High-Fidelity Sequence-Selective Duplex Formation by Recognition-Encoded Melamine Oligomers

Template-Directed Synthesis of Recognition-Encoded Melamine Oligomers Using a Base-Filling Strategy

Replication of molecular information in nature is based on the synthesis of the backbone of the copy strand by polymerization of monomers bound to a template. An alternative strategy is to use a preassembled polymer backbone devoid of sequence information as the copy strand and to attach side chains in a sequence determined by binding to a template, i.e., base-filling. Base-filling strategies were investigated for template-directed synthesis of recognition-encoded melamine oligomers (REMO) using H-bond base-pairing interactions between 4-nitrophenol and phosphine oxide side chains. A template with three 4-nitrophenol H-bond donor recognition units was used with a blank copy strand equipped with three aldehyde groups for the reversible attachment of amine recognition units via dynamic imine chemistry. Equilibration of the template and blank strands in dichloromethane in the presence of benzylamine and a phosphine oxide recognition unit equipped with an amine resulted in selective incorporation (79%) of the phosphine oxide recognition unit into the resulting copy strand. Covalent attachment of the blank strand to the template with a diester linker increased the selectivity of the base-filling process to 85%, and carrying out the experiment in toluene further increased the selectivity to 92%. The imines in the copy strand were trapped by reduction, and cleavage of the ester linkages allowed recovery of the template strand along with the kinetically stable tris-phosphine oxide copy. Fidelity of templating is determined by the concentration of the template strand, the association constant for the base-pairing interaction, and the effective molarities of the intramolecular interactions in the duplex.

The supramolecular chemistry of monodisperse 1,3,5-triazine oligomers

Organic compounds based on 1,3,5-triazine scaffolds are utilised in practical applications in agriculture, as well as in the pharmaceutical and plastic industries. In fundamental research, 1,3,5-triazines are used as building blocks for the construction of oligomers that are relevant to the areas of supramolecular chemistry, chemical biology and polymer science. Here, we review the molecular recognition and self-assembly properties of monodisperse linear and branched oligomers, macrocycles, and dendrimers of 1,3,5-triazine. We focus mainly on experimental studies conducted in solution, describing the key interactions and structural features of these systems.

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.

Recognition-Encoded Molecules: A Minimal Self-Replicator

Nucleic acids, with their unique duplex structure, which is key for information replication, have sparked interest in self-replication's role in life's origins. Early template-based replicators, initially built on short oligonucleotides, expanded to include peptides and synthetic molecules. We explore here the potential of a class of synthetic duplex-forming oligoanilines, as self-replicators. We have recently developed oligoanilines equipped with 2-trifluoromethylphenol-phosphine oxide H-bond base pairs and we investigate whether the imine formed between aniline and aldehyde complementary monomers can self-replicate. Despite lacking a clear sigmoidal kinetic profile, control experiments with a methylated donor and a competitive inhibitor support self-replication. Further investigations with the reduced aniline dimer demonstrate templated synthesis, revealing a characteristic parabolic growth. After showing sequence selective duplex formation, templated synthesis and the emergence of catalytic function, the self-replication behaviour further suggests that the unique properties of nucleic acids can be paralleled by synthetic recognition-encoded molecules.

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.

Efficient automated solid-phase synthesis of recognition-encoded melamine oligomers

Recognition-encoded melamine oligomers (REMO) are synthetic polymers with an alternating 1,3,5-triazine-piperazine backbone and side chains equipped with either a phenol or phosphine oxide recognition unit. Here, we describe an automated method for highly efficient solid-phase synthesis (SPS) of REMO of any specified length and sequence. These SPS protocols are amongst the most robust reported to date, as demonstrated by the synthesis of a mixed-sequence 42-mer, which was obtained in excellent crude purity on a 100 mg scale. Starting from loaded Wang resin and dichlorotriazine monomer building blocks, the SPS methods were automated and optimised on a commercial peptide synthesiser. Major side products were identified using LCMS, and the undesired side reactions were suppressed by the choice of resin, solvent and coupling conditions. REMO have been shown to form high-fidelity length- and sequence-selective H-bonded duplexes, analogous to nucleic acids, and automated synthesis will facilitate exploration of related functional properties, such as molecular replication and programmable self-assembly.

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.

High-Affinity Hybridization of Complementary Aromatic Oligoamide Strands in Water

We prepared a series of water-soluble aromatic oligoamide sequences all composed of a segment prone to form a single helix and a segment prone to dimerize into a double helix. These sequences exclusively assemble as antiparallel duplexes. The modification of the duplex inner rim by varying the nature of the substituents borne by the aromatic monomers allowed us to identify sequences that can hybridize by combining two chemically different strands, with high affinity and complete selectivity in water. X-ray crystallography confirmed the expected antiparallel configuration of the duplexes whereas NMR spectroscopy and mass spectrometry allowed us to assess precisely the extent of the hybridization. The hybridization kinetics of the aromatic strands was shown to depend on both the nature of the substituents responsible for strand complementarity and the length of the aromatic strand. These results highlight the great potential of aromatic hetero-duplex as a tool to construct non-symmetrical dynamic supramolecular assemblies.

