimensional, self-assembled complexes of NA. Understanding the diversity and structure of these complexes is vital for uncovering matrix and regulative biological processes in the human body and artificially influencing them for therapeutic purposes. To explore the reliability of PELDOR and MD simulations, we site-specifically attached nitroxide spin labels to oligonucleotides, which form self-assembled complexes between NA chains and exhibit significant conformational flexibility. The DNA complexes assembled from a pair of oligonucleotides with different linker sizes showed excellent agreement between the distance distributions obtained from PELDOR and calculated from MD simulations, both for the mean inter-spin distance and the distance distribution width. These results prove that PELDOR with MD simulations has significant potential for studying the structure and dynamics of conformational flexible complexes of NA.

Revealing light-induced structural shifts in G-quadruplex-porphyrin complexes: a pulsed dipolar EPR study

The binding of G-quadruplex structures (G4s) with photosensitizers is of considerable importance in medicinal chemistry and drug discovery due to their promising potential in photodynamic therapy applications. G4s can experience structural changes as a result of ligand interactions and light exposure. Understanding these modifications is essential to uncover the fundamental biological roles of the complexes and optimize their therapeutic potential. The structural diversity of G4s makes it challenging to study their complexes with ligands, necessitating the use of various complementary methods to fully understand these interactions. In this study, we introduce, for the first time, the application of laser-induced dipolar EPR as a method to characterize G-quadruplex DNA complexes containing photosensitizers and to investigate light-induced structural modifications in these systems. To demonstrate the feasibility of this approach, we studied complexes of the human telomeric G-quadruplex (HTel-22) with cationic 5,10,15,20-tetrakis(1-methyl-4-pyridinio) porphyrin tetra(p-toluenesulfonate) (TMPyP4). In addition to showcasing a new methodology, we also aimed to provide insights into the mechanisms underlying photoinduced HTel-22/TMPyP4 structural changes, thereby aiding in the advancement of approaches targeting G4s in photodynamic therapy. EPR revealed G-quadruplex unfolding and dimer formation upon light exposure. Our findings demonstrate the potential of EPR spectroscopy for examining G4 complexes with photosensitizers and contribute to a better understanding of G4s' interactions with ligands under light.

The impact of G-quadruplex dynamics on inter-tetrad electronic couplings: a hybrid computational study

The G-quadruplex is a fascinating nucleic acid motif with implications in biology, medicine, and nanotechnologies. G-quadruplexes can form in the telomeres at the edges of chromosomes and in other guanine-rich regions of the genome. They can also be engineered for exploitation as biological materials for nanodevices. Their higher stiffness and higher charge transfer rates make them better candidates in nanodevices than duplex DNA. For the development of molecular nanowires, it is important to optimize electron transport along the wire axis. One powerful basis to do so is by manipulating the structure, based on known effects that structural changes have on electron transport. Here, we investigate such effects, by a combination of classical simulations of the structure and dynamics and quantum calculations of electronic couplings. We find that this structure-function relationship is complex. A single helix shape parameter alone does not embody such complexity, but rather a combination of distances and angles between stacked bases influences charge transfer efficiency. By analyzing linear combinations of shape descriptors for different topologies, we identify the structural features that most affect charge transfer efficiency. We discuss the transferability of the proposed model and the limiting effects of inherent flexibility.

Paramagnetic Chemical Probes for Studying Biological Macromolecules

Paramagnetic chemical probes have been used in electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) spectroscopy for more than four decades. Recent years witnessed a great increase in the variety of probes for the study of biological macromolecules (proteins, nucleic acids, and oligosaccharides). This Review aims to provide a comprehensive overview of the existing paramagnetic chemical probes, including chemical synthetic approaches, functional properties, and selected applications. Recent developments have seen, in particular, a rapid expansion of the range of lanthanoid probes with anisotropic magnetic susceptibilities for the generation of structural restraints based on residual dipolar couplings and pseudocontact shifts in solution and solid state NMR spectroscopy, mostly for protein studies. Also many new isotropic paramagnetic probes, suitable for NMR measurements of paramagnetic relaxation enhancements, as well as EPR spectroscopic studies (in particular double resonance techniques) have been developed and employed to investigate biological macromolecules. Notwithstanding the large number of reported probes, only few have found broad application and further development of probes for dedicated applications is foreseen.

