Understanding self-assembly at molecular level enables controlled design of DNA G-wires of different properties.

A possible engineering of materials with diverse bio- and nano-applications relies on robust self-assembly of oligonucleotides. Bottom-up approach utilizing guanine-rich DNA oligonucleotides can lead to formation of G-wires, nanostructures consisting of continuous stacks of G-quartets. However, G-wire structure and self-assembly process remain poorly understood, although they are crucial for optimizing properties needed for specific applications. Herein, we use nuclear magnetic resonance to get insights at molecular level on how chosen short, guanine-rich oligonucleotides self-assemble into G-wires, whereas complementary methods are used for their characterization. Additionally, unravelling mechanistic details enable us to guide G-wire self-assembly in a controlled manner. MD simulations provide insight why loop residues with considerably different properties, i.e., hydrogen-bond affinity, stacking interactions, electronic effects and hydrophobicity extensively increase or decrease G-wire length. Our results provide fundamental understanding of G-wire self-assembly process useful for future design of nanomaterials with specific properties.

Supramolecular Polymorphism of (G4C2)n Repeats Associated with ALS and FTD.

Guanine-rich DNA sequences self-assemble into highly stable fourfold structures known as DNA-quadruplexes (or G-quadruplexes). G-quadruplexes have furthermore the tendency to associate into one-dimensional supramolecular aggregates termed G-wires. We studied the formation of G-wires in solutions of the sequences d(G4C2)n with n = 1, 2, and 4. The d(G4C2)n repeats, which are associated with some fatal neurological disorders, especially amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), represent a challenging research topic due to their extensive structural polymorphism. We used dynamic light scattering (DLS) to measure translational diffusion coefficients and consequently resolve the length of the larger aggregates formed in solution. We found that all three sequences assemble into longer structures than previously reported. The d(G4C2) formed extremely long G-wires with lengths beyond 80 nm. The d(G4C2)2 formed a relatively short stacked dimeric quadruplex, while d(G4C2)4 formed multimers corresponding to seven stacked intramolecular quadruplexes. Profound differences between the multimerization properties of the investigated sequences were also confirmed by the AFM imaging of surface films. We propose that π-π stacking of the basic G-quadruplex units plays a vital role in the multimerization mechanism, which might be relevant for transformation from the regular medium-length to disease-related long d(G4C2)n repeats.

GC ends control topology of DNA G-quadruplexes and their cation-dependent assembly.

GCn and GCnCG, where n = (G2AG4AG2), fold into well-defined, dimeric G-quadruplexes with unprecedented folding topologies in the presence of Na+ ions as revealed by nuclear magnetic resonance spectroscopy. Both G-quadruplexes exhibit unique combination of structural elements among which are two G-quartets, A(GGGG)A hexad and GCGC-quartet. Detailed structural characterization uncovered the crucial role of 5'-GC ends in formation of GCn and GCnCG G-quadruplexes. Folding in the presence of 15NH4+ and K+ ions leads to 3'-3' stacking of terminal G-quartets of GCn G-quadruplexes, while 3'-GC overhangs in GCnCG prevent dimerization. Results of the present study expand repertoire of possible G-quadruplex structures. This knowledge will be useful in DNA sequence design for nanotechnological applications that may require specific folding topology and multimerization properties.

Molecular recognition of a lipophilic guanosine derivative in Langmuir films at the air-water interface.

Molecular recognition of a lipophilic deoxyguanosine derivative at the air-water interface was investigated by film balance experiments and Brewster Angle Microscopy. Results showed that guanosine, despite strong tendency towards self-assembly, interacts with both complementary and noncomplementary liponucleosides (lipophilic derivatives of deoxycytidine and deoxythymidine). At surface pressures below 17mN/m, attractive and repulsive interactions were present in case of both mixed monolayers and were the strongest at guanosine molar fractions of 0.5 and 0.75. At higher values of surface pressure, deoxyguanosine-deoxycytidine interactions were strictly attractive and were present only for monolayers with guanosine molar fraction of 0.75. On the contrary, attractive and repulsive interactions remained present in case of deoxyguanosine-deoxythymidine mixed monolayers. This indicates that interactions between guanosine and cytidine are much stronger than guanosine-thymidine interactions. Interactions for none of the nucleoside pairs, however, are specific and π-stacking interactions between the aromatic planes of liponucleoside derivatives probably dominate over hydrogen bonding interactions. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.

Surface-Adsorbed Long G-Quadruplex Nanowires Formed by G:C Linkages.

G-quadruplexes connected into long, continuous nanostructures termed G-wires show properties superior to dsDNA when applied in nanotechnology. Using AFM imaging, we systematically studied surface adsorption of a set of G-rich oligonucleotides with GC-termini for their ability to form long G-wires through G:C pairing. We investigated the effects of increasing sequence length, the type of nucleotide in the side loops, and removal of the CG-3' terminus. We found that sequences with adenine in the side loops most readily form G-wires. The role of magnesium as an efficient surface-anchoring ion was also confirmed. Conversely, as resolved from dynamic light scattering measurements, magnesium had no ability to promote G-quadruplex formation in solution. These insights may help in selecting prosperous candidates for construction of G-quadruplex based nanowires and to explore them for their electronic properties.