Peptide Macrocyclization Guided by Reversible Covalent Templating

The creation of complementary products via templating is a hallmark feature of nucleic acid replication. Outside of nucleic acid-like molecules, the templated synthesis of a hetero-complementary copy is still rare. Herein we describe one cycle of templated synthesis that creates homomeric macrocyclic peptides guided by linear instructing strands. This strategy utilizes hydrazone formation to pre-organize peptide oligomeric monomers along the template on a solid support resin, and microwave-assisted peptide synthesis to couple monomers and cyclize the strands. With a flexible templating strand, we can alter the size of the complementary macrocycle products by increasing the length and number of the binding peptide oligomers, showing the potential to precisely tune the size of macrocyclic products. For the smaller macrocyclic peptides, the products can be released via hydrolysis and characterized by ESI-MS.

Sequence-selective duplex formation and template effect in recognition-encoded oligoanilines

A new family of duplex-forming recognition encoded oligomers, capable of sequence selective duplex formation and template directed synthesis, was developed. Monomers equipped with both amine and aldehyde groups were functionalized with 2-trifluoromethylphenol or phosphine oxide as H-bond recognition units. Duplex formation and assembly properties of homo- and hetero-oligomers were studied by 19F and 1H NMR experiments in chloroform. The designed backbone prevents the undesired 1,2-folding allowing sequence-selective duplex formation, and the stability of the antiparallel duplex is 3-fold higher than the parallel arrangement. Dynamic combinatorial chemistry was exploited for the templated synthesis of complementary oligomers, showing that an aniline dimer can template the formation of the complementary imine. The key role of the H-bond recognition confers to the system the ability to discriminate a mutated donor monomer incapable of H-bonding. Sequence selective duplex formation combined with the template effect makes this system an attractive target for further studies.

Directional Ionic Bonds

Covalent and ionic bonds represent two fundamental forms of bonding between atoms. In contrast to bonds with significant covalent character, ionic bonds are of limited use for the spatial structuring of matter because of the lack of directionality of the electric field around simple ions. We describe a predictable directional orientation of ionic bonds that contain concave nonpolar shields around the charged sites. Such directional ionic bonds offer an alternative to hydrogen bonds and other directional noncovalent interactions for the structuring of organic molecules and materials.

Recognition-Encoded Synthetic Information Molecules

ConspectusNucleic acids represent a unique class of highly programmable molecules, where the sequence of monomer units incorporated into the polymer chain can be read through duplex formation with a complementary oligomer. It should be possible to encode information in synthetic oligomers as a sequence of different monomer units in the same way that the four different bases program information into DNA and RNA. In this Account, we describe our efforts to develop synthetic duplex-forming oligomers composed of sequences of two complementary recognition units that can base-pair in organic solvents through formation of a single H-bond, and we outline some general guidelines for the design of new sequence-selective recognition systems.The design strategy has focused on three interchangeable modules that control recognition, synthesis, and backbone geometry. For a single H-bond to be effective as a base-pairing interaction, very polar recognition units, such as phosphine oxide and phenol, are required. Reliable base-pairing in organic solvents requires a nonpolar backbone, so that the only polar functional groups present are the donor and acceptor sites on the two recognition units. This criterion limits the range of functional groups that can be produced in the synthesis of oligomers. In addition, the chemistry used for polymerization should be orthogonal to the recognition units. Several compatible high yielding coupling chemistries that are suitable for the synthesis of recognition-encoded polymers are explored. Finally, the conformational properties of the backbone module play an important role in determining the supramolecular assembly pathways that are accessible to mixed sequence oligomers.Almost all complementary homo-oligomers will form duplexes provided the product of the association constant for formation of a base-pair and the effective molarity for the intramolecular base-pairing interactions that zip up the duplex is significantly greater than one. For these systems, the structure of the backbone does not play a major role, and the effective molarities for duplex formation tend to fall in the range 10-100 mM for both rigid and flexible backbones. For mixed sequences, intramolecular H-bonding interactions lead to folding. The competition between folding and duplex formation depends critically on the conformational properties of the backbone, and high-fidelity sequence-selective duplex formation is only observed for backbones that are sufficiently rigid to prevent short-range folding between bases that are close in sequence. The final section of the Account highlights the prospects for functional properties, other than duplex formation, that might be encoded with sequence.

Homochiral versus Heterochiral Dimeric Helical Foldamer Bundles: Chlorinated-Solvent-Dependent Self-Sorting

Aromatic oligoamide sequences programmed to fold into stable helical conformations were designed to display a linear array of hydrogen-bond donors and acceptors at their surface. Sequences were prepared by solid-phase synthesis. Solution ¹ H NMR spectroscopic studies and solid-state crystallographic structures demonstrated the formation of stable hydrogen-bond-mediated dimeric helix bundles that could be either heterochiral (with a P and an M helix) or homochiral (with two P or two M helices). Formation of the hetero- or homochiral dimers could be driven quantitatively using different chlorinated solvents-exemplifying a remarkable case of either social or narcissistic chiral self-sorting or upon imposing absolute handedness to the helices to forbid PM species.

