Journal of Nucleic Acids

Journal of Nucleic Acids / 2010 / Article
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G-Quadruplex Nucleic Acids

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Volume 2010 |Article ID 938536 | https://doi.org/10.4061/2010/938536

Paolo Neviani, Dominique Sarazin, Marc Schmutz, Christian Blanck, Nicolas Giuseppone, Gian Piero Spada, "Hierarchical Formation of Fibrillar and Lamellar Self-Assemblies from Guanosine-Based Motifs", Journal of Nucleic Acids, vol. 2010, Article ID 938536, 9 pages, 2010. https://doi.org/10.4061/2010/938536

Hierarchical Formation of Fibrillar and Lamellar Self-Assemblies from Guanosine-Based Motifs

Academic Editor: Lea Spindler
Received01 Feb 2010
Revised07 Apr 2010
Accepted27 May 2010
Published13 Jul 2010

Abstract

Here we investigate the supramolecular polymerizations of two lipophilic guanosine derivatives in chloroform by light scattering technique and TEM experiments. The obtained data reveal the presence of several levels of organization due to the hierarchical self-assembly of the guanosine units in ribbons that in turn aggregate in fibrillar or lamellar soft structures. The elucidation of these structures furnishes an explanation to the physical behaviour of guanosine units which display organogelator properties.

1. Introduction

Supramolecular self-assembly represents a key technology for the spontaneous construction of nanoarchitectures and for the fabrication of materials with enhanced physical and chemical properties [14]. In addition, a significant asset of supramolecular self-assemblies rests on their reversible formation, thanks to the kinetic lability of their noncovalent interactions. This dynamic nature can be exploited for the development of “self-healing” and “smart” materials towards the tuning of their functional properties upon various external factors [58]. One particular intriguing objective in the field is to reach a high level of control over the shape and size of the supramolecular architectures, in order to produce well-defined functional nanostructures by rational design [9]. In this direction, many investigations have been pursued toward the construction of self-assembled objects from numerous low-molecular weight scaffolds [1018], for instance, by exploiting multiple directional hydrogen-bonding interactions. In particular, nucleobases have been used as supramolecular synthons as a result of their efficiency to code for noncovalent interaction motifs [19]. Among nucleobases, guanine represents the most versatile one, because of its different H-bond donor (N1H and N2H) and acceptor sites (O6, N3, and N7) which display self-complementary patterns of interactions. Interestingly, and depending on the environmental conditions, guanosine derivatives can form various types of structures. Most of the supramolecular architectures reported so far from guanosine derivatives require the presence of a cation (alkali metal, earth-alkali, or lanthanide ions) [2031] which stabilizes, via dipole-ion interactions, the macrocyclic G-quartet that can, in turn, stack in columnar G-quadruplex arrangements (Figure 1(a)). In addition, guanosine can polymerize via hydrogen bonding to give a variety of supramolecular networks including linear ribbons such as A- and B-types (Figures 1(b) and 1(c)).

This complex supramolecular behaviour confers to the guanine-guanine interactions their upper interest among all the homonucleobases studied [20, 32]. They have been subjected to intense investigations in various areas ranging from structural biology and medicinal chemistry—guanine-rich sequences are abundant in telomeric ends of chromosomes and promoter regions of DNA and are capable of forming G-quartet based structures [3335]—to material science and nanotechnology [36, 37].

In 1998, it was reported [38] that, even in the absence of metal cations, lipophilic guanosine derivative 1 (Figure 2) is able to self-assemble in ribbon-like structures leading to the formation of a lyotropic liquid crystalline phase [39]. In the following years, the structures of the ribbons obtained from different guanosine derivatives have been characterized in solution (by NMR and ESI-MS), in the solid state (by X-ray diffraction and NMR), and at graphite-solution interface (by STM) [4046]. Two different types of ribbons, with different patterns of hydrogen bonds, have been resolved in solution. The first species (ribbon-A, Figure 1(b)) is characterised by N2HO6 and N1HN7 hydrogen bonds, and the second one (ribbon-B, Figure 1(c)) by N1HO6 and N2HN3 hydrogen bonds. In the case of 1, ribbon-A is detected in anhydrous chloroform solutions () soon after dissolving the polycrystalline powder but subsequently undergoes a structural transition towards a thermodynamically more stable ribbon-B [40]. Interestingly, in the case of the closely related chemical structure of 2, only ribbon-B has been detected in chloroform solution (even soon after dissolution) [41]. For derivative 1, the critical concentration for the formation of the gel-like phase was measured 0.596 M in chloroform, and for derivative 2  0.125 M in the same solvent.

