Double Helix Formation Research Articles

Reversible Double‐Helix–Random‐Coil Transition Process of Bis{hexa(ethynylhelicene)}s

Two compounds with two hexa(ethynylhelicene) parts connected by a flexible hexadecamethylene and a rigid butadiyne linker were synthesized. The 1H NMR spectroscopic and CD analyses and vapor-pressure osmometry (VPO) of these two compounds revealed intramolecular double-helix formation. Upon heating a 5-microM solution in toluene, the double-helix structure unfolded to form a random coil, and on cooling it folded again into a double helix. The thermodynamic stabilities of both structures were dependent on temperature, and the structural change in both compounds is due to the large enthalpies and entropies under equilibrium. The rate constants of their unfolding were obtained by assuming a pseudo-first-order reaction; the compound with a rigid linker unfolded slower than that with a flexible linker. The former has a larger activation energy, and its double-helix and random-coil conformers were separated by chromatography. The rate of folding was also faster for the flexible-linker compound with larger activation energy. The rate constants for the folding of both compounds slightly decreased with increasing temperature, which was ascribed to the presence of exothermic pre-equilibrium and rate-determining steps. The folding was markedly accelerated with increasing random-coil concentration, which suggests the involvement of self-catalysis. A mechanism of folding was proposed. The involvement of different mechanisms of folding and unfolding was suggested by the kinetic studies, and it was confirmed by the presence of hysteresis in the melting profiles. The difference in linker structure also affected the thermal-switching profiles of the double-helix-random-coil structural changes.

Chiral recognition in noncovalent bonding interactions between helicenes: right-handed helix favors right-handed helix over left-handed helix

Our studies of helicenes are summarized in regard to chiral recognition phenomenon in noncovalent bonding interactions. The interactions between helical molecules show a tendency for pairs of the same configuration of the helicenes to form more stable complexes than pairs of enantiomeric helicenes. The observations are made in charge transfer complexation, crystallization, homocoupling reaction, layer structure formation, self-aggregation, and double helix formation. The interactions between a helicene and a right-handed helical polymer, double strand DNA, are also described.

Bipyridine-modified oligonucleotides: Aggregation in the presence of metal ions

To the 5′-end of the palindromic oligonucleotide sequence d(CGCGAATTCGCG) was appended an artificial 2,2′-bipyridine-based nucleoside, resulting in the formation of regular DNA double helices that contain bidentate ligands as single-nucleotide overhangs. Due to their limited size, these duplexes are too small to be resolved by atomic force microscopy (AFM). Therefore, only a homogeneous surface can be detected after their deposition on mica. In the presence of the octahedrally coordinating transition metal ion iron(II), an entirely different surface topology is observed, however. On mica support, two types of aggregates are formed, namely a monolayer of interconnected DNA double helices and a three-dimensional disc-like structure that with time rearranges into fibers with lengths of several micrometers. On highly ordered pyrolytic graphite (HOPG), two-dimensional structures resembling a labyrinth are observed in the presence of iron(II). These observations can be explained by the formation of artificial three-way junctions between DNA double helices, mediated by octahedral iron bipyridine complexes. Hence, the incorporation of artificial ligand-containing nucleosides into oligonucleotides opens up the way to DNA-based nanostructures that assemble only in the presence of suitable metal ions.

Conformational Change Induced by Metal-Ion-Binding to DNA Containing the Artificial 1,2,4-Triazole Nucleoside

A conformational switch can be induced upon the addition of transition-metal ions to oligonucleotides that contain a row of successive artificial nucleobases flanked by complementary sequences of natural nucleobases, provided that the artificial bases cannot undergo self-pairing via hydrogen bonding but only via the formation of metal-ion-mediated base pairs. Such oligonucleotides adopt a hairpin structure in the absence of transition-metal ions, yet they show a preference for the formation of a regular double helix if the appropriate metal ions are present. We report here our experimental data on the structure of the oligonucleotide d(A7X3T7) (A=adenine, T=thymine, X=1,2,4-triazole) in the absence and presence of silver(I). This study comprising temperature-dependent UV spectroscopy, CD spectroscopy, MALDI-TOF measurements, fluorescence spectroscopy, and dynamic light scattering opens up a new approach to the generation of a large variety of metal-ion sensors with the possibility of fine-tuning their sensing capabilities, depending on the artificial nucleoside that is used.