Molecular insights into the selective binding mechanism targeting parallel human telomeric G-quadruplex

Stabilizing human telomere DNA G-quadruplex (G4) proves a promising anti-cancer strategy. Though plenty of G4 stabilizing molecules have been reported, little is known about their selective binding mechanism among various G4s. Recently, a designed monohydrazone derivative (compound 15) was reported to display specific preference in binding and stabilizing parallel human telomeric G4. To reveal the selective binding mechanism, a comparative theoretical investigation was performed on two monohydrazone derivatives (compounds 1 and 15) and three telomeric G4s showing parallel, hybrid-I, and hybrid-II conformations. Two probable binding modes, i.e. the end-stacking binding and the groove binding, were predicted by molecular dockings for each monohydrazone in its binding with the telomeric G4s. Further long-timescale molecular dynamics simulations reveal the conversion from the groove binding to the end-stacking binding for both compounds, indicating the preference of the end-stacking binding mode. Structural analysis together with binding free energy calculations show that the van der Waals interaction plays a leading role in ranking the binding affinity. By forming extensive van der Waals interactions, the parallel G4-15 binding complex shows the highest binding affinity, and the corresponding compound 15 exhibits the strongest stabilizing effect to the telomeric G4. These findings agree well with the experimental observations. Through characterizing the selective binding between monohydrazones and telomeric G4s at the atomic level, the current study provides support to the design of novel selective stabilizers targeting telomeric G4s.

Interaction of a Short Peptide with G-Quadruplex-Forming Sequences: An SRCD and CD Study

G-quadruplex (G4) forming DNA sequences were recently found to play a crucial role in the regulation of genomic processes such as replication, transcription and translation, also related to serious diseases. Therefore, systems capable of controlling DNA and RNA G-quadruplex structures would be useful for the modulation of various cellular events. In particular, peptides represent good candidates for targeting G-quadruplex structures, since they are easily tailored to enhance their functionality. In this work, we analyzed, by circular dichroism and synchrotron radiation circular dichroism spectroscopies, the interaction of a 25-residue peptide deriving from RHAU helicases (Rhau25) with three G-quadruplex-forming oligonucleotide sequences, in both sodium- and potassium-containing buffers, the most relevant monovalent cations in physiological conditions. The peptide displayed greater affinity for the G4 sequences adopting a parallel structure. However, it showed the ability to also interact with antiparallel or hybrid G-quadruplex structures, inducing a conformation conversion to the parallel structure. The stability of the oligonucleotide structure alone or in presence of the Rhau25 peptide was studied by temperature melting and UV denaturation experiments, and the data showed that the interaction with the peptide stabilized the conformation of oligonucleotide sequences when subjected to stress conditions.

Precise Distance Measurements in DNA G-Quadruplex Dimers and Sandwich Complexes by Pulsed Dipolar EPR Spectroscopy

DNA G-quadruplexes show a pronounced tendency to form higher-order structures, such as π-stacked dimers and aggregates with aromatic binding partners. Reliable methods for determining the structure of these non-covalent adducts are scarce. Here, we use artificial square-planar Cu(pyridine)4 complexes, covalently incorporated into tetramolecular G-quadruplexes, as rigid spin labels for detecting dimeric structures and measuring intermolecular Cu2+ -Cu2+ distances via pulsed dipolar EPR spectroscopy. A series of G-quadruplex dimers of different spatial dimensions, formed in tail-to-tail or head-to-head stacking mode, were unambiguously distinguished. Measured distances are in full agreement with results of molecular dynamics simulations. Furthermore, intercalation of two well-known G-quadruplex binders, PIPER and telomestatin, into G-quadruplex dimers resulting in sandwich complexes was investigated, and previously unknown binding modes were discovered. Additionally, we present evidence that free G-tetrads also intercalate into dimers. Our transition metal labeling approach, combined with pulsed EPR spectroscopy, opens new possibilities for examining structures of non-covalent DNA aggregates.

