Helix-specific interactions induce condensation of guanosine four-stranded helices in concentrated salt solutions

Guanosine hydrogels in focus: A comprehensive analysis through mid-infrared spectroscopy

Guanosine nucleosides and nucleotides have the peculiar ability to self-assemble in water to form supramolecular complex architectures from G-quartets to G-quadruplexes. G-quadruplexes exhibit in turn a large liquid crystalline lyotropic polymorphism, but they eventually cross-link or entangle to form a densely connected 3D network (a molecular hydrogel), able to entrap very large amount of water (up to the 99% v/v). This high water content of the hydrogels enables tunable softness, deformability, self-healing, and quasi-liquid properties, making them ideal candidates for different biotechnological and biomedical applications. In order to fully exploit their possible applications, Attenuated Total Reflection-Fourier Transform InfraRed (ATR-FTIR) spectroscopy was used to unravel the vibrational characteristics of supramolecular guanosine structures. First, the characteristic vibrations of the known quadruplex structure of guanosine 5'-monophosphate, potassium salt (GMP/K), were investigated: the identified peaks reflected both the chemical composition of the sample and the formation of quartets, octamers, and quadruplexes. Second, the role of K+ and Na+ cations in promoting the quadruplex formation was assessed: infrared spectra confirmed that both cations induce the formation of G-quadruplexes and that GMP/K is more stable in the G-quadruplex organization. Finally, ATR-FTIR spectroscopy was used to investigate binary mixtures of guanosine (Gua) and GMP/K or GMP/Na, both systems forming G-hydrogels. The same G-quadruplex-based structure was found in both mixtures, but the proportion of Gua and GMP affected some features, like sugar puckering, guanine vibrations, and base stacking, reflecting the known side-to-side aggregation and bundle formation occurring in these binary systems.

Self-oriented anisotropic structure of G-hydrogels as a delicate balance between attractive and repulsive forces

Guanine (G) hydrogels are very attractive materials made by the supramolecular organization of G-derivatives in water. In this paper, hydrogels composed of guanosine 5'-monophosphate (GMP) and guanosine (Gua), that make long, flexible and knotted G-quadruplexes, were investigated by small- and wide-angle X-ray scattering (SAXS and WAXS) to comprehend the origin of their unique orientational properties. The SAXS intensity, analysed at a fixed scattering vector modulus Q as a function of polar angle, allowed us to derive the Maier-Saupe orientation parameter m. The strong dependence of m on hydrogel composition and temperature demonstrated that the preferred orientation is controlled by the quadruplex surface charge and flexibility. Indeed, a possible correlation between the orientation parameter m and the quadruplex-to-quadruplex lateral interactions was explored. Results confirmed that the balance between attractive and repulsive interactions plays a main role in the orientational anisotropy: quadruplex clusters lose their orientational properties when attractive interactions decrease. The key role of the number of negative charges per unit length of the G-quadruplex filaments was confirmed by Atomic Force Microscopy (AFM) observations. Indeed, directionality histograms showed that in the presence of a large amount of Gua, G-quadruplexes follow preferential orientations other than those related to the strong interactions with the K+ pattern on the mica surface. The fact that lateral quadruplex-to-quadruplex interactions, even in the presence of external (opposing) forces, can tune the hydrogel alignment in a given preferred direction provides novel possibilities for scaffold/3D printing applications.

Self-assembled guanosine-hydrogels for drug-delivery application: Structural and mechanical characterization, methylene blue loading and controlled release

It is known that guanosine derivatives (G) self-assemble in water forming long, flexible, and interacting aggregates (the so-called G-quadruplexes): by modulating the quadruplex charges, e.g. simply using a mixture of guanosine 5'-monophosphate (GMP) and guanosine (Gua), multi-responsive, self-healing hydrogels can be obtained. In this paper, the potential application of G-hydrogels as drug delivery systems has been assessed. Hydrogels were prepared at different Gua:GMP molar ratios. The photosensitizer Methylene Blue and the pro-apoptotic protein cytochrome C were used as cargo molecules. Small angle x-ray scattering and atomic force microscopy experiments confirmed the presence of G-quadruplexes disposed in swollen matrices with different mesh-sizes. Rheology measurements showed that the Gua:GMP molar ratio leads to specific drug release mechanisms, as the gel strength is finely tuned by electrostatic repulsion and van der Waals attraction between G-quadruplexes. Noteworthy, the gel cohesion and the drug release were pH responsive. Swelling, self-healing and cell viability features were also investigated: the results qualify the Gua:GMP hydrogel as an excellent biomaterial that can entrap and deliver key biomolecules in a sustained and responsive release manner.

