Duplex Oligomers Defined via Covalent Casting of a One-Dimensional Hydrogen-Bonding Motif

Abstract

Hydrogen-bonded tapes comprised of monomeric molecular precursors are used to define structural parameters for the design of related oligomers encoded with predetermined modes of assembly. Application of this "covalent casting" strategy vis-à-vis the one-dimensional H-bonding motif expressed by 2-amino-4,6-dichlorotriazine has enabled the design of high-affinity duplex molecular strands. Dimeric, trimeric, and tetrameric duplex oligomers are prepared through an iterative synthetic protocol involving sequential homologation of the oligo(aminotriazine). The mode of assembly and interstrand affinity of homologous oligomers are established in solution by (1)H NMR dilution experiments, isothermal titration calorimetry (ITC), vapor pressure osmometry (VPO), cross-hybridization experiments involving the analysis of dye-labeled strands via thin-layer chromatography (TLC), and in the solid state by X-ray crystallographic analysis. Binding free energy per unimer (-Delta G degrees/n) increases significantly upon extension from monomer to dimer to trimer, signifying a strong positive cooperative effect. Nanomolar binding affinity (K(d) = 1.44 +/- 0.50 nM) was determined for the duplex trimer by ITC in 1,2-dichloroethane at 20 degrees C. In-register duplex formation is not observed for the tetramer, which appears to adopt an alternative binding mode. These data give insight into the structural and interactional features of the oligomers required for high-affinity, high-specificity binding and define a platform for the design of second-generation systems and related duplex strands for use in nanoscale assembly.

Double versus single helical structures of oligopyridine-dicarboxamide strands. Part 1: Effect of oligomer length

“…For instance, this is the case in nucleic acids double helices and their analogs, and in several synthetic oligomers based on hydrogen bonding. 5,7,11 To explain these results, we first hypothesized that the attractive interactions leading to duplex formation in oligopyridine dicarboxamides may not match over long strands. However, molecular models of long double helices built on the basis of the crystal structures of short double helices 19 show no alteration of the double helical motif (Fig.…”

“…Several non-natural hydrogen bond arrays have also been designed. 1,[5][6][7][8][9][10][11][12] The three dimensional structures of these molecular duplexes have not always been characterized in detail but the two strands are most often supposed to adopt a ladder (or zipper) like linear conformation. Another common way to direct the assembly of a molecular duplex or triplex is to use metal ions 1,13 or anions 14 as templates around which two or three strands wind upon establishing selective interactions.…”

Recycling polyethylene from automotive fuel tanks

“…Supramolecular polymerization,1–3 that is, the self‐assembly of polymer‐like materials through the utilization of the noncovalent bond, has been a developing area of research over the last decade, with a number of groups investigating how different facets of noncovalent chemistry can be used to induce the formation of polymeric aggregates4–13 and nanoparticles 14, 15. Such supramolecular polymers potentially have a number of interesting properties: (1) they form spontaneously, without the need for an initiation process (or catalyst); (2) they are dynamic, that is, they are formed under reversible conditions, thus imparting the potential of such materials to be thermally self‐repairing;16, 17 and (3) termination processes during the polymerization (self‐assembly) are limited.…”

Synthesis of [CH2C(CO2Et)2CH2Ar]n polymers and their unique optical properties by through‐space interactions between Ar and CO groups

“…A mixture of diethyl malonate and di(propargyl) malonate was treated with α,α′‐dibromo‐ p ‐xylene in the presence of NaH in dimethyl sulfoxide (DMSO) to furnish the corresponding random copolymer P6 [ M n = 4.57 × 10 3 , M w / M n = 2.12 by GPC (THF, polystyrene standard), m:n = 8:1 (determined by 1 H NMR)] in 29% yield after twice reprecipitation from a THF solution by the addition of methanol. The resulting copolymer P6 was subjected to the Hüisgen reaction (Click reaction)20 in the presence of an excess amount of 5‐((3‐azidopropyl)sulfonyl)‐ N , N ‐dimethylnaphthalen‐1‐amine ( 5 )21 to yield copolymer P7 [54% yield, M n = 5.88 × 10 3 , M w / M n = 2.14 by GPC (THF, polystyrene standard), m:n = 8:1 (determined by 1 H NMR)].…”