In both ribbon-like polymers A and B, the glycosidic bond adopts an anti conformation [4246]. However, the two ribbons possess a different symmetry and, as a consequence, while ribbon-A does present a permanent dipole moment, it is not the case for ribbon-B. This feature has been exploited in organic electronic prototype devices [4749], and more generally, linear ribbons from guanosine derivatives are considered as potential scaffolds for functional materials [5054]. Although the formations of the linear ribbons and their H-bonding patterns have been demonstrated in solution [40, 41] (as well as in the crystal state and on graphite surface), only very few investigations have been performed so far toward the determination of the length of these supramolecular polymers, as well as on their possible hierarchical self-assemblies in higher scale structures. NMR spectroscopic indications of the supramolecular polymerisation only come from the shifting and broadening of the resonance signals upon concentration of the solution. In addition, the observation of negative enhancements (or positive cross-peaks) in NOE (or NOESY) experiments indicates that guanosine derivatives behave as large molecules with () [3840].

In this paper we report on the investigation of the supramolecular polymerisation of 1 and 2 in chloroform by using light scattering technique as well as transmission electronic microscopy (TEM). This line of studies reveals the formation of supramolecular polymers with high molecular weights that produce hierarchical structuring of very soft self-assemblies displaying either fibrillar (1) or lamellar (2) organizations.

2. Results and Discussion

2.1. Static Light Scattering

The multiangle laser light scattering is the common technique [55, 56] for determining the shape of the polymers through the mean square radius of gyration and their structure through the particle scattering factor , the molecular weight , and the second virial coefficient . Theory took great interests long time ago giving statistical sense to these parameters [5561]. When is near zero and solutions considered as athermal according to general polymer theories [61] one may deal with the apparent molecular weight and use the so-called statistical dimensions determined at discrete concentrations [59, 60] instead of the one extrapolated at . Looking at the variation of versus concentration or temperature allows equilibrium constant to be evaluated which open fields to dynamics of the scaffolds and to their assembly ability. The form factor may be also useful to determine structural changes of the objects during the diffusion process of elementary unimers [59, 60]. The form factor may derive from calculations especially when the structure of the coil is well known. Theoretical aspects are shortly reviewed at the end of the paper (Section 4). There is shown typical processes for data calculations leading to Zimm plot which yields to the molecular dimensions and solution thermodynamics [5558]. All the data obtained for guanosines 1 and 2 are summarized in Table 1.


𝑀 𝑊
g/mole
𝑅 2 𝑔 𝑍 1 / 2
nm
𝐴 2
mol ml/g2
𝑑 𝑛 / 𝑑 𝑐

Guanosine 13620573.5 1 0 4 0.0769
Guanosine 25.93 1 0 4 43−6.4 1 0 4 0.083

The Zimm plot obtained from guanosine 1 at C in CHCl3 for different concentrations is shown in Figure 3. In this range of concentration, the apparent molecular weight was determined to be relatively stable below the gelation threshold. The linear regression reveals a modest molecular weight of 3620 (corresponding to an aggregation number of 6 to 7 units) but with a radius of gyration of 57 nm which indicates the presence of large objects. The discrepancy between these two parameters is explained by the high polydispersity of the supramolecular polymer with an average of small ribbons together with a smaller population of large objects. Indeed, the gyration radius being determined from , the importance of the large structures becomes predominant.

The molecular weight of the polymers depends largely on the concentration range and a study between 2.88 and 2.88  gmL-1 reveals a power law of 0.75 (see Figure 4) which is higher than the value (0.6) for regular swollen coils and which is the signature for rigid objects of about 200 nm in length [57, 62].

Finally, the association constant between two monomers in the supramolecular B-type ribbon (see Figure 1(c)) was determined by plotting the apparent molecular weight as a function of the concentration (Figure 5) and shows a relatively small value [59, 60].

When the polymer is homogeneous, Flory Krigbaum [63] derived the more realistic model for introducing the enthalpy and entropy parameter, respectively. By comparison with the Flory-Huggins theory [64] these parameters are seen to be related by where is the Flory Huggins interaction parameters. For ideal behaviour and so the theta point is reached, with theta temperature being given by where T is the absolute temperature. The theory leads to some basics which are the equivalent size of the solvent and monomers, respectively, and a number of association for statistical calculations.