K vs. Na Effects on the Self-Assembly of Guanosine 5'-Monophosphate: A Solution SAXS Structural Study+. NANOMATERIALS (BASEL, SWITZERLAND) 2020;10:E629. [PMID: 32231081 PMCID: PMC7221663 DOI: 10.3390/nano10040629]

The hierarchical process of guanosine (G) self-assembly, leading in aqueous solution and in the presence of metal cations to the formation of G-quadruplexes, represents an intriguing topic both for the biological correlation with telomerase activity and for the nano-technological applications, as demonstrated by the current measured in a quadruplex wire 100 nm long. Similar to G-rich DNA sequences and G-oligonucleotides, the guanosine 5'-monophosphate (GMP) self-aggregates in water to form quadruplexes. However, due to the absence of a covalent axial backbone, this system can be very useful to understand the chemical-physical conditions that govern the guanosine supramolecular aggregation. We have then investigated by in-solution Synchrotron Small Angle X-ray Scattering technique the role of different cations in promoting the quadruplex formation as a function of concentration and temperature. Results show how potassium, with its peculiar biological traits, favours the G-quadruplex elongation process in respect to other cations (Na + , but also NH 4 + and Li + ), determining the longest particles in solution. Moreover, the formation and the elongation of G-quadruplexes have been demonstrated to be controlled by both GMP concentration and excess cation content, even if they specifically contribute to these processes in different ways. The occurrence of condensed liquid crystalline phases was also detected, proving that excess cations play also unspecific effects on the effective charges on the G-quadruplex surface.

On the structural stability of guanosine-based supramolecular hydrogels

Supramolecular hydrogels formed from the self-assembly of low molecular weight derivatives are very attractive systems, because of their potential applications in nano- and bio-technology. In this paper, the stable and transparent hydrogels observed in binary mixtures of guanosine derivatives (G), namely guanosine 5'-monophosphate (GMP) and guanosine (Gua), dissolved in water (at volume fractions larger than 0.95), were investigated by microscopy techniques and Small Angle X-ray Scattering (SAXS). The results confirm the presence of G-quadruplexes, chiral cylindrical rods obtained by the regular stacking of self-assembled planar cyclic guanosine quartets. However, the addition of Gua determines the formation of very stable hydrogels able to trap large amounts of water (up to a volume fraction of 0.99) and characterised by an unusual anisotropic order. A modified lateral helix-to-helix interaction pattern, tuned by Gua, is suggested to be responsible for the supramolecular gelation and the stability of the hydrogels during swelling.

Functional architectures derived from guanine quartets

This paper highlights recent developments in the design and construction of functional materials such as supramolecular hydrogels and ion channels using a guanine motif as a self-assembling building block.

G-quadruplexes: Emerging roles in neurodegenerative diseases and the non-coding transcriptome

G-rich sequences in DNA and RNA have a propensity to fold into stable secondary structures termed G-quadruplexes. G-quadruplex forming sequences are widespread throughout the human genome, within both, protein coding and non-coding genes, and regulatory regions. G-quadruplexes have been implicated in multiple cellular functions including chromatin epigenetic regulation, DNA recombination, transcriptional regulation of gene promoters and enhancers, and translation. Here we will review the evidence for the occurrence of G-quadruplexes both in vitro and in vivo; their role in neurological diseases including G-quadruplex-forming repeat expansions in the C9orf72 gene in frontotemporal dementia and amyotrophic lateral sclerosis and loss of the G-quadruplex binding protein FMRP in the intellectual disability fragile X syndrome. We also review mounting evidence that supports a role for G-quadruplexes in regulating the processing or function of a range of non-coding RNAs. Finally we will highlight current perspectives for therapeutic interventions that target G-quadruplexes.

