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

Oligoamides of 2,6-diaminopyridine and 2,6-pyridinedicarboxylic acid were previously shown to fold into single helical monomers and to hybridize into double helical dimers. A new series of these oligomers comprising 5 to 15 pyridine units, 4-decyloxy residues, and benzylcarbamate end groups were synthesized using a new convergent scheme that involves an early disymmetrization of the diamine and of the diacid. The hybridization of these compounds into double helices was studied by ¹H NMR spectroscopy in chloroform solutions at various temperatures. Somewhat unexpectedly, these studies revealed that dimerization increases with oligomer length up to a certain point, and then decreases down to undetectable levels for the longest strands. NMR studies show that both double helices and single helices become more stable when strand length increases. The measured values of enthalpy and entropy of hybridization for oligomers of various length show that the enthalpic gain constantly decreases with strand length. This can be interpreted as being the result of an increasing enthalpic price of the spring-like extension that the strand undergoes upon hybridization as its length increases. On the other hand, the entropic loss of hybridization also constantly decreases with strand length. Presumably, the helical preorganization of the monomers increases with strand length, which allows the longer strands to hybridize with a minimal loss of motional freedom, that is to say at a low entropic price. The competiton between these two factors results in a maximum of hybridization for the strands having an intermediate length.     

Dynamic chemical devices: generation of reversible extension/contraction molecular motion by ion-triggered single/double helix interconversion

The polyheterocyclic strands 1-H and 2-H adopt a helical shape enforced by the pyridine-pyrimidine helicity codon. The crystal structure of 2-H shows the formation of stacks of dimers of right- and left-handed individual helices. Treatment of 1-H and 2-H with silver triflate results in the generation of double-helical entities 1-DH and 2-DH, containing two strands and two silver ions. NMR studies and determination of the crystal structure of 2-DH indicate that the duplex is stabilized by coordination of each Ag(+) ion to two terminal bipyridine units, one from each strand, and by pronounced pi-pi stacking interactions between the internal heterocycles of the strands, yielding a very robust double helical structure. Reversible interconversion of the single and double helix may be achieved by addition of a cryptand capable of sequestering Ag(+) and releasing it by protonation. Thus, successive addition of acid and base leads to reversible interconversion between the shorter ( approximately 3.6 A) single helix and the longer ( approximately 10.3 A) double helix, resulting in the generation of pronounced extension/contraction motion. The system 1,2-H/1,2-DH represents a dynamic chemical device undergoing ionic modulation of reversible molecular mechanical motion fueled by acid/base neutralization.     

Helical molecular programming: supramolecular double helices by dimerization of helical oligopyridine-dicarboxamide strands

Helically preorganized oligopyridine-dicarboxamide strands are found to undergo dimerization into double helical supramolecular architectures. Dimerization of single helical strands with five or seven pyridine rings has been characterized by NMR and mass spectrometry in various solvent/ temperature conditions. Solution studies and stochastic dynamic simulations consistently show an increasing duplex stability with increasing strand length. The double helical structures of three different dimers was characterized in the solid phase by X-ray diffraction analysis. Both aromatic stacking and hydrogen bonding contribute the double helical arrangement of the oligopyridinedicarboxamide strand. Inter-strand interactions involve extensive face-to-face overlap between aromatic rings, which is not possible in the single helical monomers. Most hydrogen bonds occur within each strand of the duplex and stabilize its helical shape. Some inter-strand hydrogen bonds are found in the crystal structures. Dynamic studies by NMR as well as by molecular modeling computations yield structural and kinetic information on the double helices and on monomer-dimer interconversion. In addition, they reveal the presence of a spring-like extension/compression as well as rotational displacement motions.     

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.     