Molecular Dynamics Study on the Binding of an Anticancer DNA G-Quadruplex Stabilizer, CX-5461, to Human Telomeric, c-KIT1, and c-Myc G-Quadruplexes and a DNA Duplex

DNA G-quadruplex (G4) stabilizer, CX-5461, is in phase I/II clinical trials for advanced cancers with BRCA1/2 deficiencies. A FRET-melting temperature increase assay measured the stabilizing effects of CX-5461 to a DNA duplex (∼10 K), and three G4 forming sequences negatively implicated in the cancers upon its binding: human telomeric (∼30 K), c-KIT1 (∼27 K), and c-Myc (∼25 K). Without experimentally solved structures of these CX-5461-G4 complexes, CX-5461's interactions remain elusive. In this study, we performed a total of 73.5 μs free ligand molecular dynamics binding simulations of CX-5461 to the DNA duplex and three G4s. Three binding modes (top, bottom, and side) were identified for each system and their thermodynamic, kinetic, and structural nature were deciphered. The molecular mechanics/Poisson Boltzmann surface area binding energies of CX-5461 were calculated for the human telomeric (-28.6 kcal/mol), c-KIT1 (-23.9 kcal/mol), c-Myc (-22.0 kcal/mol) G4s, and DNA duplex (-15.0 kcal/mol) systems. These energetic differences coupled with structural differences at the 3' site explained the different melting temperatures between the G4s, while CX-5461's lack of intercalation to the duplex explained the difference between the G4s and duplex. Based on the interaction insight, CX-5461 derivatives were designed and docked, showing higher selectivity to the G4s over the duplex.

Recent developments in empirical atomistic force fields for nucleic acids and applications to studies of folding and dynamics

Nucleic acids play critical roles in carrying genetic information, participating in catalysis, and preserving chromosomal structure. Despite over a century of study, efforts to understand the dynamics and structure-function relationships of DNA and RNA at the atomic level are still ongoing. Molecular dynamics (MD) simulations augment experiments by providing atomistic resolution and quantitative relationships between structure and conformational energy. Steady advancements in computer hardware, software, and atomistic force fields (FFs) over 40 years have facilitated new discoveries. Here, we review nucleic acid FF development with emphasis on recent refinements that have improved descriptions of important nucleic acid properties. We then discuss several key examples of successes and challenges in modeling nucleic acid structure and dynamics using the latest FFs.

Posttranscriptional site-directed spin labeling of large RNAs with an unnatural base pair system under non-denaturing conditions

Site-directed spin labeling (SDSL) of large RNAs for electron paramagnetic resonance (EPR) spectroscopy has remained challenging to date.

Site-directed spin labeling (SDSL) of large RNAs for electron paramagnetic resonance (EPR) spectroscopy has remained challenging to date. We here demonstrate an efficient and generally applicable posttranscriptional SDSL method for large RNAs using an expanded genetic alphabet containing the NaM-TPT3 unnatural base pair (UBP). An alkyne-modified TPT3 ribonucleotide triphosphate (rTPT3^COTP) is synthesized and site-specifically incorporated into large RNAs by in vitro transcription, which allows attachment of the azide-containing nitroxide through click chemistry. We validate this strategy by SDSL of a 419-nucleotide ribonuclease P (RNase P) RNA from Bacillus stearothermophilus under non-denaturing conditions. The effects of site-directed UBP incorporation and subsequent spin labeling on the global structure and function of RNase P are marginal as evaluated by Circular Dichroism spectroscopy, Small Angle X-ray Scattering, Sedimentation Velocity Analytical Ultracentrifugation and enzymatic assay. Continuous-Wave EPR analyses reveal that the labeling reaction is efficient and specific, and Pulsed Electron–Electron Double Resonance measurements yield an inter-spin distance distribution that agrees with the crystal structure. The labeling strategy as presented overcomes the size constraint of RNA labeling, opening new avenues of spin labeling and EPR spectroscopy for investigating the structure and dynamics of large RNAs.