How soft are biological helices? A measure of axial and lateral force constants in folate quadruplexes by high-pressure X-ray diffraction

Alkaline folates self-associate in aqueous solutions to form columnar lyotropic phases. Such phases are made by quadruplexes, which are supramolecular helicoidal structures formed by a stacked array of folate tetramers. High-pressure synchrotron X-ray diffraction is used to analyze alkaline folate quadruplex stability and energetics. Diffraction data show that both inter-helical lateral and tetramer stacking distances decrease as a function of pressure. Lateral and axial quadruplex compressibilities and force constants have been derived and strong correlation between the strength of tetramer stacking and pressure effects demonstrated. In particular, quadruplex rigidity increases by changing Na+ to K+ and by adding excess KCl, as a consequence of increased stacking interactions and quadruplex elongation.

Guanosine quadruplexes in solution: a small-angle x-ray scattering analysis of temperature effects on self-assembling of deoxyguanosine monophosphate

We investigated quadruplex formation in aqueous solutions of 2′-deoxyriboguanosine 5′-monophosphate, d(pG), which takes place in the absence of the covalent axial backbone. A series of in-solution small angle X-ray scattering experiments on d(pG) have been performed as a function of temperature in the absence of excess salt, at a concentration just above the critical one at which self-assembling occurs. A global fit approach has been used to derive composition and size distribution of the scattering particles as a function of temperature. The obtained results give thermodynamical justification for the observed phase-behavior, indicating that octamer formation is essential for quadruplex elongation. Our investigation shows that d(pG) quadruplexes are very suitable to assess the potential of G-quadruplex formation and to study the self-assembling thermodynamics.

Structure and gelation mechanism of tunable guanosine-based supramolecular hydrogels

The mechanism of gelation of 50/50 w/w mixtures of guanosine (G) and 2',3',5'-tri-O-acetylguanosine (TAcG) in aqueous 0.354 M KCl was investigated using a combination of static light scattering (SLS), polarized and depolarized dynamic light scattering (VV and VH DLS), small-angle neutron and X-ray scattering (SANS and SAXS), and viscometric experiments. SLS and viscometry show a dramatic increase in apparent molecular weight and hydrodynamic volume at 0.2 wt % and 0.3 wt %, respectively, indicating the critical concentration for self-association of G/TAcG quartets into columnar assemblies lies below 0.2 wt %. Above this concentration, SANS and SAXS generate complementary information on the structure of the individual columnar stacks. VV and VH DLS results indicate bimodal correlation functions, whose properties suggest, respectively, translational and rotational diffusion of a bimodal distribution of particles. The fast mode appears to originate from fibrillar agglomerates of G/TAcG columnar quartet assemblies, while the slow mode comes from microgel domains. Guinier plot analysis of the SLS data probes the internal structure of the microgel domains. Collectively, the results suggest that sol and microgel phases coexist below the macroscopic gel point, and that the sol phase contains individual columnar stacks of G/TAcG quartets and fibrillar aggregates formed via lateral aggregation of these columnar assemblies. With increasing concentration, the DLS data indicate a progressive increase in the volume fraction of microgel domains, which ultimately leads to macroscopic gelation. Prior observation of a transient network contribution to the gel rheology at low temperature is attributed to the presence of individual columnar stacks within the gel network.

Small angle X-ray scattering analysis of deoxyguanosine 5'-monophosphate self-assembing in solution: nucleation and growth of G-quadruplexes

To solve details of the self-assembling process of guanosine in diluted aqueous solution and to derive a thermodynamical model for quadruplex formation, the structural behavior of deoxyguanosine 5'-monophosphate has been analyzed by in-solution small angle X-ray scattering. The experiments have been performed as a function of guanosine concentration and at fixed guanosine concentration but in the presence of varying amounts of KCl. As a result, the self-assembling process, in terms of both aggregate particle fractions and aggregate length, has been observed to be strongly dependent on composition and largely affected by excess potassium ions in the solution. In particular, the different aggregate forms have been resolved and their concentration derived as a function of sample composition. In accordance with a hierarchical aggregation process, a nucleation and elongation mechanism has been used to derive the thermodynamical parameters for self-assembling. The results show that the annealing and fragmentation steps play an important role in the aggregation process.

