Parallel Double Helices Research Articles

Amylose Dimerization in Solution Can Be Studied Using a Model System.

Amylose, the linear polymer of α-1,4-linked glucopyranose units, is known to crystallize as a parallel double helix, but evidence of this duplex forming in solution has remained elusive for decades. We show how the dimerization of short amylose chains can be detected in solution using NMR spectroscopy when the glucans are labeled at the reducing-end with an aromatic moiety that overcomes chemical shift degeneracy leading to distinct signals for the single-stranded and duplex amylose. A set of α-1,4 glucans with varying lengths of 6, 12, 18, and 22 glucose units and a 4-aminobenzamide label were synthesized, enabling the first systematic thermodynamic study of the association of amylose in solution. The dimerization is enthalpically driven, entropically unfavorable and beyond a minimum length of 12, each additional pair of glucose residues stabilizes the duplex by 0.85 kJ mol-1 . This fundamental knowledge provides a basis for a quantitative understanding of starch structure, gelation and enzymatic digestion, and lays the foundations for the strategic use of α-1,4-glucans in the development of self-assembled materials.

Chiral Sum Frequency Generation Spectroscopy Detects Double-Helix DNA at Interfaces.

Many DNA-based technologies involve the immobilization of DNA and therefore require a fundamental understanding of the DNA structure-function relationship at interfaces. We present three immobilization methods compatible with chiral sum frequency generation (SFG) spectroscopy at interfaces. They are the "anchor" method for covalently attaching DNA on a glass surface, the "island" method for dropcasting DNA on solid substrates, and the "buoy" method using a hydrocarbon moiety for localizing DNA at the air-water interface. Although SFG was previously used to probe DNA, the chiral and achiral SFG responses of single-stranded and double-stranded DNA have not been compared systemically. Using the three immobilization methods, we obtain the achiral and chiral C-H stretching spectra. The results introduce four potential applications of chiral SFG. First, chiral SFG gives null response from single-stranded DNA but prominent signals from double-stranded DNA, providing a simple binary readout for label-free detection of DNA hybridization. Second, with heterodyne detection, chiral SFG gives an opposite-signed spectral response useful for distinguishing native (D-) right-handed double helix from non-native (L-) left-handed double helix. Third, chiral SFG captures the aromatic C-H stretching modes of nucleobases that emerge upon hybridization, revealing the power of chiral SFG to probe highly localized molecular structures within DNA. Finally, chiral SFG is sensitive to macroscopic chirality but not local chiral centers and thus can detect not only canonical antiparallel double helix but also other DNA secondary structures, such as a poly-adenine parallel double helix. Our work benchmarks the SFG responses of DNA immobilized by the three distinct methods, building a basis for new chiral SFG applications to solve fundamental and biotechnological problems.

The Effect of Calcium and Halide Ions on the Gramicidin A Molecular State and Antimicrobial Activity.

Gramicidin A (gA) forms several convertible conformations in different environments. In this study, we investigated the effect of calcium halides on the molecular state and antimicrobial activity of gramicidin A. The molecular state of gramicidin A is highly affected by the concentration of calcium salt and the type of halide anion. Gramicidin A can exist in two states that can be characterized by circular dichroism (CD), mass, nuclear magnetic resonance (NMR) and fluorescence spectroscopy. In State 1, the main molecular state of gramicidin A is as a dimer, and the addition of calcium salt can convert a mixture of four species into a single species, which is possibly a left-handed parallel double helix. In State 2, the addition of calcium halides drives gramicidin A dissociation and denaturation from a structured dimer into a rapid equilibrium of structured/unstructured monomer. We found that the abilities of dissociation and denaturation were highly dependent on the type of halide anion. The dissociation ability of calcium halides may play a vital role in the antimicrobial activity, as the structured monomeric form had the highest antimicrobial activity. Herein, our study demonstrated that the molecular state was correlated with the antimicrobial activity.

