Oligoamide Strands Research Articles

High‐Affinity Hybridization of Complementary Aromatic Oligoamide Strands in Water

AbstractWe 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.

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.

Hydrogen-Bonded Duplexes with Lengthened Linkers.

Connecting basic hydrogen-bonding units with lengthened flexible or rigid linkers generates oligoamide strands that carry new H-bonding sequences and association specificity, leading to H-bonded homo- and heteroduplexes with association constants in the 104 M-1 range in chloroform. Computational and experimental studies indicate that in duplexes with rigid aromatic linkers the oligoamide strands adopt bent conformations that allow the formation of interstrand H-bonds and accommodate the introduced aromatic liners, offering a new series of association units.

A novel H-bonding self-assembly heteromeric molecular duplex bearing host and guest energy transfer units as high-performance electroluminescent material

Two oligoamide strands with complementary H-bonding sequences bearing 4HB-NIM and 4HB-CzNI were synthesized. 4HB-NIM and 4HB-CzNI could be self-assembled into a heterodimeric dyad (namely 4HB-NIM-CzNI)via quadruple H-bond interactions. Photoluminescence measurements revealed that in both dilute solution and doped film states, more efficient host-guest energy transfer processes could be observed in the duplex 4HB-NIM-CzNI than the physical blends of the small molecular guest reference compound NIM and the host single strand 4HB-CzNI, which should be attributed to the shortened spatial distances in 4HB-NIM-CzNI. In addition, in comparison with NIM and the guest single strand 4HB-NIM, 4HB-NIM-CzNI shows much higher photoluminescence quantum yield [0.53 vs 0.04 (NIM) or 0.35 (4HB-NIM)] in neat-film state, indicative of the more alleviated concentration quenching of the guest fluorophore in 4HB-NIM-CzNI than 4HB-NIM and NIM. As a consequence, an organic light-emitting diode (OLED) with 4HB-NIM-CzNI as the light-emitting dopant shows much more improved electroluminescent performance than its 4HB-NIM-based reference OLED: with lower turn-on voltage (5.0 vs 5.9 V), higher maximum luminance (5260 vs 2980 cd m−2) and current efficiency (3.5 vs 3.0 cd A−1) as well as lower efficiency roll-off. All these results indicated that the integration of both host and guest fluorophores into H-bonding self-assembled material should be an effective strategy to construct high performance supramolecular electroluminescent materials.

Multiple hydrogen bonds-mediated formation of supramolecular polysiloxanes based on oligoamide duplexes

Formation of supramolecular polysiloxane polymers was studied by using oligoamide strands 1a, 2a, and 3a bearing multiple hydrogen bonds as association units. According to SEM and TEM studies one polymeric strand associated into supramolecular spherical assemblies via duplex formation. The results demonstrated the effect of such complementary oligoamides upon constructing main-chain supramolecular polymers.

A Red‐Emissive Sextuple Hydrogen‐Bonding Self‐Assembly Molecular Duplex Bearing Perylene Diimide Fluorophores for Warm‐White Organic Light‐Emitting Diode Application

AbstractA novel sextuple hydrogen‐bonding (HB) self‐assembly molecular duplex bearing red‐emitting perylene diimide (PDI) fluorophores, namely PDIHB, was synthesized, and its molecular structure was confirmed by 1H NMR, 13C NMR, TOF‐MS and 2D NMR. Compared with the small molecular reference compound PDI, PDIHB shows one time enhanced fluorescence efficiency in solid state (4.1% vs. 2.1%). More importantly, the presence of bulky HB oligoamide strands in PDIHB could trigger effective spatial separation between guest and host fluorophores in thin solid film state, hence inefficient energy transfer occurs between the blue‐emitting host 2TPhNIHB and red guest PDIHB in the 2 wt% guest/host blending film. As a result, a solution‐processed organic light‐emitting diode (OLED) with quite simple device structure of ITO/PEDOT:PSS (40 nm)/PVK (40 nm)/PDIHB (2 wt%): 2TPhNIHB (50 nm)/LiF (0.8 nm)/Al (100 nm) could emit bias‐independent warm‐white electroluminescence with stable Commission Internationale de L'Eclairage coordinates of (0.42, 0.33), and the maximum brightness and current efficiency of this device are 260 cd·m−2 and 0.49 cd·A−1, respectively. All these results indicated that HB self‐assembly supramolecular fluorophores could act as prospective materials for white OLED application.