Guanosine gel for sequence-dependent separation of polymorphic ssDNA

The separation of fluorescent-labeled ssDNA fragments of equal length based on differences in sequence was achieved through the use of guanosine gels (G-gels) formed by guanosine-5'-monophosphate (GMP) in capillary gel electrokinetic chromatography (CGEKC) with LIF detection. Baseline resolution was achieved for homodimers and homopentamers of A, T, and C. G-gel CGEKC provided better resolution than CZE, MEKC, or a sieving gel in CGE. Resolution improved with increasing GMP, indicating that the interaction is linked to structural organization of the G-gel. Fluorescence intensity and anisotropy show that the order of interaction with G-gels is T>C>A. We then investigated four conformationally similar, polymorphic 76-mers with A/G substitutions that are utilized in forensic DNA typing. Resolution was achieved by CGEKC but not CZE or CGE. In CGEKC, the negatively charged G-gels and oligonucleotides electromigrate toward the positive inlet while being driven by EOF to the negative outlet. The net forward velocity is the greatest for oligonucleotides most closely associated with the slower, more cumbersome G-gel network. For the 76-mers, resolution increases with increasing difference in guanosine content between strands and, for a given difference, with increasing total guanosines in the strands.

Locating counterions in guanosine quadruplexes: a contrast-variation neutron diffraction experiment in condensed hexagonal phase

Guanosine, one of the primary components of nucleic acids, self-associates in water to form G-quadruplexes, four-stranded helicoidal aggregates, made by stacked planar tetramers, consisting of four planar guanine molecules. Essential for the stability of these supramolecular aggregates is the presence of monovalent cations. As G-quadruplexes show a lyotropic polymorphism, neutron diffraction, in combination with the H2O/D2O contrast variation technique, has been applied to study the cation structural features of quadruplexes in hexagonal phase at different hydrations and counterion concentrations. The guanosine 5'-monophosphate, dipotassium salt, was considered and G-quadruplexes in hexagonal phase were prepared in the different experimental conditions (contrast, hydration and KCl solution concentration) by using the osmotic stress technique. The calculated scattering length density distribution maps show that counterions fill the helix inner cavity and that atmospheric cations are bound to a second site, close to the external phosphate groups. The site occupancy turned out to be very high: we found on the inner site 0.87 K ions per tetramer in G-quadruplexes prepared in pure water and 0.97 K ions per tetramer in G-quadruplexes prepared in KCl 0.5 M, while in all cases 6 ions per unit cell were detected to occupy the outer sites, partially neutralizing the two formal negative charges per phosphate group. The very large K ions concentration difference between the binding sites and the bulk solution demonstrates that counterions are structurally involved in the formation and in the stabilization of the helices.

Detection of DNA hybridization using the near-infrared band-gap fluorescence of single-walled carbon nanotubes

We demonstrate the optical detection of DNA hybridization on the surface of solution suspended single-walled carbon nanotubes (SWNTs) through a SWNT band gap fluorescence modulation. Hybridization of a 24-mer oligonucleotide sequence with its complement produces a hypsochromic shift of 2 meV, with a detection sensitivity of 6 nM. The energy shift is modeled by correlating the surface coverage of DNA on SWNT to the exciton binding energy, yielding an estimated initial fractional coverage of 0.25 and a final coverage of 0.5. Hybridization on the nanotube surface is confirmed using Forster resonance energy transfer of fluorophore-labeled DNA oligonucleotides. This detection is enabled through a new technique to suspend SWNTs using adsorption of single-stranded DNA and subsequent removal of free DNA from solution. While the kinetics of free DNA hybridization are relatively fast (<10 min), the kinetics of the process on SWNTs are slower under comparable conditions, reaching steady state after 13 h at 25 degrees C. A second-order kinetic model yields a rate constant of k = 4.33 x 10(5) (M h)(-1). This optical, selective detection of specific DNA sequences may have applications in the life sciences and medicine as in vitro or in vivo detectors of oligonucleotides.