Parallel poly(A) homo- and hetero-duplex formation detection with an adapted DNA nanoswitch technique

Polyriboadenylic [poly(rA)] strands of sufficient length form parallel double helices in acidic and/or ammonium-containing conditions. Poly(rA) duplexes in acidic conditions are held together by A+–A+ base-pairing also involving base interactions with the phosphate backbone. Traditional UV-melting studies of parallel poly(A) duplexes have typically examined homo-duplex formation of a single nucleic acid species in solution. We have adapted a technique utilizing a DNA nanoswitch that detects interaction of two different strands either with similar or differing lengths or modifications. Our method detected parallel duplex formation as a function of length, chemical modifications, and pH, and at a sensitivity that required over 100-fold less concentration of sample than prior UV-melting methods. While parallel polyriboadenylic acid and poly-2′-O-methyl-adenylic acid homo-duplexes formed, we did not detect homo-duplexes of polydeoxyriboadenylic acid strands or poly-locked nucleic acid (LNA)-adenylic strands. Importantly however, a poly-locked nucleic acid (LNA)-adenylic strand, as well as a poly-2′-O-methyl-adenylic strand, formed a hetero-duplex with a polyriboadenylic strand. Overall, our work validates a new tool for studying parallel duplexes and reveals fundamental properties of poly(A) parallel duplex formation. Parallel duplexes may find use in DNA nanotechnology and in molecular biology applications such as a potential poly(rA) tail capture tool as an alternative to traditional oligo(dT) based purification.

Out-of-Plane Aptamer Functionalization of RNA Three-Helix Tiles.

Co-transcriptionally folding RNA nanostructures have great potential as biomolecular scaffolds, which can be used to organize small molecules or proteins into spatially ordered assemblies. Here, we develop an RNA tile composed of three parallel RNA double helices, which can associate into small hexagonal assemblies via kissing loop interactions between its two outer helices. The inner RNA helix is modified with an RNA motif found in the internal ribosome entry site (IRES) of the hepatitis C virus (HCV), which provides a 90° bend. This modification is used to functionalize the RNA structures with aptamers pointing perpendicularly away from the tile plane. We demonstrate modifications with the fluorogenic malachite green and Spinach aptamers as well with the protein-binding PP7 and streptavidin aptamers. The modified structures retain the ability to associate into larger assemblies, representing a step towards RNA hybrid nanostructures extending in three dimensions.

Interaction of carbohydrate binding module 20 with starch substrates.

CBM20s are starch-binding domains found in many amylolytic enzymes, including glucoamylase, alpha-amylase, beta-amylases, and a new family of starch-active polysaccharide monooxygenases (AA13 PMOs). Previous studies of CBM20–substrate interaction only concerned relatively small or soluble amylose molecules, while amylolytic enzymes often work on extended chains of insoluble starch molecules. In this study, we utilized molecular simulation techniques to gain further insights into the interaction of CBM20 with substrates of various sizes via its two separate binding sites, termed as BdS1 and BdS2. Results show that substrate binding at BdS1 involving two conserved tryptophan residues is about 2–4 kcal mol−1 stronger than that at BdS2. CBM20 exhibits about two-fold higher affinity for helical substrates than for the amylose random coils. The affinity for amylose individual double helices does not depend on the helices' length. At least three parallel double helices are required for optimal binding. The binding affinity for a substrate containing 3 or more double helices is ∼−15 kcal mol−1, which is 2–3 kcal mol−1 larger than that for individual double helices. 100 ns molecular dynamics simulations were carried out for the binding of CBM20 to an extended substrate containing 3 layers of 9 60-unit double helices (A3L). A stable conformation of CBM20–A3L was found at BdS1. However, when CBM20 binds A3L viaBdS2, it moves across the surface of the substrate and does not form a stable complex. MD simulations show that small amylose helices are quickly disrupted upon binding to CBM20. Our results provide some important molecular insights into the interactions of CBM20 with starch substrates, which will serve as the basis for further studies of CBM20-containing enzymes, including AA13 PMOs.

Mechanotransduction by PCDH15 Relies on a Novel cis-Dimeric Architecture

The tip link, a filament formed by protocadherin 15 (PCDH15) and cadherin 23, conveys mechanical force from sound waves and head movement toopen hair-cell mechanotransduction channels. Tip-link cadherins are thought to have acquired structural features critical for their role in mechanotransduction. Here, we biophysically and structurally characterize the unusual cis-homodimeric architecture of PCDH15. We show that PCDH15 molecules form double-helical assemblies through cis-dimerization interfaces in the extracellular cadherin EC2-EC3 domain region and in a unique membrane-proximal domain. Electron microscopy studies visualize the cis-dimeric PCDH15 assembly and reveal the PCDH15 extracellular domain as a parallel double helix with cis cross-bridges at the two locations we defined. Thehelical configuration suggests the potential forelasticity through helix winding and unwinding. Functional studies in hair cells show that mutations that perturb PCDH15 dimerization contacts affect mechanotransduction. Together, these data reveal the cis-dimeric architecture of PCDH15 and show that dimerization is critical for sensing mechanical stimuli.