Structural dynamics of propeller loop: towards folding of RNA G-quadruplex

We have carried out an extended set of standard and enhanced-sampling MD simulations (for a cumulative simulation time of 620 μs) with the aim to study folding landscapes of the rGGGUUAGGG and rGGGAGGG parallel G-hairpins (PH) with propeller loop. We identify folding and unfolding pathways of the PH, which is bridged with the unfolded state via an ensemble of cross-like structures (CS) possessing mutually tilted or perpendicular G-strands interacting via guanine-guanine H-bonding. The oligonucleotides reach the PH conformation from the unfolded state via a conformational diffusion through the folding landscape, i.e. as a series of rearrangements of the H-bond interactions starting from compacted anti-parallel hairpin-like structures. Although isolated PHs do not appear to be thermodynamically stable we suggest that CS and PH-types of structures are sufficiently populated during RNA guanine quadruplex (GQ) folding within the context of complete GQ-forming sequences. These structures may participate in compact coil-like ensembles that involve all four G-strands and already some bound ions. Such ensembles can then rearrange into the fully folded parallel GQs via conformational diffusion. We propose that the basic atomistic folding mechanism of propeller loops suggested in this work may be common for their formation in RNA and DNA GQs.

Quantum Mechanical Investigation of the G-Quadruplex Systems of Human Telomere

The three G-quadruplexes involved in the human telomere have been studied with an accurate quantum mechanical approach, and the possibility of reducing them to a simpler model has been tested. The similarities and the differences of these three systems are shown and discussed. Each system has been analyzed through different properties and compared to the others. In particular, we have considered: (1) the shape of the cavity and the atomic charges around it; (2) the electric field in and out of the cavity; (3) the stabilization energy due to the stacking of G-tetrads, to the H-bonds and to the ion interactions; and, finally, (4) to study the mechanism of the process of the ion inclusion in the cavity, the curves of potential energy due to the movement of the Na+ and K+ ions toward the cavity. The results suggest that a detailed study is essential in order to obtain the quantitative properties of these complex systems, but also that some qualitative behaviors can be schematized. Our study makes it clear that the entry of an ion in the cavity of these systems is a complex process, where it is possible to find stable structures with the ion out and in the cavity. Moreover, it is possible that more than one diabatic state is involved in this process.

Di-copper(ii) DNA G-quadruplexes as EPR distance rulers

Paramagnetic Cu(ii) complexes, immobilized via four-point-attachment to both ends of G-quadruplexes, serve as EPR-based distance rulers for studying DNA structure.

In What Ways Do Synthetic Nucleotides and Natural Base Lesions Alter the Structural Stability of G-Quadruplex Nucleic Acids?

Synthetic analogs of natural nucleotides have long been utilized for structural studies of canonical and noncanonical nucleic acids, including the extensively investigated polymorphic G-quadruplexes (GQs). Dependence on the sequence and nucleotide modifications of the folding landscape of GQs has been reviewed by several recent studies. Here, an overview is compiled on the thermodynamic stability of the modified GQ folds and on how the stereochemical preferences of more than 70 synthetic and natural derivatives of nucleotides substituting for natural ones determine the stability as well as the conformation. Groups of nucleotide analogs only stabilize or only destabilize the GQ, while the majority of analogs alter the GQ stability in both ways. This depends on the preferred syn or anti N-glycosidic linkage of the modified building blocks, the position of substitution, and the folding architecture of the native GQ. Natural base lesions and epigenetic modifications of GQs explored so far also stabilize or destabilize the GQ assemblies. Learning the effect of synthetic nucleotide analogs on the stability of GQs can assist in engineering a required stable GQ topology, and exploring the in vitro action of the single and clustered natural base damage on GQ architectures may provide indications for the cellular events.