An Artificial Base Pair, Mediated by Hydrogen Bonding and Metal‐Ion Binding

Silver service: Addition of silver(I) to an oligonucleotide comprising 1-deazaadenine and thymine nucleobases leads to the formation of a Hoogsteen-type double helix with specific binding of one metal ion per base pair (see scheme). Each base pair is mediated by one hydrogen bond and by two coordination bonds. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2007/z700315_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.

Structural Study of the DNA Dipalmitoylphosphatidylcholine Complex at the Air−Water Interface

We present here results that demonstrate the formation of a complex of DNA with zwitterionic dipalmitoylphosphatidylcholine (DPPC) monolayer at the air-water interface in the presence of Ca2+ ions; in particular, we show that the presence of Ca2+ cations is essential for the formation of the complex of DPPC with DNA. We characterize the resulting structure by X-ray reflectivity and by null-ellipsometry. We show that DNA maintains its native double helix form when attached to the zwitterionic lipid monolayer, at difference with the case of ammine containing monolayers. Our findings are discussed in view of other works that recently appeared on the interaction of DNA with zwitterionic phospholipids, emphasizing the role of DPPC as a potential vector for transfer of genetic material into mammalian cells by nonviral gene therapy and also suggesting Langmuir/Blodgett layers of zwitterionic phospoholipids as a method for nonconventional DNA immobilization.

DNA Made of Purines Only

The DNA double helix, containing both purine and pyrimidine bases, has evolved as the universal genetic system. In this issue of Chemistry & Biology , Battersby and colleagues describe the formation of double helix that is comprised solely of naturally occurring purine-nucleotides [1] .

Gelation mechanism and network structure of mixed solution of low- and high-acyl gellan studied by dynamic viscoelasticity, CD and NMR measurements

The gelation mechanism and the change of the network structure during cooling of the mixed solution of high-acyl (HA) and low-acyl (LA) gellan (containing 0.5% HA gellan and 0.5% LA gellan; hereafter called “mixed solution”) were elucidated on the basis of the results of dynamic viscoelasticity, circular dichroism (CD), and NMR measurements, which provide information about the network formation, the structural change due to random coil-double helix (C–H) transition, and the chain mobility of gellan, respectively. It was demonstrated that HA gellan chains in the mixed solution underwent C–H transition individually to form a network structure at the transition temperature for 1% HA gellan solution (75 °C), where storage modulus G′ and loss modulus G″ were steeply increased and the chain mobility of the HA gellan was restricted. The structural change of the HA gellan chains proceeded gradually with further cooling. At 25 °C, which is the C–H transition temperature for 1% LA gellan solution, LA gellan chains in the mixed solution formed a double helix, where G′ and G″ were slightly increased and the chain mobility of LA gellan was restricted. The results suggest that the double helix formation involves only the same kind of gellan chains even in the mixed solution, and that LA gellan chains decrease the mobility and promote the double helix formation of HA gellan chains, and vice versa.

Mismatches and Bubbles in DNA

Single mismatches in the DNA double helix form nucleation sites for bubbles. Although the overall melting temperature of the duplex is affected to different degrees depending on the probe length, the statistical weights of the bubble states around the defect are always strongly affected. Here we show experimentally that a single mismatch has indeed a dramatic effect on the distribution of intermediate (bubble) states in the melting transition of DNA oligomers. For probe lengths in the range 20–40 bases, the mismatch transforms a transition with many intermediates into a nearly two-state transition. One surprising consequence is the existence of a regime where the sensitivity of a mismatch detection assay based on monitoring intermediate states would increase with probe length. Our results provide experimental constraints on how mismatches should be implemented in models of DNA melting, such as the widely used thermodynamic nearest neighbor model, to which we compare our data.