ChemInform Abstract: Cavity‐Containing, Backbone‐Rigidified Foldamers and Macrocycles

AbstractReview: synthesis and characterization; 101 refs.

Molecular Duplexes with Encoded Sequences and Stabilities

Through specific molecular shapes and repeating polymeric sequences, biomacromolecules encode information about both structure and function. Inspired by DNA molecules, we have conceived a strategy to encode linear molecular strands with sequences that specify intermolecular association, and we and our collaborators have supported this idea through our experimental work. This Account summarizes the design and development of a class of molecular duplexes with programmable hydrogen-bonding sequences and adjustable stabilities. The specific system involves oligoamide strands synthesized from readily available monomeric modules based on standard amide (peptide) chemistry. By covalently linking three types of basic building blocks in different orders, we create oligoamide strands with various arrangements of amide O and H atoms that provide arrays of hydrogen bonding sequences. Because one of the two edges of these molecules presents the sequences of hydrogen-bond donors and acceptors, these oligoamide strands associate via their hydrogen-bonding edges into double-stranded pairs or duplexes. Systematic studies have demonstrated the strict sequence specificity and tunable stability of this system. These structurally simple duplexes exhibit many features associated with DNA sequences such as programmable sequence specificity, shape and hydrogen-bonding complementarity, and cooperativity of multipoint interactions. Capable of specifying intermolecular associations, these duplexes have formed supramolecular structures such as β-sheets and non-covalent block copolymers and have templated chemical reactions. The incorporation of dynamic covalent interactions into these H-bonded duplexes has created association units that undergo sequence-specific association and covalent ligation in both nonpolar solvents and polar media including water. These new association units may facilitate the development of new dynamic covalent structures, and new properties are emerging from these structures. For example, we discovered hydrogen-bonded duplexes that could gelate different organic solvents, and we could tune the gelatinization by adjusting the multiple side chains attached to the duplexes. In addition, we have recently designed duplexes whose formation and dissociation are controlled by changes in external stimuli such as acidity. With their programmable specificity and tunable stability, these molecular duplexes have provided a systematic approach for the association of different structural units. Further development of this system could facilitate the creation of many supramolecular and dynamic covalent structures. Because these duplexes are easily modifiable and information is easily encoded and retrieved, this system may address some of the remaining challenges facing information-storing molecules including self-replication.

Cavity-containing, backbone-rigidified foldamers and macrocycles

This Feature Article gives an account for a host of readily available foldamers and macrocycles with well-defined shapes and non-deformable cavities that appeared over the last decade. Efforts to create porous molecular structures have led to the establishment of an effective strategy for enforcing the folding of unnatural aromatic oligoamide strands based on an especially robust three-center (bifurcated) hydrogen-bonding interaction. Based on such a strategy, aromatic oligoamides adopting crescent and helical conformations that contain non-collapsible cavities of tunable diameters have been created. Extending the same folding principle to the preparation of aromatic polyamides that would adopt pore-containing helical conformation instead led to the discovery of a highly efficient, one-pot macrocyclization process. Such a one-pot macrocyclization process has been successfully applied to the preparation of macrocycles with aromatic amide, hydrazide, urea and other backbones. Mechanistic study indicates that the high efficiencies observed for the formation of these macrocycles are due to the folding of the corresponding uncyclized oligomeric precursors of the corresponding macrocycles. Oligoamide macrocycles, along with their uncyclized, cavity-containing counterparts, i.e., crescent oligoamides, bind guests such as guanidinium (G) and octylguanidinium (OG) ions with tunable selectivity. Recent studies revealed that these rigid macrocycles tend to engage in extraordinarily strong, directional aggregation, leading to nanotubular assemblies containing pores of fixed sizes. Consistent with the presence of self-assembling nanopores, oligoamide macrocycles were found to assemble into transmembrane channels with high conductance.