Programmed self-assembly of a quadruplex DNA nanowire.

The ability to produce, reproducibly and systematically, well-defined quadruplex DNA nanowires through controlled rational design is poorly understood despite potential utility in structural nanotechnology. The programmed hierarchical self-assembly of a long four-stranded DNA nanowire through cohesive self-assembly of GpC and CpG "sticky" ends is reported. The encoding of bases within the quadruplex stem allows for an uninterrupted π-stacking system with rectilinear propagation for hundreds of nanometers in length. The wire is mechanically stable and features superior nuclease resistance to double-stranded DNA. The study indicates the feasibility for programmed assembly of uninterrupted quadruplex DNA nanowires. This is fundamental to the systematic investigation of well-defined DNA nanostructures for uses in optoelectronic and electronic devices as well as other structural nanotechnology applications.

Meeting report: Guanosines and quadruplexes (London, September 15-17, 2010).

The meeting entitled "Guanosines and quadruplexes" was held in London on September 2010. It attracted over 80 participants from all over the world, combining researchers interested in nucleoside/nucleotide self-assembly and nucleic acids structures, working in fields ranging from chemistry, biology, physics, theory to material sciences and nanotechnology.

Effect of base sequence on g-wire formation in solution.

The formation and dimensions of G-wires by different short G-rich DNA sequences in solution were investigated by dynamic light scattering (DLS) and polyacrilamide gel electrophoresis (PAGE). To explore the basic principles of wire formation, we studied the effects of base sequence, method of preparation, temperature, and oligonucleotide concentration. Both DLS and PAGE show that thermal annealing induces much less macromolecular self-assembly than dialysis. The degree of assembly and consequently length of G-wires (5-6 nm) are well resolved by both methods for DNA sequences with intermediate length, while some discrepancies appear for the shortest and longest sequences. As expected, the longest DNA sequence gives the longest macromolecular aggregates with a length of about 11 nm as estimated by DLS. The quadruplex topologies show no concentration dependence in the investigated DNA concentration range (0.1 mM-0.4 mM) and no structural change upon heating.

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.

Self-organization of guanosine 5'-monophosphate on mica.

Self-assembled aggregates of guanosine 5'-monophosphate (GMP) on the surface of muscovite mica were investigated by atomic force microscopy (AFM). Aqueous solutions of sodium, potassium and ammonium GMP salts were studied. For solution concentrations c < 0.005 wt% only small islands of deposited material are present on the surface. For c approximately 0.02 wt%, in addition to the islands and patches, also linear aggregates called G-wires are formed. The wire-like aggregates are on average 1.9 nm high and can be several micrometers long. They exhibit a profound directional growth along the six main crystallographic axes of the basal plane of mica. For c > 0.1 wt% flat terraces with the height of 2.5 nm appear. They are formed of G-wires lying with their long axis parallel to the substrate and stacking in a hexagonal arrangement. The morphology of the adsorbates is independent of the type of salt used to prepare the initial solution. This signifies that intrinsic potassium ions from the substrate play much more important role in the GMP adsorption than cations from the solution.

Disodium guanosine 5'-monophosphate self-associates into nanoscale cylinders at pH 8: a combined diffusion NMR spectroscopy and dynamic light scattering study.

We report a combined NMR and dynamic light scattering (DLS) study on the size of supramolecular structures formed by disodium guanosine 5'-monophosphate, Na(2)(5'-GMP), at pH 8. In general, two distinct types of aggregate species are present in an aqueous solution of Na(2)(5'-GMP). One type consists of stacking 5'-GMP monomers, and the other contains stacking G-quartets. Both types of aggregates can be modeled as rodlike cylinders. The cylinder diameter is 10 and 26 A for monomer aggregates and quartet aggregates, respectively. For Na(2)(5'-GMP) concentrations between 18 and 34 wt %, the cylinders formed by stacking G-quartets have an average length between 8 and 30 nm, corresponding to a stack of approximately 24-87 G-quartets. These nanoscale aggregates are significantly larger than what had previously been believed for Na(2)(5'-GMP) self-association at pH 8. The length of both types of 5'-GMP aggregates was found to increase with Na(2)(5'-GMP) concentration but was insensitive to the added NaCl in solution. While the aggregate size for monomer aggregates increases with a decrease in temperature, the size of G-quartet aggregates is essentially independent of temperature. We found that the size of G-quartet aggregates is slightly larger in D(2)O than in H(2)O, whereas the size of monomer aggregates remains the same in D(2)O and in H(2)O. We observed a linear relationship between the axial ratio of the 5'-GMP cylinders and the Na(2)(5'-GMP) concentration for both types of 5'-GMP aggregates, which suggests a common stacking mechanism for monomers and G-quartets.