Double Helix-to-Double Helix Transformation, Using Platinum(II) Acetylide Complexes as Surrogate Linkers

We describe novel optically active double helices consisting of complementary strands stabilized by amidinium-carboxylate salt bridges. The m-terphenyl groups of each strand are joined by trans-Pt(II) acetylide complexes with pendant PPh(3) ligands as the surrogate linker, which converts to cis counterparts by a ligand exchange reaction with cis-1,2-bis(diphenylphosphino)ethylene, resulting in the formation of double helices with different structures. Subsequent iodine-promoted reductive elimination on the Pt(II) atoms generates the fully organic, enantiomerically pure double helices. [structure: see text]

Oligoresorcinols Fold into Double Helices in Water

We report the first double helices with a controlled helicity in water based on oligoresorcinols as a new, simplest water-soluble structural motif. The molecular strands of the oligoresorcinols self-assemble into double helices with the aid of aromatic interactions in water as characterized by 1H NMR and absorption spectroscopies together with the X-ray crystallographic study of the pentamer. The double helix formation is sensitive to the chain length, solvent composition, and temperature. Moreover, a bias in the screw sense of the double helices was achieved by covalently attaching chiral substituents to both ends of the molecular strands.

Imaging of High-Amylose Starch Tablets. 3. Initial Diffusion and Temperature Effects

The penetration of water into cross-linked high amylose starch tablets was studied at different temperatures by nuclear magnetic resonance (NMR) imaging, which follows the changes occurring at the surface and inside the starch tablets during swelling. It was found that the swelling was anisotropic, whereas water diffusion was almost isotropic. The water proton image profiles at the initial stage of water penetration were used to calculate the initial diffusion coefficient. The swelling and water concentration gradients in this controlled release system show significant temperature dependence. Diffusion behavior changed from Fickian to Case II diffusion with increasing temperature. The observed phenomena are attributed to the gelatinization of starch and the pseudo-cross-linking effect of double helix formation.

Escherichia coli single-strand binding protein?DNA interactions on carbon nanotube-modified electrodes from a label-free electrochemical hybridization sensor

An electrochemical hybridization biosensor based on the intrinsic oxidation signals of nucleic acids and proteins has been designed, that makes use of the unique binding event between Escherichia coli single-strand binding protein (SSB) and single-stranded DNA (ssDNA). The voltammetric signal from guanine oxidation significantly decreased upon binding of SSB to single-stranded oligonucleotides (probe), anchored on a single-walled carbon nanotube (SWCNT) -modified screen-printed carbon electrode (SPE). Simultaneously, oxidation of the tyrosine (Tyr) and tryptophan (Trp) residues of the SSB protein increased upon binding of the SSB protein to ssDNA and ss-oligonucleotides. After the hybridization, SSB did not bind to the double helix form, and the guanine signal could be observed along with the disappearance of the oxidation signal of the protein. The amplification of intrinsic guanine and protein oxidation signals by SWCNT, and a washing step with sodium dodecylsulfate, enabled the specific detection of a point mutation. Monitoring the changes in the guanine and protein signals upon hybridization greatly simplified the detection procedure. The detection limit of 0.15 microg/ml target DNA can be applied to genetic assays. To the best of our knowledge, this is the first work that utilizes the monitoring of SSB-DNA interactions on a solid transducer for the electrochemical detection of DNA hybridization by using intrinsic oxidation signals.