Hydrogen-Bonded Oligoamide Duplexes as Programmable Molecular Recognition Units: A Systematic Approach Towards Directed Self-Assembly and Controlled Non-Covalent Synthesis

Association units with high strength and specificity are getting increasing attention in the construction of well-defined selfassembling systems, which are making controlled non-covalent synthesis a reality. A class of hydrogen-bonded duplexes consisting of oligoamide strands carrying various combinations (sequences) of hydrogen-bond donors and acceptors has exhibited superb ability as intermolecular association units. These duplexes are featured by programmable sequence-specificity, predictable binding strength, ready synthetic availability and modifiability. With association constants ranging from ∼104 to 109M-1, these hydrogen-bonded duplexes offer a diverse set of association units capable of specifying intermolecular association in a controlled and directed manner. The efficacy of these molecules as molecular assembler has already been demonstrated by a number of examples such as the construction of supramolecular block copolymers, the templation of β-sheets, directed chemical reactions such as olefin metathesis and disulfide exchange. By integrating hydrogen bonding with dynamic covalent interactions, covalently linked duplexes are formed sequence-specifically in a selfassembling fashion in highly competitive media, which represents a major progress in creating association units combining the strength of covalent bonds and the specificity of multiple hydrogen bonds. Recently, hydrogen-bonded and/or covalent crosslinked duplexes have been found to serve as gelators for organic solvents, which may open a new avenue for developing novel materials. Keywords: Hydrogen-bonded duplex, oligoamide strand, association unit, multiple hydrogen bonds, sequence-specificity, non-covalent interactions, self-assembly, supramolecular polymer, hydrogen bonding, stacking, electrostatic, van der Waals, hydrophobic forces, homo-duplexes, hetero-duplexes

Alternative Strategy for Adjusting the Association Specificity of Hydrogen-Bonded Duplexes

A strategy for creating new association specificity of hydrogen-bonded duplexes by varying the spacings between neighboring hydrogen bonds is described. Incorporation of naphthalene-based residues has provided oligoamide strands that pair into duplexes sharing the same H-bonding sequences (e.g., DDAA) but differing in the spacings between their intermolecular hydrogen bonds, leading to homo- or heteroduplexes. The ability to manipulate association-specificity as demonstrated by this work may be extended to other multiple hydrogen bonded systems, thereby further enhancing the diversity of multiple hydrogen-bonded association units for constructing supramolecular structures.

A hydrogen bonding motif for forming extended assemblies

Oligoamide strands containing tertiary amide groups were found to share a basic structural motif that promotes the formation of H-bonded, chain- or tape-like supramolecular assemblies.

Engineering hydrogen‐bonded duplexes

AbstractBased on several simple, readily available building blocks, oligoamide strands carrying various arrays of hydrogen‐bond donors and acceptors, i.e. hydrogen‐bonding sequences, have been designed and synthesized. Detailed characterization indicates that these oligoamide strands associate via their hydrogen‐bonding edges into doubled stranded pairs (duplexes), which are characterized by programmable sequence specificity and adjustable stability. Using these hydrogen‐bonded duplexes as association units, supramolecular structures, such as β‐sheets and non‐covalent block copolymers, are obtained by simply mixing the corresponding components. Recently, by incorporating reversible covalent interactions into these hydrogen‐bonded duplexes, sequence‐specific formation of covalently linked structures has been realized under thermodynamic conditions, which has opened an entirely new avenue to the development of previously unknown dynamic covalent structures such as various block copolymers. Copyright © 2007 Society of Chemical Industry

Sequence-Specific Association in Aqueous Media by Integrating Hydrogen Bonding and Dynamic Covalent Interactions

Oligoamide strands that associate in a sequence-specific fashion into hydrogen-bonded duplexes in nonpolar solvents were converted into disulfide cross-linked duplexes in aqueous media. Thus, by incorporating trityl-protected thiol groups, which allows the reversible formation of disulfide bonds, into the oligoamide strands, only duplexes consisting of complementary hydrogen-bonding sequences were formed in aqueous solution as well as in methanol. The sequence-specific cross-linking of oligoamide strands was confirmed by MALDI-TOF, reverse-phase HPLC, and by isolating a cross-linked duplex. This study demonstrates that the sequence-specificity characteristic of multiply hydrogen-bonded systems can be extended into competitive media through the interplay of H-bonding and reversible covalent interactions, based on which a new class of molecular associating and ligating units that are compatible with both polar and nonpolar environments can be conveniently obtained.

