Recognition-Encoded Synthetic Information Molecules

Cooperativity in the assembly of H-bonded duplexes of synthetic recognition-encoded melamine oligomers

Recognition-encoded melamine oligomers (REMO) are synthetic polymers composed of repeating triazine-piperazine units and equipped with phenol and phosphine oxide side-chains. Short oligomers have previously been shown to form length- and sequence-selective H-bonded duplexes in non-polar solvents. Here, automated solid phase synthesis was used to prepare homo-sequence REMO with either twelve phenol recognition units or twelve phosphine oxide recognition units. The ends of the oligomers were functionalised with an azide and an alkyne group to allow investigation of duplex formation by covalent trapping with copper-catalysed azide-alkyne cycloaddition (CuAAC) reactions. The oligomers were also functionalised with a dansyl fluorophore or a dabcyl quencher dye to allow investigation of duplex formation by Förster resonance energy transfer (FRET). Covalent trapping showed that the duplex is the major species present in a 1 : 1 mixture of the phenol 12-mer and phosphine oxide 12-mer at micromolar concentrations in dichloromethane. FRET titration experiments showed that the association constant for duplex formation is greater than 108 M-1 in chloroform, and DMSO denaturation experiments showed that duplex formation is highly cooperative. The Hill coefficient for denaturation of the 12-mer duplex was 4.6, which is significantly higher than the value measured for the corresponding 6-mer duplex (1.9). This behaviour mirrors that observed for nucleic acid duplexes, where denaturation becomes increasingly cooperative as more base-pairs are added to the duplex.

Sequence-selective pulldown of recognition-encoded melamine oligomers using covalent capture on a solid support

The covalent capture of recognition-encoded melamine oligomers (REMO) with a target attached to a solid support was investigated. Sequence-selective pulldown of complementary oligomers was observed when the target was challenged with a randomised library of oligomers. The approach provides an affinity selection method for the discovery of functional REMO sequences.

Investigation of Host-Guest Interactions in 2-Ureido-4-ferrocenylpyrimidine Derivatives

In the present study, synthesis, conformational behavior, host-guest complex formation, and electrochemical properties of novel 6-substituted-2-ureido-4-ferrocenylpyrimidines were explored. A comprehensive NMR spectroscopic investigation was carried out to confirm the structure and conformational equilibrium of the ureidopyrimidines through studying the temperature- and concentration dependence of NMR spectra. Low-temperature NMR measurements were used to clarify structural changes inflicted by a 2,6-diaminopyridine guest. Association constant (Kassoc) values of host-guest complexes were calculated based on low-temperature titrations. It was shown that the introduction of a pyridin-2-yl substituent in the pyrimidine ring in host 10 induced a considerable change not only in the conformational equilibrium of the host itself but also in that of the host-guest complex. Geometries and relative stabilities of the conformers of host 10 as well as its host-guest complexes were determined by quantum chemical calculations. Electrochemical behavior of ureidopyrimidine hosts and host-guest complexes was investigated by cyclic voltammetry (CV) and linear sweep voltammetry (LSV) measurements. Two ureidopyrimidine derivatives were immobilized on the surface of spectral graphite electrodes, and their electrochemical response on the addition of 2,6-diaminopyridine was compared. These results also supported the importance of the pyridin-2-yl substituent in the efficient sensing of the guest.

Length and Sequence-Selective Polymer Synthesis Templated by a Combination of Covalent and Noncovalent Base-Pairing Interactions

Information can be encoded and stored in sequences of monomer units organized in linear synthetic polymers. Replication of sequence information is of fundamental importance in biology; however, it represents a challenge for synthetic polymer chemistry. A combination of covalent and noncovalent base pairs has been used to achieve high-fidelity templated synthesis of synthetic polymers that encode information as a sequence of different side-chain recognition units. Dialkyne building blocks were attached to the template by using ester base pairs, and diazide building blocks were attached to the template by using H-bond base pairs. Copper-catalyzed azide-alkyne cycloaddition reactions were used to zip up the copy strand on the template, and the resulting duplex was cleaved by hydrolyzing the covalent ester base pairs. By using recognition-encoded melamine oligomers with either three phosphine oxide or three 4-nitrophenol recognition units to form the noncovalent base pairs, exceptionally high affinities of the diazides for the template were achieved, allowing the templated polymerization step to be carried out at low concentrations, which promoted on-template intramolecular reactions relative to competing intermolecular processes. Two different templates, a 7-mer and an 11-mer, were used in the three-step reaction sequence to obtain the sequence-complementary copy strands with minimal amounts of side reaction.