Conformational properties of DNA containing (CCA)n and (TGG)n trinucleotide repeats

We have used CD spectroscopy, polyacrylamide gel electrophoresis, and UV absorption spectroscopy to study conformational properties of DNA fragments containing (CCA)n and (TGG)n repeats, which are the most length-polymorphic microsatellite sequences of the human genome. The (CCA)n fragments are random single strands at neutral and alkaline pH but they fold into intramolecular intercalated cytosine tetraplexes at mildly acid pH values. More acid values stabilize intermolecular tetraplex formation. The behavior of (TGG)n repeats is more complex. They form hairpins or antiparallel homoduplexes in low salt solutions which, however, are transformed into parallel-stranded guanine tetraplexes at physiological KCl concentrations. Their molecularity depends on the repeat number: (TGG)4 associates into an octameric complex, (TGG)8 forms tetramolecular complexes. (TGG)n with odd repeat numbers (5, 7, and 9) generate bimolecular and tetramolecular tetraplexes. The only (TGG)7 folds into an intramolecular tetraplex at low KCl concentrations, which is antiparallel-stranded. Moreover, the (TGG)(n) fragments provide various mutually slipped conformers whose population increases with salt concentration and with the increasing repeat number. However, the self-structures of both strands disappear in the presence of the complementary strand because both (TGG)n and (CCA)n prefer to associate into the classical heteroduplex. We suppose that the extreme conformational variability of the DNA strands stands behind the length polymorphism which the (CCA)n/(TGG)n repeats exhibit in the human genome.

Information content and complexity in the high-order organization of DNA

Nucleic acids are characterized by a vast structural variability. Secondary structural conformations include the main polymorphs A, B, and Z, cruciforms, intrinsic curvature, and multistranded motifs. DNA secondary motifs are stabilized and regulated by the primary base sequence, contextual effects, environmental factors, as well as by high-order DNA packaging modes. The high-order modes are, in turn, affected by secondary structures and by the environment. This review is concerned with the flow of structural information among the hierarchical structural levels of DNA molecules, the intricate interplay between the various factors that affect these levels, and the regulation and physiological significance of DNA high-order structures.

A Reversible Gel for Chiral Separations

The use of a guanosine gel as a chiral selector in capillary electrophoresis is introduced. Guanosine gels are reversible organized media that are formed through the self-association of guanosine compounds. Their degree of organization and their physicochemical properties can be modulated through variations in guanosine monomer concentration, pH, temperature, and cation content. Baseline resolution of the d and l enantiomers of propranolol was achieved using a reversible biogel formed by 5'-guanosine monophosphate as the run buffer in capillary electrophoresis. Conditions were optimized to provide enantiomeric resolution of 2.1-2.3 in less than 5 min. The reversibility of the gel network offers potential advantages for chiral separations, including the possibility of using thermal or chemical dissociation of the gel network to remove the nucleoside monomers from the separated enantiomers, thereby eliminating the chiral selector as a source of physical contamination of the enantiomerically pure products and spectral background in UV absorbance detection.

Dynamic light scattering and 31P NMR study of the self-assembly of deoxyguanosine 5'-monophosphate: the effect of added salt

Self-assembling and dynamical properties of deoxyguanosine 5'-monophosphate in isotropic aqueous solutions were studied by (31)P NMR spectroscopy and dynamic light scattering (DLS). All solutions had the same c = 4 wt% guanosine concentration, while the added KCl molarity ranged from 0 to 1.5 M. (31)P NMR measurements show that potassium ions strongly enhance the stacking process of guanosine tetramers until a saturation is reached at 0.1 M KCl with more than 70% of the molecules aggregated. Polarized light scattering reveals the presence of a fast relaxation mode that arises from the translational dynamics of the self-assembled stacks. The diffusion coefficient of this mode shows a strong dependence on molarity of added salt, which can be described in terms of the coupled mode and counterion condensation theories for polyelectrolyte solutions. Depolarized light scattering reveals the rotational dynamics of the self-assembled stacks which exhibits a pronounced slowing down with increasing the added salt content.