Preparation of oligoamide‐ended poly(ethylene glycol) and hydrogen‐bonding‐assisted formation of aggregates and nanoscale fibers

AbstractAn oligoamide‐ended poly(ethylene glycol) (PEG) with a PEG weight‐average molecular weight of 5000 (PEG‐5000‐oligoamide), with 3,5‐bis‐[2‐(5‐acetylamino‐2‐isobutoxy‐benzoylamino)‐acetylamino]‐benzoyl as the oligoamide, was synthesized. PEG‐5000‐oligoamide aggregated in chloroform or toluene via hydrogen‐bonding interactions among the oligoamide strands as a core and PEG, which was soluble in the solvents, as a shell. When a chloroform solution of PEG‐5000‐oligoamide at a concentration of approximately 0.06 g/L was cast onto a silicon wafer or a mica plate, rapid solvent evaporation induced its self reassembly as nanofibers. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 1119–1128, 2005

Diversity of interstrand π— stacking motifs in the double helices of pyridinedicarboxamide oligomers

Winding of oligoamide strands of 2,6-diaminopyridine and 2,6-pyridinedicarboxylic acid into molecular duplexes is illustrated by two new crystal structures of double helical dimers. The relative positions of the two strands within the double helices in these two structures are different; they also differ from the structures reported previously. Unlike the single helical structure of the monomeric strands, the double helical motif is not highly stable in the solid state. This implies that the interactions that lead to duplex formation are not directional. It suggests that the two strands have a significant motional freedom in the duplex.

Duplex foldamers from assembly induced folding.

Oligoamide strands 1, 2, and 3, consisting of 4-H-bond units, were originally designed to form noncovalent polymers based on the expectation that they would adopt an extended conformation. Instead of assembling into the expected supramolecular polymer through their 4-H-bond units, the 1:1 mixture of 1 and 2 was found to form a highly stable dimeric species. To dimerize, the H-bonding sequences of 1 and 2 can only adopt a folded (stacked) conformation. The self-assembly of 3 was also found to adopt a similar folded duplex conformation. These novel duplex foldamers are very stable. They were characterized by 1D and 2D 1H NMR, VPO, and mass spectral (ESI) studies.

PNA complexes of polynucleotides and polyamides: Structure of two- and three-stranded chimeric helices revealed by conformational analysis

We have performed a conformational analysis of double-stranded (dA:pT)5 and triple-stranded (dA:pT · pT)5 helices for all possible variants of mutual orientation of oligoamide and oligonucleotide strands by means of AMBER 3.0. Computation results showed that the conformational flexibility of chimeric helices is practically like the DNA flexibility, although orientation of atoms around the amide bond is almost planar. cis- and trans-orientations are close in energy. Permissible changes in helical parameters of chimeric helices practically coincide with the corresponding parameters of double- and triple-stranded DNA helices. Double-stranded chimeric helices exhibit a tendency to twist accompanied by helical pitch decreasing. Three-stranded chimeric complexes, on the contrary, exhibit a tendency to unwinding. Energy gain of chimeric helices is noticeable. Thus, double-stranded chimeras are characterized by the energy of 20 kcal/mol per monomer unit lower than double-stranded DNAs. The energy gain of triple-stranded chimeric complexes is about 40 kcal/mol per monomer unit. There is qualitative correlation between the experimentally obtained enthalpy of chimeric complexes and their calculated potential energy. It fully explained the ability of oligoamides to interact with DNA following oligoamide strand invasion of the duplex through D-loop formation. The dependence of energy on mutual strand orientation in chimeric duplexes is weak. Energy penalty of duplexes with parallel orientation of 5′ → 3′ and N → C chain vectors is about 0,7 kcal/mol per monomer unit. The dependence of energy on mutual strand orientation in chimeric triplexes is much more appreciable. The most advantageous is parallel orientation of 5′ → 3′ and N → C vectors of Watson–Crick chains accompanied by antiparallel orientation of the Hoogsteen oligoamide chain. It was shown that the stability of double-stranded oligonucleotides may be increased as a result of oligoamide insert of three or four monomer units in one of the oligonucleotide chains. The length and base sequence in the insert allowed one to modulate the degree of duplex stabilization. It is important that such stabilization may be obtained without any distortion in vector character of nucleotide duplex formation. It is evident that this method of stabilization of helices is suitable also for triplexes. Moreover, in this way, one can overcome the difficulties connected with the low penetration ability of PNA in living cells. © 1994 John Wiley & Sons, Inc.