Pressure effects on the structural,electronic, and optical properties of Sin@SWCNTs

Well‐ordered single, double/four parallel, three/four‐strands helical chains, and five‐strand helical chain with a single atom chain at the center of Si nanowires (NWs) inside single‐walled carbon nanotubes (Si_n@SWCNTs) are obtained by means of molecular dynamics. On the basis of these optimized structures, the structural evolution of Si_n@SWCNTs subjected to axial stress at low temperature is also investigated. Interestingly, the double parallel chains depart at the center and transform into two perpendicular parts, the helical shell transformed into chain, and the strand number of Si NWs increases during the stress load. Through analyzis of pair correlation function (PCF), the density of states (DOS), and the z‐axis polarized absorption spectra of Si_n@SWCNTs, we find that the behavior of Si_n@SWCNTs under stress strongly depends on SWCNTs' symmetry, diameter, as well as the shape of NWs, which provide valuable information for potential application in high pressure cases such as seabed cable. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Chalcogen-Bond-Induced Double Helix Based on Self-Assembly of a Small Planar Building Block

As a rule, helical structures at the molecular level are formed by non-planar units. This makes the design of helices, starting from planar building blocks via self-assembly, even more fascinating. Until now, however, this has only been achieved in rare cases, where hydrogen and halogen bonds were involved. Here, we show that the carbonyl-tellurium interaction motif is suitable to assemble even small planar units into helical structures in solid phase. We found two different types of helices: both single and double helices, depending on the substitution pattern. In the double helix, the strands are connected by additional Te⋅⋅⋅Te chalcogen bonds. In the case of the single helix, a spontaneous enantiomeric resolution occurs in the crystal. This underlines the potential of the carbonyl-tellurium chalcogen bond to generate complex three-dimensional patterns.     

Molecular electrotatic potential of a triple stranded helix: Poly(dT)·poly(dA)·poly(dT)

The molecular electrostatic potential of the triple helix poly(dT)·tpoly(dA)·poly(dT) is calculated, and the results are examined in relation to those obtained for its component double and single helical parts. For the double helix presenting the standard Watson–Crick hydrogen bonds, the deepest potentials are formed on the side of the major groove, a situation similar to that observed in the A-DNA duplex. For the double helix presenting Hoogsteen-type hydrogen bonds the deepest potentials lie in the major groove, on the side of the pyrimidine strand. In the triple helix the deepest potentials are located in the major groove in a narrow zone over the thymine bases of the Watson–Crick pair.     

Double-stranded helical polymers consisting of complementary homopolymers

Two complementary homopolymers of chiral amidines and achiral carboxylic acids with m-terphenyl-based backbones were synthesized by the copolymerization of a p-diiodobenzene derivative with the diethynyl monomers bearing a chiral amidine group and a carboxyl group using the Sonogashira reaction, respectively. Upon mixing in THF, the homopolymer strands assembled into a preferred-handed double helix through interstrand amidinium-carboxylate salt bridges, as evidenced by its absorption, circular dichroism, and IR spectra. In contrast, when mixed in less polar solvents, such as chloroform, the complementary strands kinetically formed an interpolymer complex with an imperfect double helical structure containing a randomly hybridized cross-linked structure, probably because of strong salt bridge formations. This primary complex was rearranged into the fully double helical structure by treatment with a strong acid followed by neutralization with an amine. High-resolution atomic force microscopy revealed the double-stranded helical structure and enabled the determination of the helical sense.     

Increasing the Size of an Aromatic Helical Foldamer Cavity by Strand Intercalation

The postsynthetic modulation of capsules based on helical aromatic oligoamide foldamers would be a powerful approach for controlling their receptor properties without altering the initial monomer sequences. With the goal of developing a method to increase the size of a cavity within a helix, a single‐helical foldamer capsule was synthesized with a wide‐diameter central segment that was designed to intercalate with a second shorter helical strand. Despite the formation of stable double‐helical homodimers (K_dim>10⁷ M ^?1) by the shorter strand, when it was mixed with the single‐helical capsule sequence, a cross‐hybridized double helix was formed with K_a>10⁵ M ^?1. This strategy makes it possible to direct the formation of double‐helical heterodimers. On the basis of solution‐ and solid‐state structural data, this intercalation resulted in an increase in the central‐cavity size to give a new interior volume of approximately 150 ų.     

Hybridization energies of double strands composed of DNA, RNA, PNA and LNA

The electronic properties of double strands composed of trimeric LNA, PNA, DNA and RNA single strands were investigated by density-functional molecular orbital calculations. The computed hybridization energies for the double strands involving PNA or LNA are larger than those for DNA-DNA and RNA-RNA. The larger stability is attributed to the presence of a larger positive charge of the hydrogen atoms contributing to the hydrogen bonds in the PNA-DNA and LNA-DNA double-strands. These results are comparable to the experimental finding that PNA and LNA single strands display high affinity toward a complementary DNA or RNA single strand.     