Effect of Monovalent Ion Parameters on Molecular Dynamics Simulations of G-Quadruplexes

G-quadruplexes (GQs) are key noncanonical DNA and RNA architectures stabilized by desolvated monovalent cations present in their central channels. We analyze extended atomistic molecular dynamics simulations (∼580 μs in total) of GQs with 11 monovalent cation parametrizations, assessing GQ overall structural stability, dynamics of internal cations, and distortions of the G-tetrad geometries. Majority of simulations were executed with the SPC/E water model; however, test simulations with TIP3P and OPC water models are also reported. The identity and parametrization of ions strongly affect behavior of a tetramolecular d[GGG]₄ GQ, which is unstable with several ion parametrizations. The remaining studied RNA and DNA GQs are structurally stable, though the G-tetrad geometries are always deformed by bifurcated H-bonding in a parametrization-specific manner. Thus, basic 10-μs-scale simulations of fully folded GQs can be safely done with a number of cation parametrizations. However, there are parametrization-specific differences and basic force-field errors affecting the quantitative description of ion-tetrad interactions, which may significantly affect studies of the ion-binding processes and description of the GQ folding landscape. Our d[GGG]₄ simulations indirectly suggest that such studies will also be sensitive to the water models. During exchanges with bulk water, the Na⁺ ions move inside the GQs in a concerted manner, while larger relocations of the K⁺ ions are typically separated. We suggest that the Joung-Cheatham SPC/E K⁺ parameters represent a safe choice in simulation studies of GQs, though variation of ion parameters can be used for specific simulation goals.

Structure, Properties, and Biological Relevance of the DNA and RNA G-Quadruplexes: Overview 50 Years after Their Discovery

G-quadruplexes (G4s), which are known to have important roles in regulation of key biological processes in both normal and pathological cells, are the most actively studied non-canonical structures of nucleic acids. In this review, we summarize the results of studies published in recent years that change significantly scientific views on various aspects of our understanding of quadruplexes. Modern notions on the polymorphism of DNA quadruplexes, on factors affecting thermodynamics and kinetics of G4 folding–unfolding, on structural organization of multiquadruplex systems, and on conformational features of RNA G4s and hybrid DNA–RNA G4s are discussed. Here we report the data on location of G4 sequence motifs in the genomes of eukaryotes, bacteria, and viruses, characterize G4-specific small-molecule ligands and proteins, as well as the mechanisms of their interactions with quadruplexes. New information on the structure and stability of G4s in telomeric DNA and oncogene promoters is discussed as well as proof being provided on the occurrence of G-quadruplexes in cells. Prominence is given to novel experimental techniques (single molecule manipulations, optical and magnetic tweezers, original chemical approaches, G4 detection in situ, in-cell NMR spectroscopy) that facilitate breakthroughs in the investigation of the structure and functions of G-quadruplexes.

Quantum mechanical investigation of G-quartet systems of DNA

Minima of the electric field and positions of K⁺ and Na⁺ (zero of the x-coordinate is the center of the cavity).

Folding of guanine quadruplex molecules-funnel-like mechanism or kinetic partitioning? An overview from MD simulation studies

BACKGROUND

Guanine quadruplexes (GQs) play vital roles in many cellular processes and are of much interest as drug targets. In contrast to the availability of many structural studies, there is still limited knowledge on GQ folding.

SCOPE OF REVIEW

We review recent molecular dynamics (MD) simulation studies of the folding of GQs, with an emphasis paid to the human telomeric DNA GQ. We explain the basic principles and limitations of all types of MD methods used to study unfolding and folding in a way accessible to non-specialists. We discuss the potential role of G-hairpin, G-triplex and alternative GQ intermediates in the folding process. We argue that, in general, folding of GQs is fundamentally different from funneled folding of small fast-folding proteins, and can be best described by a kinetic partitioning (KP) mechanism. KP is a competition between at least two (but often many) well-separated and structurally different conformational ensembles.

MAJOR CONCLUSIONS

The KP mechanism is the only plausible way to explain experiments reporting long time-scales of GQ folding and the existence of long-lived sub-states. A significant part of the natural partitioning of the free energy landscape of GQs comes from the ability of the GQ-forming sequences to populate a large number of syn-anti patterns in their G-tracts. The extreme complexity of the KP of GQs typically prevents an appropriate description of the folding landscape using just a few order parameters or collective variables.

GENERAL SIGNIFICANCE

We reconcile available computational and experimental studies of GQ folding and formulate basic principles characterizing GQ folding landscapes. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.