These statistical basics hold for guanosine 2 but comments on guanosine 1 may lie in the expression of idealized lattice model for second virial coefficient. It is obvious that one of the optimal conditions for association is an athermal solution which is what we have found for guanosine 2 (Table 1). In the case of guanosine 2, the light scattering reveals a quite different behavior of the self-assembly process. The Zimm plot in Figure 6 shows a smaller polidispersity than what is measured for guanosine 1 together with higher molecular weights (, and the degree of polymerisation ), but with a close radius of gyration (43 nm) which might correlate with the formation of more compact objects. This expectation is confirmed by plotting the in the range of concentration and . The experimentally determined power law of 0.3 (see Figure 7) is the signature for very compact objects such as spheres [57, 62]. Finally, the determination of the equilibrium constant [59, 60] for guanosine 2 shows a strong association process () and a complex behaviour of a sigmoid type (Figure 8). This nonlinear effect indicates a cooperative process and the hierarchical association between the linear supramolecular ribbons with their organization in higher-ordered self-assembled structures that in turn stabilize the primary association.

2.2. Transmission Electron Microscopy

Structural observation of self-assembled system can easily be achieved by TEM approaches, as widely used and described in the literature [65, 66].

Guanosine derivative 1 in bromoform () forms small short fibers (Figure 9(a)). Bromoform was used for technical reasons regarding the evaporation rate at room temperature which is too high for chloroform thus changing the concentration of the sample during the preparation step. The dielectric constants are very close to each other for chloroform and bromoform (4,8 and 4,4 at C, resp.), and the gelation concentration was observed to be similar in both cases. These fibers present a diameter of 6 nm and a length of approximatively 200 nm. Indeed, the precise length cannot be determined as the fibers present a high entanglement ratio. This length corresponds to the distance between the nodes of the networks and was also observed from time to time on individual filaments (see Figure 9(b)). It is also in agreement with the light scattering data. The small individual fibers self-assemble in larger ones to form bundles of 30 nm. These latter can be formed during the preparation step as the diameter of the bundles varies from one experiment to another. The distribution of the fibers within a clear network illustrates the organogelator properties of guanosine 1.

Guanosine derivative 2 in bromoform () forms small aggregates and small lamellar structures. On Figure 10, large aggregates consisting of the superposition of small (100 nm) lamellar structures are observed (see arrows). These structures show no define contours and are the results of the aggregations of the smaller domains. No internal features inside the small domains are visible at the resolution of the technique. The aggregation within highly compact lamellar structures is also in good agreement with the light scattering experiments that indicate mainly the presence of pseudospherical objects with a strong cooperative effect occurring between the ribbons and their higher-scale self-assemblies.

3. Conclusions

We have determined the hierarchical polymeric natures of the self-assemblies obtained from the ribbon forming [40, 41] guanosine derivatives 1 and 2. The light scattering measurements appeared as an appropriate technique for the molecular weight determination versus the structure of these objects that are both concentration sensitive. The main conclusions were confirmed by TEM. Lipophilic guanosine 1 forms very soft fibrillar objects of 6 nm of diameter and 200 nm in length and that in turn produces bundles of networked fibers with 30 nm of diameter. Despite its closely related structure, guanosine 2 forms much longer ribbons with molecular weights up to that in turn fold in very compact aggregates with lamellar structures. This process has been shown to be highly cooperative by the determination of the molecular weight as a function of the concentration.

Interestingly, while both derivatives show the same motif of H-bonding in the formation of the first level of supramolecular assembly (the B-type ribbon), their hierarchical organization is quite different. This finding points out the role of other structural aspects in addition to the H-bond recognition pattern (e.g., the number and length of tails) in determining the shape and dimension of the object obtained at the nanoscale level.

These investigations furnish an explanation to the gelation properties of these two derivatives and can be used to rationalize the synthesis of functional guanosine-based soft materials.

4. Materials and Methods

4.1. Experimental Details for the Synthesis of Guanosine Derivatives

,-O-Didecanoyl--Deoxyguanosine 1
Compound 1 was prepared in 94% yield starting from -deoxyguanosine (Fluka) (1 mmol) and decanoic anhydride (2.2 mmol) according to the literature procedure for ,-O-dipropanyl--deoxyguanosine [67]. 1H NMR (300 MHz, [D6]DMSO): (tt, 6H; 2 CH3), (m, 24H; 12 CH2), (m, 4H; 2 CH2–CH2–CO), (tt, 4H; 2 CH2–CO), 2.42 and 2.93 (mm, 2H, H-/H-), (m, 3H; H-/H-/H-), 5.35 (m, 1H; H-), 6.17 (m, 1H; H-), 6.45 (bs, 2H; NH2), 7.9 (s, 1H; H-8), 10.65 (s, 1H; NH); ES-MS: m/z (%): 576.8 (100) [1+ +H].

