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• W2124879324 abstract "Double plane: Base pairing mediates sterically induced, cooperative self-assembly of complementary nucleotides on a template formed from amphiphilic bis(ZnII–cyclen) derivatives ordered on thiolated surface. Real-time monitoring of binding events proved precise harboring of equal amounts of A and U nucleotides from their arbitrary combinations in solution into planar bilayers (see picture). This paper describes a two-dimensional chemical system in which a divalent “template” guides and controls the stepwise and cooperative self-assembly mediated by base pairing of adenosine and uridine nucleotides. Multiple hydrogen bonding and base pairing constitute one of the most widely studied classes of noncovalent interactions in supramolecular chemistry.1 The precision with which nature utilizes complementary weak bonding to guide self-assembly of complex structures remains a fascinating challenge for surface chemistry that aims to develop novel approaches to interfacial sensing and nanofabrication.2 To date, attempts to use base pairing as a basis for planar molecular-recognition systems have focused on self-assembled monolayers (SAMs)3, 4 or Langmuir monolayers5 that are formed from compounds bearing nucleobases or their synthetic analogues. Although exceptionally useful in the precise vertical alignment of oligo/polynucleotides on solid supports,6 the SAM-based methods are unsuitable for lateral tailoring of recognition surfaces with different types of bases. This is mostly because of steric hindrance and phase separation of monolayer constituents.3, 7 On the other hand, Langmuir monolayers enable fine-tuning of steric conditions in highly ordered films comprised of different entities at air/water interfaces,8 but their practical applicability is severely limited. Herein, we use a novel surface-design scheme that combines the advantages of SAM-based and Langmuir-Blodgett (LB) monolayer approaches. This allows for precise harboring of arbitrary combinations of complementary nucleotides in planar films through sterically induced, cooperative self-assembly on a surface presenting divalent bis(ZnII–cyclen) complexes.9–12 These complexes have been previously used for selective recognition of thymidine and uridine bases in polynucleotides and natural DNA.13 Furthermore, they have a use as highly efficient divalent receptors for thymidine and uridine nucleotides that interact with the bis-cyclic host through simultaneous binding of terminal phosphate and imide groups to complementary macrocyclic fragments.14 In our system, the selective formation of bis(ZnII–cyclen)-nucleotide aggregates promotes cooperative nucleotide self-assembly on a recognition surface. We ordered amphiphilic bis(ZnII–cyclen) derivatives (hereafter, ZnII–BC) into a planar matrix through LB transfer of ZnII–BC monolayers from an aqueous subphase onto a gold-coated surface covered with a loosely packed SAM of octanethiol (Figure 1). This simple combination of SAM and LB techniques preserves a uniform order of the precursor monolayer and gives a stable, interdigitated bilayer with macrocyclic fragments exposed to the solution. According to our preliminary studies, ZnII–BC immobilized in such a film is capable of binding nucleotide constituents modeled with uracil and an inorganic phosphate dianion while being inactive to adenine or monoanionic phosphates (for details see the Supporting Information).15 The nucleotide assembly on functionalized SAM/LB plates was investigated in aqueous solutions of monovalent adenosine 5′-mono-, di- or triphosphates (hereafter, 5′-AXPs, where X=M (mono), D (di), or T (tri)) and/or divalent uridine 5′-mono-, di- or triphosphates (5′-UXPs, where X=M (mono), D (di), or T (tri)) at pH 7.5 through surface plasmon resonance (SPR) as a most appropriate tool for real-time monitoring of binding events. Schematically drawn structure of a SAM-supported monolayer of ZnII–BC on a gold-coated surface. The SPR sensograms in Figure 2 a,b2 illustrate typical kinetics of the stepwise assembly of 0.02 mM 5′-AXPs and 5′-UXPs for different orders of nucleotide addition (i.e., UTP probing followed by the subsequent addition of ATP and UTP (a) and adsorption of ATP, followed by UTP and UDP(b)). SPR sensograms for stepwise adsorption of a 5′-ATP/5′-UTP binary combination on a SAM-ZnII–BC surface. a) The experiment started by probing with UTP (0.02 mm) followed by subsequent addition of ATP (0.02 mm) and of UTP (0.02 mm), b) the “vice versa” subsequent binding of ATP (0.02 mm) and UTP (0.02 mm) finalized by probing with UDP (0.05 mM); pH 7.5. Initially, ZnII–BC surfaces responded slowly to both types of nucleotides. The first-stage binding translated into an SPR maximal response, Δα1, that falls within a range of 1.8–2.7 angle min;16 the absolute values of Δα1 increased with the molecular weight of the measured nucleotides.15 In addition, the kinetics and values of Δα1 determined for 5′-AXPs were similar to those measured for similar 5′- UXPs (here, 2.5–2.7 angle min for UTP and ATP). After the completion of initial adsorption, similar probes of complementary nucleotides (0.02 mm) were added. The kinetics of secondary binding of either 5′-AXP or 5′-UXP at the surface with an already-adsorbed complementary partner was very different from that of initial recognition—the SPR signal increased rapidly and reached its maximal value Δα2, which was twice that of Δα1. Again, the Δα2 value varied from 3.6 to 5.4 angle min in proportion to the nucleotide's molecular weight, and