In-situ Observation of DNA Hybridization in Aqueous Solution by Multiple Internal Reflection Infrared Absorption Spectroscopy

We have observed in-situ the hybridization (double helix formation) and denaturation (separation of double helix at elevated temperatures) of DNA in aqueous solution using infrared absorption spectroscopy (IRAS) in the multiple internal reflection (MIR) geometry. We demonstrated that conformational changes of DNA strands due to hybridization and denaturation are reflected in the infrared absorption spectra of the bases of DNA. Comparing with the results of ab-initio cluster calculation, we found that hybridization produces the specific C=O stretching vibration modes in the hydrogen-bonded bases, and also that the C=O stretching vibration modes of the bases of a single strand may be greatly influenced by its surrounding water molecules that interact with the bases.

Hydration of the amylopectin branch point. Evidence of restricted conformational diversity of the alpha-(1-->6) linkage.

The hydration behavior of a model compound for the amylopectin branch point, methyl 6'-alpha-maltosyl-alpha-maltotrioside, was investigated by combining molecular dynamics simulations in explicit water, 500 MHz NMR spectroscopy, including pulsed field gradient diffusion measurements, and exploratory multivariate data analysis. In comparison with results on a tetrasaccharide analogue, the study reveals that the conformational diversity of the three-bond alpha-(1-->6) linkage becomes quite limited in aqueous solution upon the addition of a fifth glucose residue that elongates the alpha-(1-->6) branch. This investigation reveals two plausible starch branch point structures, one that permits the formation of double helices and one that is adapted for interconnection of double helices. The apparent rigidity of the former is explained by the presence of water pockets/bridges in the vicinity of the branch point that lock the pentasaccharide structure into one conformational family that is able to accommodate the creation of the double-helical amylopectin structure.

Effects of α-Amylases from Different Sources on the Firming of Concentrated Wheat Starch Gels: Relationship to Bread Staling

The firming and carbohydrate fractions of concentrated starch gels supplemented with four alpha-amylases from different sources were evaluated. Correlations were found between the firmness data and results for the carbohydrate fractions extracted from the gels. The thermostable (TBA) and intermediate temperature stability (ISBA) bacterial alpha-amylases were most effective in decreasing the rate of firming. The cereal alpha-amylase at the high level (CAH) was also effective. The CAH produced the largest quantity of dextrins at storage time zero and the thermostable bacterial alpha-amylase at the high level (TBAH) after storage for 5 days. None of the maltooligosaccharides appeared to be responsible for the decreased rate of firming of the gels. The results indicated that the TBA and ISBA most effectively inhibited firming because they degraded the external branches and the intercluster regions of amylopectin during storage. Consideration of previously reported differential scanning calorimetry and X-ray crystallography results leads to the conclusion that the antifirming action of the TBA and ISBA is due to their ability to degrade the amylopectin and amorphous regions of the gels during storage, which inhibits the formation of double helices and decreases the strength of the starch gel matrix. Gels supplemented with the TBA and ISBA were most crystalline but firmed to a lesser extent. These results are similar to those previously reported by other researchers for bread and strongly suggest that starch retrogradation plays a primary role in bread staling.

Effect of alpha-amylases from different sources on the retrogradation and recrystallization of concentrated wheat starch gels: relationship to bread staling.

Concentrated starch gels were supplemented with four alpha-amylases from different sources. The retrogradation and recrystallization of the gels were evaluated using differential scanning calorimetry (DSC) and X-ray crystallography. Correlations between the retrogradation data and the carbohydrate fractions extracted from these gels were determined. The thermostable (TBA) and intermediate temperature stability (ISBA) bacterial alpha-amylases were most effective in decreasing the rate of retrogradation of the starch in the gels. The cereal alpha-amylase at the high level (CAH) was also effective. Supplementation with the alpha-amylases increased the crystallinity of the gels. Gels supplemented with TBA or ISBA were most crystalline and retrograded to a lesser extent. The results indicated that DSC gives not only a measure of recrystallized amylopectin but also a measure of total order (recrystallized amylopectin and double-helical content). The maltooligosaccharides produced by the enzymes did not appear to be responsible for the reduced rates of retrogradation, but they appeared to be an expression of the degree of starch modification that was responsible for the inhibition of retrogradation. The crystallinity and retrogradation data were similar to results reported for bread and strongly suggest that bread staling is caused by the retrogradation of starch. The results also indicate that alpha-amylases decrease the rate and extent of retrogradation of starch gels by inhibiting the formation of double helices.