DNA double helices recognize mutual sequence homology in a protein free environment

The structure and biological function of the DNA double helix are based on interactions recognizing sequence complementarity between two single strands of DNA. A single DNA strand can also recognize the double helix sequence by binding in its groove and forming a triplex. We now find that sequence recognition occurs between intact DNA duplexes without any single-stranded elements as well. We have imaged a mixture of two fluorescently tagged, double helical DNA molecules that have identical nucleotide composition and length (50% GC; 294 base pairs) but different sequences. In electrolytic solution at minor osmotic stress, these DNAs form discrete liquid-crystalline aggregates (spherulites). We have observed spontaneous segregation of the two kinds of DNA within each spherulite, which reveals that nucleotide sequence recognition occurs between double helices separated by water in the absence of proteins, consistent with our earlier theoretical hypothesis. We thus report experimental evidence and discuss possible mechanisms for the recognition of homologous DNAs from a distance.     

Triple Helix Formation in a Topologically Controlled DNA Nanosystem

In the present study, we demonstrate single‐molecule imaging of triple helix formation in DNA nanostructures. The binding of the single‐molecule third strand to double‐stranded DNA in a DNA origami frame was examined using two different types of triplet base pairs. The target DNA strand and the third strand were incorporated into the DNA frame, and the binding of the third strand was controlled by the formation of Watson–Crick base pairing. Triple helix formation was monitored by observing the structural changes in the incorporated DNA strands. It was also examined using a photocaged third strand wherein the binding of the third strand was directly observed using high‐speed atomic force microscopy during photoirradiation. We found that the binding of the third strand could be controlled by regulating duplex formation and the uncaging of the photocaged strands in the designed nanospace.     

Supramolecular control of unwinding and rewinding of a double helix of oligoresorcinol using cyclodextrin/adamantane system

The double helix of the oligoresorcinol nonamer formed in water was unwound by beta-cyclodextrin (beta-CD), and the resulting single strands of the nonamer threaded the beta-CD to form a twisted [3]-pseudorotaxane with a controlled helicity. Upon the addition of an adamantane, the single strand of the oligoresorcinol nonamer was expelled out of the beta-CD wheels, thus regenerating the double helix. This supramolecularly controlled, reversible unwinding and rewinding of the double helix is unique and can be readily monitored by spectroscopic techniques.     

Molecular design and synthesis of artificial double helices

This account describes novel artificial double helices recently developed by our group. We have designed and synthesized the double helices consisting of two complementary, m-terphenyl-based strands that are intertwined through chiral amidinium-carboxylate salt bridges. Due to the chiral substituents on the amidine groups, the double helices adopted an excess one-handed helical conformation in solution as well as in the solid state. By extending the modular strategy, we have synthesized double helices bearing Pt(II) linkers, which underwent the double helix-to-double helix transformations through the chemical reactions of the Pt(II) complex moieties. In addition, artificial double-stranded metallosupramolecular helical polymers were constructed by combining the salt bridges and metal coordination. In contrast to the design-oriented double helices based on salt bridges, we have serendipitously developed a spiroborate-based double helicate bearing oligophenol strands. The optical resolution of the helicate was successfully attained by a diastereomeric salt formation. We have also unexpectedly found that oligoresorcinols consisting of a very simple repeating unit self-assemble into double helices with the aid of aromatic interactions in water. Furthermore, a bias in the twist sense of the double helices can be achieved by incorporating chiral substituents at both ends of the strands.     

Diversity of interstrand π—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.     

Interpenetrating single helical capsules

An aromatic oligoamide sequence designed to adopt a helically folded conformation surrounding a hollow space is shown to undergo hybridization into a double helical duplex in which the two strands fill each other's hollow.     