Stimuli-Responsive Molecular Duplexes Displaying Duplex-to-Duplex Switching

Synthetic duplexes with high stabilities have promising potential for mimicking biomolecular functions and developing supramolecular smart materials. Herein, we describe the synthesis and stimuli-responsive properties of molecular duplexes derived from indolocarbazole-pyridine (I-P) oligomers. These duplexes adopt nonclassical helical structures, stabilized by I-P hydrogen-bonding pairs in anhydrous chlorinated solvents. Notably, the longest duplex 62 (11-mer)2 displays remarkable stability, forming twenty hydrogen bonds; its exchange energy barrier was determined to be ΔG≠=22.0 kcal ⋅ mol-1 at 75 °C in anhydrous (CDCl2)2. Upon the addition of water, a hydrated duplex 62 (11-mer)2⊃10H2O was formed, with one water molecule inserted between each I-P hydrogen-bonding pair. The Hill coefficient (n) for this process is 6.1, demonstrating extremely positive cooperativity. Conversely, the hydrated duplex 62 (11-mer)2⊃10H2O was completely converted into the original anhydrous duplex 62 (11-mer)2 when the temperature was increased. Interconversion between these two distinct duplexes can be repeatedly carried out by varying the temperature. Furthermore, reversible switching between hetero-duplexes and homo-duplexes was also demonstrated by controlling the temperature, with concomitant changes in the characteristic emission signals.

Duplex-forming oligocarbamates with tunable nonbonding sites

In biopolymers such as proteins and nucleic acids, monomer sequence encodes for highly specific intra- and intermolecular interactions that direct self-assembly into complex architectures with high fidelity. This remarkable structural control translates into precise control over the properties of the biopolymer. Polymer scientists have sought to achieve similarly precise control over the structure and function of synthetic assemblies. A common strategy for achieving this goal has been to exploit existing biopolymers, known to associate with specific geometries and stoichiometries, for the assembly of synthetic building blocks. However, such systems are neither scalable nor amenable to the relatively harsh conditions required by various materials science applications, particularly those involving non-aqueous environments. To overcome these limitations, we have synthesized sequence-defined oligocarbamates (SeDOCs) that assemble into duplexes through complementary hydrogen bonds between thymine (T) and diaminotriazine (D) pendant groups. The SeDOC platform makes it simple to incorporate non-hydrogen-bonding sites into an oligomer's array of recognition motifs, thereby enabling an investigation into this unexplored handle for controlling the hybridization of complementary ligands. We successfully synthesized monovalent, divalent, and trivalent SeDOCs and characterized their self-assembly via diffusion ordered spectroscopy, 1H-NMR titration, and isothermal titration calorimetry. Our findings reveal that the binding strength of monovalent oligomers with complementary pendant groups is entropically driven and independent of monomer sequence. The results further show that the hybridization of multivalent oligomers is cooperative, that their binding enthalpy (ΔH) and entropy (TΔS) depend on monomer sequence, and that sequence-dependent changes in ΔH and TΔS occur in tandem to minimize the overall change in binding free energy.

Selective Duplex Formation in Mixed Sequence Libraries of Synthetic Polymers

Recognition-encoded melamine oligomers (REMO) are synthetic polymers that feature an alternating 1,3,5-triazine-piperazine backbone and side-chains equipped with either a phenol or phosphine oxide recognition unit. An automated method for the solid-phase synthesis (SPS) of REMO of any specified sequence has been developed starting from dichlorotriazine monomer building blocks. Complementary homo-oligomers with either six phenols or six phosphine oxides were synthesized and shown to form a stable duplex in nonpolar solvents by NMR denaturation experiments. The duplex was covalently trapped by equipping the ends of the oligomers with an azide and an alkyne group and using a copper-catalyzed alkyne-azide cycloaddition (CuAAC) reaction. The SPS methodology was adapted to synthesize mixed sequence libraries by using a mixture of two different dichlorotriazine building blocks in each coupling cycle of an oligomer synthesis. The resulting libraries contain statistical mixtures of all possible sequences. The self-assembly properties of these libraries were screened by using the CuAAC reaction to trap any duplexes present. In mixed sequence libraries of 6-mers, the trapping experiments showed that only sequence-complementary oligomers formed duplexes at micromolar concentrations in dichloromethane. The automated synthesis approach developed here provides access to large libraries of mixed sequence synthetic polymers, and the covalent trapping experiment provides a convenient tool for screening functional properties of mixtures. The results suggest high-fidelity sequence-selective duplex formation in mixtures of 6-mer sequences of the REMO architecture.