Macromolecular Information Transfer

Macromolecular information transfer can be defined as the process by which a coded monomer sequence is communicated from one macromolecule to another. In such a transfer process, the information sequence can be kept identical, transformed into a complementary sequence or even translated into a different molecular language. Such mechanisms are crucial in biology and take place in DNA→DNA replication, DNA→RNA transcription and RNA→protein translation. In fact, there would be no life on Earth without macromolecular information transfer. Mimicking such processes with synthetic macromolecules would also be of major scientific relevance because it would open up new avenues for technological applications (e.g. data storage and processing) but also for the creation of artificial life. In this important context, this minireview summarizes recent research about information transfer in synthetic oligomers and polymers. Medium- and long-term perspectives are also discussed.

Folding and Duplex Formation in Sequence-Defined Aniline Benzaldehyde Oligoarylacetylenes

In all known genetic polymers, molecular recognition via hydrogen bonding between complementary subunits underpins their ability to encode and transmit information, to form sequence-defined duplexes, and to fold into catalytically active forms. Reversible covalent interactions between complementary subunits provide a different way to encode information, and potentially function, in sequence-defined oligomers. Here, we examine six oligoarylacetylene trimers composed of aniline and benzaldehyde subunits. Four of these trimers self-pair to form two-rung duplex structures, and two form macrocyclic 1,3-folded structures. The equilibrium proportions of these structures can be driven to favor each of the observed structures almost entirely depending upon the concentration of trimers and an acid catalyst. Quenching the acidic trimer solutions with an organic base kinetically traps all species such that they can be isolated and characterized. Mixtures of complementary trimers form exclusively sequence-specific 3-rung duplexes. Our results suggest that reversible covalent bonds could in principle guide the formation of more complex folded conformations of longer oligomers.

H-Bond Templated Oligomer Synthesis Using a Covalent Primer

Template-directed synthesis of nucleic acids in the polymerase chain reaction is based on the use of a primer, which is elongated in the replication process. The attachment of a high affinity primer to the end of a template chain has been implemented for templating the synthesis of triazole oligomers. A covalent ester base-pair was used to attach a primer to a mixed sequence template. The resulting primed template has phenol recognition units on the template, which can form noncovalent base-pairs with phosphine oxide monomers via H-bonding, and an alkyne group on the primer, which can react with the azide group on a phosphine oxide monomer. Competition reactions between azides bearing phosphine oxide and phenol recognition groups were used to demonstrate a substantial template effect, due to H-bonding interactions between the phenols on the template and phosphine oxides on the azide. The largest rate acceleration was observed when a phosphine oxide 2-mer was used, because this compound binds to the template with a higher affinity than compounds that can only make one H-bond. The 31P NMR spectrum of the product duplex shows that the H-bonds responsible for the template effect are present in the product, and this result indicates that the covalent ester base-pairs and noncovalent H-bonded base-pairs developed here are geometrically compatible. Following the templated reaction, it is possible to regenerate the template and liberate the copy strand by hydrolysis of the ester base-pair used to attach the primer, thus completing a formal replication cycle.

Folding and duplex formation in mixed sequence recognition-encoded m-phenylene ethynylene polymers

Oligomers equipped with complementary recognition units have the potential to encode and express chemical information in the same way as nucleic acids. The supramolecular assembly properties of m-phenylene ethynylene polymers equipped with H-bond donor (D = phenol) and H-bond acceptor (A = phosphine oxide) side chains have been investigated in chloroform solution. Polymerisation of a bifunctional monomer in the presence of a monofunctional chain stopper was used for the one pot synthesis of families of m-phenylene ethynylene polymers with sequences ADnA or DAnD (n = 1-5), which were separated by chromatography. All of the oligomers self-associate due to intermolecular H-bonding interactions, but intramolecular folding of the monomeric single strands can be studied in dilute solution. NMR and fluorescence spectroscopy show that the 3-mers ADA and DAD do not fold, but there are intramolecular H-bonding interactions for all of the longer sequences. Nevertheless, 1 : 1 mixtures of sequence complementary oligomers all form stable duplexes. Duplex stability was quantified using DMSO denaturation experiments, which show that the association constant for duplex formation increases by an order of magnitude for every base-pairing interaction added to the chain, from 103 M-1 for ADA·DAD to 105 M-1 for ADDDA·DAAAD. Intramolecular folding is the major pathway that competes with duplex formation between recognition-encoded oligomers and limits the fidelity of sequence-selective assembly. The experimental approach described here provides a practical strategy for rapid evaluation of suitability for the development of programmable synthetic polymers.