,-O-Isopropylidene--Decanoylguanosine 2
Compound 2 was prepared in 86% yield starting from ,-O-isopropylideneguanosine (Sigma) (0.77 mmol) and decanoic anhydride (1.2 equiv) according to the literature procedure [41].

4.2. Experimental Details Concerning the Static Light Scattering Technique

The light scattering experiments were carried out with an in-house apparatus [61] equipped with (i) a red He-Ne laser of wavelength in vacuum, (ii) a discrete-angle goniometer acting within the range from to , (iii) a Hamamatsu type photomultiplier as detector, (iv) a photocounting device, and (v) a toluene matching bath. The vertical polarization of the incident beam with respect to the scattering plane has been used and is written V. The analyzer, arranged between the measuring cell and the photomultiplier, is vertically oriented and is written . This optical setup allows measurement of the isotropic scattering intensity [68]. The excess of light scattering intensity was measured as a function of scattering vector with an accuracy of 1% (θ the scattering angle, n the solvent refractive index). The values of Rayleigh excess scattering intensity R(q) were obtained through the calibration of with a benzene standard. The intensities , after normalization of the raw data, can be written for the vertically polarized scattering light through an analyzer.

Use the following formula for stray light : where is the molecular weight, c is the concentration of the polymer, P(q) is the form factor, and S(q) the long range interference from distant scatterers, where for dilute solution S(q) 1 and is the optical factor for the system including the refractive index increment of the polymer as follows, where is the optical contrast calibrated with benzene standard (the suffix gives the polarization of incident beam and stray light).

The calibration of the spectrometer was made by evaluating the optical constant or as follows: NA is Avogadro Number, is the wavelength in vacuum, is the benzene refractive index, and is the benzene Rayleigh ratio for vertically polarised incident light.

The chloroform refractive index and the average refractive index increment of the assembly for 1 to CHCl3 are equal to and , respectively.

The chloroform refractive index and the average refractive index increment of the assembly for 2 to CHCl3 are equal to and respectively.

According to Yamakawa [62] the ratio may be read versus q as where is the normalized scattering intensity from vertically incident beam analyzed vertically, and is the second virial coefficient.

Using the formalism of Debye [55] and Zimm [56], (2) gives the following:

is the excess Rayleigh ratio of the polymer comparatively to the solvent. The inverse of the form factor (q) leads after a MacLaurin transform at low q vector to (5). Here we get the second moment of the mass distribution which is the statistic z average mean radius of gyration [57, 58] as follows:

For extrapolation at and (4) leads to the determination of the molecular mass and the second virial coefficient . When the thermodynamic forces applied on the coil equilibrate, we can write . This athermal condition for binary mixture allows the determination of the apparent molecular mass for each concentration [59, 60]:

Equation (6) contains all information on the shape and the conformation of the isolated polymer in solution. The determination of the radius of gyration is only valid in the guinier range where the architectures of the polymers are barely distinguishable.

The plot of (5) versus , called Zimm-plot, allows a simultaneous extrapolation to and , which yields as the ordinate intercept and as the initial slope of (6) and the second viral coefficient from (5).

The value of the second viral coefficient is in our case of an athermal binary mixture and thus neglected: So we get a good evaluation of the variation for versus the concentration C.

Following the calculation of Huglin [59] and Elias [60] we obtain Here is the molecular weight of the initial monomer and is the weight average molecular weight determined through (7).

Measurements of each sample have been carried out after various dilutions with precise volume of clarified solvent obtained by filtration through millipore filters size 0.45 m. All the samples are directly processed in the measurements vial to avoid dust pollution.

4.3. Experimental Details Concerning the TEM Technique

The samples are prepared in standard conditions as described in literature [69].

Acknowledgments

This work was supported by the COST Network G4-NET (MPNS Action MP0802). P. Neviani thanks the University of Bologna for a Marco Polo Fellowship supporting his staying in Strasbourg. N. Giuseppone and M. Schmutz thank the icFRC for financial support.

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Copyright © 2010 Paolo Neviani et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


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