the magnitudes of responses to 5′-AXP and 5′-UXP were similar (5.4 and 5.3 angle min for ATP and UTP, respectively). Importantly, because the magnitude of the SPR signal is proportional to the amount of adsorbed analyte, it appears that the initial binding of one molecule of either monovalent 5′-AXP or divalent 5′-UXP by ZnII–BC film promotes further assembly of not one but two complementary molecules. Furthermore, when equilibrated after secondary binding, the sensing surfaces were still capable of specific recognition; the films responded to the nucleotides that were complementary to the one bound at the second stage (Figure 2 a). Moreover, maximal third-stage responses Δα3 were close to Δα1, that is, the efficiency of final adsorption was comparable with that observed at the initial stage. On the other hand, addition of a nucleotide containing a base similar to that used in second-stage binding caused no significant increase in the SPR signal even at increasing concentrations (Figure 2 b). The specificity of the third-stage responses and their absolute values suggest that this stage proceeds with complementary recognition of incoming nucleotides (UTP on Figure 2 a) by only half of the potentially available complementary partners already present on the surface (ATP on Figure 2 a). To understand the mechanism of nucleotide assembly, we make several observations related to the inhibition of secondary binding events. Firstly, as illustrated by Figure 3 a, the protective binding of adenine to the ZnII–BC monolayer with initially adsorbed 5′-UDP inhibited further assembly of 5′-ATP on the surface. Importantly, the response, Δα2, to adenine (which does not interact itself with ZnII–BC) was almost exactly three-times lower than Δα1 for UDP. As adenine's molecular weight is also three-times lower than that of UDP, the registered signal difference corresponds to a 1:1 UDP–adenine binding ratio. The inhibitory effect of this binding on further 5′-AXP recognition suggests that phosphate coordination is the first-stage binding mode even for potentially divalent 5′-UXPs (except for UMP, which is discussed below); moreover, the immobilized nucleotides are well preorganized for the interactions with suitable complementary partners. The effect also points to the mediating role of base pairing in secondary recognition of complementary nucleotides—it is hindered when complementary H-bonding is “switched off”. Inhibition of secondary recognition of 5′-ATP at SAM-ZnII–BC sensing film. a) Initial adsorption of 5′-UDP (0.02 mm) at pH 7.5 followed by subsequent addition of adenine (0.05 mm; pH 7.9) and 5′-ATP (0.02 mm), b) the assembly of 5′-UMP (0.02 mm) followed by the probing with 5′-ATP (0.02 mm). The secondary recognition of adenosine phosphates was also inhibited by preliminary adsorption of UMP—the smallest divalent nucleotide studied herein (Figure 3 b).18 The distance between cyclic “heads” of ZnII–BC is presumably well matched to UMP's molecular geometry thus allowing for simultaneous intramolecular coordination of phosphate and imide groups to the neighboring macrocycles. The surface with bound UMP becomes inactive with respect to other incoming nucleotides as both macrocyclic moieties in ZnII–BC are occupied and therefore, the UMP nucleobase involved in this divalent binding mode is unavailable for base pairing. These observations support a mechanism involving stepwise self-assembly of complementary nucleotides at ZnII–BC monolayers (Figure 4). Specifically, irrespective of the nucleotide used, the first binding event is mediated by the coordination of the terminal phosphate to one of the “heads” of the ZnII-BC template (Figure 4 a). The geometry of the ZnII–BC molecule prevents simultaneous divalent binding of 5′-UXPs with a distance between the base and terminal phosphate longer than that in 5′-UMP. These first-step interactions, however, cause steric crowding at the opposite ZnII–cyclen, thus shielding the free macrocycle from similar nucleotides and hindering their binding to the same ZnII–BC molecule. Schematic diagrams illustrating the possible mechanism of the stepwise self-assembly of complementary nucleotides on a SAM-ZnII–BC template (one ZnII–BC unit is shown). a) Phosphate attachment of a nucleotide to the one of ZnII–cyclen units, b) base pairing accompanied by the guiding of terminal phosphate of complementary nucleotide to the opposite ZnII–cyclen, c) firm attachment of the complementary nucleotide to ZnII–BC and dissociation of the base pair, d) base pairing of incoming nucleotides with complementary partners already immobilized on the template. Incoming complementary nucleotides recognize the already bound partner through base pairing.19 Nucleotide coupling results in a spatial arrangement of the interacting components that favors simultaneous orientation (“guiding”) of the terminal phosphate of a complementary nucleotide to the free “head” of the ZnII–BC molecule (Figure 4 b). The cooperative action of the template and both nucleotides is, most likely, assisted by base stacking. Although the base stacking interactions stabilize the ordering layer significantly, the energetic contribution of hydrogen bonding is rather small compared with the phosphate-anion coordination. Therefore, dissociation of the base pair, exposing the hydrogen-bond donor and acceptor sites to the solution, is expected to be in equilibrium (Figure 4 c). Disengaged bases, in turn, form complementary pairs with other incoming nucleotides.20 This chain of consecutive interactions results in the formation of a bilayer structure