Paranemic crossover DNA: a generalized Holliday structure with applications in nanotechnology

Paranemic crossover (PX) DNA is a four-stranded coaxial DNA complex containing a central dyad axis that relates two flanking parallel double helices. The strands are held together exclusively by Watson-Crick base pairing. The key feature of the structure is that the two adjacent parallel DNA double helices form crossovers at every point possible. Hence, reciprocal crossover points flank the central dyad axis at every major or minor groove separation. This motif has been modeled and characterized in an oligonucleotide system; a minor groove separation of five nucleotide pairs and major groove separations of six, seven, or eight nucleotide pairs produce stable PX DNA molecules; a major groove separation of 9 nucleotide pairs is possible at low concentrations. Every strand undergoes a crossover every helical repeat (11, 12, 13, or 14 nucleotides), but the structural period of each strand corresponds to two helical repeats (22, 24, 26, or 28 nucleotides). Nondenaturing gel electrophoresis shows that the molecules are stable, forming well-behaved complexes. PX DNA can be produced from closed dumbbells, demonstrating that the molecule is paranemic. Ferguson analysis indicates that the molecules are similar in shape to DNA double crossover molecules. Circular dichroism spectra are consistent with B-form DNA. Thermal transition profiles suggest a premelting transition in each of the molecules. Hydroxyl radical autofootprinting analysis confirms that there is a crossover point at each of the positions expected in the secondary structure. These molecules are generalized Holliday junctions.     

Pyridinedicarboxamide strands form double helices via an activated slippage mechanism

The intertwining process of two strands of oligo-pyridinecarboxamides to form a double helix (Nature 2000, 407, 720) is found to consist of a series of discrete steps, where the tail of one of the strands proceeds inside the other single helix in an eddy-like process. While a plethora of minima can be located along the pathway, they exist only for a few, well-defined supramolecular arrangements of the two molecules. The initial transition state for the introduction of one molecule in the pitch of the other has the largest barrier and is therefore the rate-determining step of an activated slippage mechanism, which is characterized by a series of roller-coasting hills. Along the entire pathway, the intramolecular energy that stabilizes the single helices is slowly transformed into intermolecular energy that finally provides the necessary stabilization only near the end of the entwining process. Solvent or other chemical factors, such as the presence of ions, able to destabilize the full formation of the double helix may therefore drastically affect its formation.     

Completely geometrically optimized DFT/ONIOM triple-helical collagen-like structures containing the ProProGly, ProProAla, ProProDAla, and ProProDSer triads

We report completely optimized ONIOM DFT/AM1 molecular orbital calculations on several collagen-like triple helices based upon the repeating triad, ProProGly. The requirement of Gly as every third amino acid in collagen can be attributed to its enantiomorphic nature, as it behaves as a Damino acid in collagen. We, therefore, explored related collagen-like triple helices with one of the central Gly's mutated to either L or DAla; l-Ala appreciably destabilizes, while d-Ala slightly stabilizes the triple helical structure. Mutation of the same Gly to DSer, which is simply DAla with an OH in place of one of the methyl H's, induces a much greater stabilization due to an additional H-bond formed between this OH and a C=O on an adjacent peptide strand. Energies are presented for the triple helices and their component strands (both optimized and distorted to their triple helical geometries) relative to the component amino acids. The variation of relative energies with the chosen reference is delineated.     

Mode of binding of camptothecins to double helix oligonucleotides

We report an NMR study on the interaction of topotecan (Tpt) and other camptothecins (Cpts) with several double helix and single strand oligonucleotides. The results obtained by (31)P NMR spectroscopy, nuclear Overhauser experiments (NOE) and molecular dynamics (MD) simulations show that Cpt drugs do not intercalate into the double helix, as suggested by many authors. Phosphorus NMR spectra indicated that no deformation occurs at any level of the phosphodiester backbone, while 2D NOESY experiments allowed the detection of several contacts between the aromatic protons of Cpts and those of the double helix. Models of the drug/oligonucleotide complexes, built on the basis of NOE data, show that the drug is located at the end of the double helix, by stacking the A and B rings with the guanine or cytidine of the terminal CG base pairs, with a preference for the 3[prime or minute]-terminal end sites. Cpts interact with double strand, as well as with single strand oligomers, as can be seen from the NMR shift variation observed on the drug protons; but this shielding effect cannot be an evidence of intercalation, as it is largely due to external non-specific interactions of the positively charged drug with the negatively charged ionic surface of the oligonucleotide. The molecular weight of one of the complexes was obtained from the correlation time value. The conformational behaviour of the DNA fragment d(CGTACG)(2) was studied by MD simulations on a ns time scale in the presence of water molecules and Na(+) ions. Different models were examined and the deformations induced on the phosphodiester backbone by molecules that are known to intercalate, were monitored by MD simulations.