Sequence recognition in the pairing of DNA duplexes

Pairing of DNA fragments with homologous sequences occurs in gene shuffling, DNA repair, and other vital processes. While chemical individuality of base pairs is hidden inside the double helix, x ray and NMR revealed sequence-dependent modulation of the structure of DNA backbone. Here we show that the resulting modulation of the DNA surface charge pattern enables duplexes longer than approximately 50 base pairs to recognize sequence homology electrostatically at a distance of up to several water layers. This may explain the local recognition observed in pairing of homologous chromosomes and the observed length dependence of homologous recombination.

Biomesogenic matrix systems

The bifunctionally reactive nucleoside and distant nucleoside analogs adenosine (Ado), S-[(adenine-9-yl)methoxyethyl]-L-cysteine (Na-salt) (cysA) and 9-vinyladenine (vA) in aqueous solutions assemble on complementary polyuridylic acid templates to form complex lyomesophases. The systems are investigated by polarizing microscopy, differential scanning calorimetry (DSC) and 1H- and 31P-nmr spectroscopies, assisted by molecular modeling studies. The results indicate the importance of biomesogenic (pre)ordering in nucleic acid native and artificial matrix reactions.

Electrostatic interaction between long, rigid helical macromolecules at all interaxial angles

We derive formulas for the electrostatic interaction between two long, rigid macromolecules that may have arbitrary surface charge patterns and cross at an arbitrary interaxial angle. We calculate the dependence of the interaction energy on the interaxial angle, on the separation, and on the precise alignment of the charge pattern on one molecule with respect to the other. We focus in particular on molecules with helical charge patterns. We report an exact, explicit expression for the energy of interaction between net-neutral helices in a nonpolar medium as well as an approximate result for charged helices immersed in an electrolyte solution. The latter result becomes exact in the asymptotic limit of large separations. Molecular chirality of helices manifests itself in a torque that tends to twist helices in a certain direction out of parallel alignment and that has a nontrivial behavior at small interaxial angles. We illustrate the theory with the calculation of the torque between layers of idealized, DNA-like double helices in cholesteric aggregates. We propose a mechanism of the observed cholesteric-to-columnar phase transition and suggest an explanation for the observed macroscopic (0.4-5 microm) pitch of the cholesteric phase of B-DNA.

Self-assembly of disk-shaped molecules to coiled-coil aggregates with tunable helicity

A disk-shaped molecule with chiral tails is shown to form long fibers of molecular diameter and micrometer length by self-assembly in chloroform. The molecules are derived from crown ethers and contain a phthalocyanine ring. In the fibers, they have a clockwise, staggered orientation that leads to an overall right-handed helical structure. These structures, in turn, self-assemble to form coiled-coil aggregates with left-handed helicity. Addition of potassium ions to the fibers leaves their structure intact but blocks the transfer of the chirality from the tails to the cores, leading to loss of the helicity of the fibers. These tunable chiral materials have potential in optoelectronic applications and as components in sensor devices.

Symmetry laws for interaction between helical macromolecules

The power of symmetry laws is applied in many scientific areas from elementary particle physics to structural biology. The structures of many biological helices, including DNA, were resolved with the use of pertinent symmetry constraints. It was not recognized, however, that similar constraints determine cardinal features of helix-helix interactions vital for many recognition and assembly reactions in living cells. We now formulate such symmetry-determined interaction laws and apply them to explain DNA "over-winding" from 10.5 base pairs per turn in solution to 10 in hydrated fibers, counterion specificity in DNA condensation, and forces observed over the last 15 A of separation between DNA, collagen, and four-stranded guanosine helices.

DNA--DNA interactions

The forces that govern DNA double helix organization are being finally systematically measured. The non-specific longer-range interactions--such as electrostatic interactions, hydration, and fluctuation forces--that treat DNA as a featureless rod are reasonably well recognized. Recently, specific interactions--such as those controlled by condensing agents or those consequent to helical structure-are beginning to be recognized, quantified and tested.