that harbors equal amounts of complementary nucleotides (Figure 4 d). The above mechanism suggests that nucleotide self-assembly is independent from the formation path—that is, stepwise recognition of complementary nucleotides in an arbitrary order as well as their one-step self-assembly from an equimolar mixture should give the same nucleotide pattern on ZnII–BC surfaces. To prove this assumption, we studied both continuous and interrupted adsorption of ATP/UTP equimolar mixtures (0.02 mM of each nucleotide) on ZnII–BC templates. One-step ATP/UTP adsorption translated into a maximal increase in the SPR signal Δαone step=9.0 angle min (data not shown; an SPR curve is given in the Supporting Information). This value is more than twofold greater when compared with Δα=3.9 angle min, which was measured for the adsorption of ATP from a solution with a double concentration of nucleotide (0.04 mM).15 This correlates well to Δαmultistep=10.4, which was determined from Figure 2 a for the stepwise binding of the ATP/UTP combination. Figure 5 describes interrupted adsorption of a similar mixture, followed by stepwise surface probing with ATP (0.02 mm) followed by UTP (0.02 mm) solutions. The ATP/UTP mixed solution was replaced by one of ATP (0.02 mm) when Δα reached 6.5 angle min greater than 1/2Δαmultistep≅5.2 angle min. This value assumes that more than half of the nucleotides that constitute the final bilayer were already immobilized on a surface. After the completion of ATP binding, UTP (0.02 mm) was added. We observed almost equal SPR maximal signals for individual solutions; an overall increase in the SPR signal Δαmax amounted to 9.4 angle min. Close agreement between maximal SPR responses registered for one-step and stepwise modes of assembly indicates that constant amounts of nucleotide bind to the surface irrespective of the procedure used. Some of the differences between Δαone step and Δαmultistep may be attributed to steric crowding at the interface in more concentrated mixtures. Such crowding results in the formation of structures that are not-so-rigorously defined, presumably because some base pairs between the nucleotide layer attached to the template and the complementary top layer are uncompleted. Furthermore, equal SPR signals measured in subsequent probing with individual nucleotides in Figure 5 prove the alteration of the binding mode in the course of self-assembly; when the ZnII–BC template is saturated with bound nucleotides and a bottom layer is formed, further completion of the bilayer structure proceeds through 1:1 base recognition. SPR sensogram for the interrupted adsorption of 5′-ATP/5′-UTP equimolar mixture (0.02 mM of each nucleotide) replaced by ATP (0.02 mm) at Δα=6.5 angle min and completed with the addition of UTP (0.02 mm). In summary, we described sterically induced cooperative assembly of complementary nucleotides progressing through the chain of consecutive mono- and divalent interactions on a surface presenting artificial ZnII–BC receptors. We believe that the approach utilized herein might be extended to other types of planar patterns of complementary nucleotides, as well as for the preparation of other artificial systems preorganized for efficient molecular recognition and further bottom-up self-assembly of synthetic molecules containing suitable fragments. All nucleotides (adenosine 5′-monophosphate, adenosine 5′-diphosphate disodium salt hydrate, adenosine 5′-triphosphate disodium salt hydrate, uridine 5′-monophosphate disodium salt hydrate, uridine 5′-diphosphate disodium salt hydrate, and uridine 5′-triphosphate trisodium salt hydrate) are of analytical-reagent grade and were obtained from Acros Organics (Belgium). Nucleotides and organic bases (uracil and adenine) were dissolved in water that was deionized to 16 MΩ cm resistivity and preliminarily adjusted to pH 7.5 by the addition of a small amount of sodium hydroxide; these solutions were used for SPR measurements immediately after their preparation. Platform preparation: TF-1 glass supports covered with a Cr adhesion sublayer (5 nm) and a polycrystalline Au layer (50 nm) supplied by Analytical-μSystem were modified by immersion into an absolute ethanol solution of octanethiol (1 mM) for 2 min. The monolayers of ZnII–BC were spread from 10−5 M chlorophorm solution onto basic subphase with pH 8.52, compressed to 17 mN m−1, and vertically transferred (the down-stroke mode of transfer was applied) onto thiolated support at a constant speed of 0.5 mm min−1. SPR monitoring: The SPR Kretschmann-type spectrometer Biosuplar-2 (Analytical-μSystem; a light-emitting diode light source λ=670 nm) equipped with a peristaltic pump (flow rate 0.3 mL min−1) was used for kinetic monitoring; freshly prepared solutions were added in 15 mL portions to the pump vessel when the previous portion was nearly all used. The SPR cell was rinsed with pure water for 15–20 min prior to the addition of each next probe. Other experimental details are given in the Supporting Information. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2006/z600450_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article." @default.
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• W2124879324 date "2006-08-07" @default.
• W2124879324 modified "2023-10-17" @default.
• W2124879324 title "Cooperative Self-Assembly of Adenosine and Uridine Nucleotides on a 2D Synthetic Template" @default.
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• W2124879324 doi "https://doi.org/10.1002/anie.200600450" @default.
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