Synthetically encoded complementary oligomers

Creating the next generation of advanced materials will require controlling molecular architecture to a degree typically achieved only in biopolymers. Sequence-defined polymers take inspiration from biology by using chain length and monomer sequence as handles for tuning structure and function. These sequence-defined polymers can assemble into discrete structures, such as molecular duplexes, via reversible interactions between functional groups. Selectivity can be attained by tuning the monomer sequence, thereby creating the need for chemical platforms that can produce sequence-defined polymers at scale. Developing sequence-defined polymers that are specific for their complementary sequence and achieve their desired binding strengths is critical for producing increasingly complex structures for new functional materials. In this Review Article, we discuss synthetic platforms that produce sequence-defined, duplex-forming oligomers of varying length, strength and association mode, and highlight several analytical techniques used to characterize their hybridization.

Replication of synthetic recognition-encoded oligomers by ligation of trimer building blocks

The development of methods for replication of synthetic information oligomers will underpin the use of directed evolution to search new chemical space. Template-directed replication of triazole oligomers has been achieved using a covalent primer in conjunction with non-covalent binding of complementary building blocks. A phenol primer equipped with an alkyne was first attached to a benzoic recognition unit on a mixed sequence template via selective covalent ester base-pair formation. The remaining phenol recognition units on the template were then used for non-covalent binding of phosphine oxide oligomers equipped with an azide. The efficiency of the templated CuAAC reaction between the primer and phosphine oxide building blocks was investigated as a function of the number of H-bonds formed with the template. Increasing the strength of the non-covalent interaction between the template and the azide lead to a significant acceleration of the templated reaction. For shorter phosphine oxide oligomers intermolecular reactions compete with the templated process, but quantitative templated primer elongation was achieved with a phosphine oxide 3-mer building block that was able to form three H-bonds with the template. NMR spectroscopy and molecular models suggest that the template can fold, but addition of the phosphine oxide 3-mer leads to a complex with three H-bonds between phosphine oxide and phenol groups, aligning the azide and alkyne groups in a favourable geometry for the CuAAC reaction. In the product duplex, 1H and 31P NMR data confirm the presence of the three H-bonded base-pairs, demonstrating that the covalent and non-covalent base-pairs are geometrically compatible. A complete replication cycle was carried out starting from the oligotriazole template by covalent attachment of the primer, followed by template-directed elongation, and hydrolysis of the the ester base-pair in the resulting duplex to regenerate the template and liberate the copy strand. We have previously demonstrated sequence-selective oligomer replication using covalent base-pairing, but the trimer building block approach described here is suitable for replication of sequence information using non-covalent binding of the monomer building blocks to a template.

Flexible Self-Powered Sensing System Based on Novel DNA Circuit Strategy and Graphdiyne for Thalassemia Gene by Rapid Naked-Eye Tracking and Open-Circuit Voltage

Based on the controllable instantaneous self-assembly ability of long-chain branched DNA nanostructures and the synergistic effect between nucleic acid amplification without enzymes, a highly sensitive and highly specific self-powered biosensing platform is developed. Two-dimensional graphdiyne is prepared, modified on flexible carbon cloth, and then functionalized with gold nanoparticles. When DNA mi-tubes are applied on it, target thalassemia gene CD122 triggers a dual-catalytic hairpin assembly reaction. The generated nanoscale DNA is precisely captured by the DNA mi-tube, exposing binding sites and activating the hybridization chain reaction to form long-chain branched DNA. Double-stranded DNA, along with dendritic DNA carrying a large number of guanine bases, precisely captures the signal molecule methylene blue (MB), generating a significant electrochemical signal. The redox reaction of MB also causes a proportional change in the system's color, achieving a colorimetric detection functionality. An efficient dual-mode self-powered sensing platform, therefore, is established for detecting the thalassemia gene CD122. The linear response range of target concentration to open-circuit voltage and RGB Blue value is 0.0001-10,000 pM. The detection limit under electrochemical mode is 36.3 aM (S/N = 3), and under colorimetric mode, it is as low as 12.1 aM (S/N = 3). The new method exhibits high sensitivity, excellent selectivity, and high accuracy, providing a universal strategy for designing novel biosensing platforms that can be extended to the detection of other biomolecules.