Unzipping Mechanism of the Double-stranded DNA Unwinding by a Hexameric Helicase: Quantitative Analysis of the Rate of the dsDNA Unwinding, Processivity and Kinetic Step-size of the Escherichia coli DnaB Helicase Using Rapid Quench-flow Method

Kinetics of the double-stranded (ds) DNA unwinding by the Escherichia coli replicative helicase DnaB protein has been examined under single-turnover conditions using the chemical quench-flow technique. The unwinding reaction proceeds through an initial conformational transition followed by the unwinding catalytic steps and the release of the single-stranded (ss) DNA. Analyses of the reaction as a function of the number of base-pairs in the dsDNA reveal that the number of catalytic steps is not strictly proportional to the length of the dsDNA. As the helicase approaches the end of the substrate, the remaining approximately 11 bp of the DNA melts without catalytic participation of the enzyme. The kinetic step-size of the DnaB helicase, i.e. the number of the base-pairs unwound in a single catalytic step is only 1.4(+/- 0.2). The low value of the step-size indicates that the helicase unwinds a single base-pair in a single catalytic step. Thus, the DnaB helicase unzips the dsDNA in a reverse process to the zipping mechanism of the non-enzymatic double helix formation. The protein is a fast helicase that at 25 degrees C unwinds approximately 291 bp/s, much faster than previously thought, and the unwinding rate can be much higher at higher temperatures. However, the ATP-state of the enzyme has an increased dissociation rate, resulting in only a moderate unwinding processivity, P = 0.89(+/- 0.03), little dependent on the temperature. The conformational transition of the DnaB helicase-DNA complex, preceding the unwinding, is an intrinsic transition of the enzyme from the stationary conformation to the ATP-state of the helicase.

Formation and propagation of oscillating bubbles in DNA initiated by structural distortions

The initiation of the transcription process in DNA is linked with the dynamics originating from structural distortions of the double helix. It was proposed that such deformations might be caused by a ‘hit and run’ mechanism which is associated with the temporary attachment of some proteins, constituting activator factors, to regions of the DNA leaving it in deformed shape. In a nonlinear model approach we demonstrate that there exist such structural distortions of the double helix that appropriately serve to activate the formation of open regions in the form of oscillating bubble. The structure of the double helix form of DNA is modeled by a oscillator network model. We show that the underlying nonlinear dynamics supports localized solutions in the form of radial breathers and kink-shaped angular patterns. It is demonstrated that the radial breathers, which are attributed to localized H-bond deformations of the DNA molecule, move coherently along the double chain. We further illustrate that the breathers sustain the impact of heterogeneity due to the genetic code inscribed in DNA. Moreover, mobility of the breathers is also preserved when, the positions of the nucleotides are (randomly) modulated through fluctuational modes of the chemical environment, and energy dissipation due to non-elasticity damping of the motion of the nucleotides is incorporated. The amplitudes, oscillation periods and spatial extensions of the radial breathers resembles those found for the oscillating bubbles in real DNA molecules.

Coiling instabilities of multilamellar tubes.

Myelin figures are densely packed stacks of coaxial cylindrical bilayers that are unstable to the formation of coils or double helices. These myelin figures appear to have no intrinsic chirality. We show that such cylindrical membrane stacks can develop an instability when they acquire a spontaneous curvature or when the equilibrium distance between membranes is decreased. This instability breaks the chiral symmetry of the stack and may result in coiling. A unilamellar cylindrical vesicle, on the other hand, will develop an axisymmetric instability, possibly related to the pearling instability.