Silver-Mediated Double Helix: Structural Parameters for a Robust DNA Building Block.

The DNA double helix is a versatile building block used in DNA nanotechnology. To potentiate the discovery of new DNA nanoscale assemblies, recently, silver cations have been introduced to pair DNA strands by base–Ag+–base bonding rather than by Watson–Crick pairing. In this work, we study the classical dynamics of a parallel silver-mediated homobase double helix and compare it to the dynamics of the antiparallel double helix. Our classical simulations show that only the parallel double helix is highly stable through the 100 ns simulation time. A new type of H-bond previously proposed by our collaboration and recently observed in crystal-determined helices drives the physicochemical stabilization. Compared to the natural B-DNA form, the metal-mediated helix has a contracted axial base pair rise and smaller numbers of base pairs per turn. These results open the path for the inclusion of this robust metal-mediated building block into new nanoscale DNA assemblies.

ナノ物質の輸送を目指した DNA オリガミによるナノマシンの設計

In this report, a new method to fabricate nano-machine which can swim in the liquid was proposed. DNA Origami whose characteristic is DNA self-assembly was made used of to construct a spiral structure in the size of several micrometers in length and tens of nanometers in diameter. Multiple parallel DNA double helix structure build up a DNA bundle, and the amount of base pairs in the bundle were increased or decreased to approach a spiral structure. By spattering nickel on the surface to magnetize DNA spiral structure, so that the spiral can be excited by an external magnetic field in which nano-machine can rotate and propel nano-material into the target location. This method permits a non-contact way to control nano-machine in the liquid that greatly reduces the erosion of organism.

7-Deaza-2'-deoxyguanosine: Selective Nucleobase Halogenation, Positional Impact of Space-Occupying Substituents, and Stability of DNA with Parallel and Antiparallel Strand Orientation.

The positional impact of phenyl or phenyltriazolyl residues on the properties of 7-deaza-2'-deoxyguanosine, such as fluorescence, sugar conformation, and stability in DNA and DNA-RNA double helixes was studied. To this end, regioselective iodination protocols were developed for 7-deaza-2'-deoxyguanosine affording the 7- and 8-iodo isomers. The aromatic side chains were introduced by Suzuki-Miyaura cross-coupling or click reaction. Only the 8-phenyl nucleoside shows strong fluorescence in polar aprotic solvents accompanied by solvatochromism. The conformation of the sugar moiety was shifted toward S due to the bulky 8-substituent. Phosphoramidite building blocks and oligonucleotides were synthesized. 8-Substituted 7-deaza-2'-deoxyguanosines destabilize canonical (aps) DNA as well as DNA with parallel strand (ps) orientation. The base pair stability was maintained when the space-occupying substitutes were located at the 7-position. Unexpectedly, the bulky phenyltriazolyl "click" residue is well-accommodated at the 7-position of ps DNA and even led to a stabilization of the parallel double helix. CD spectra indicate that functionalization leads only to local distortion of the double helix while the overall structure of aps and ps DNA is maintained.

Flexible Wire-Shaped Supercapacitors in Parallel Double Helix Configuration with Stable Electrochemical Properties Under Static/Dynamic Bending

Wire-shaped flexible supercapacitors (SCs) have aroused much attention due to their small size, light weight, high flexibility and deformability. However, the previously reported wire-shaped SCs usually involve complex assembly process and encounter potential structural instability, and the influence of dynamic bending on the electrochemical stability of wire-shaped SCs is also not clear. Here, a parallel double helix wire-shaped supercapacitor (PDWS) protocol has been developed with two symmetric titanium@MnO2 fiber electrodes winded on a flexible nylon fiber by a simple and reliable process. The PDWSs show an operate voltage of 0.8 V, a high capacitance of 15.6 mF cm-2 and an energy density of 1.4 μWh cm-2. Due to rational structure design, the PDWSs demonstrate excellent mechanical and electrochemical stability under both static and dynamic deformations. Over 3500 bending cycles, 88.0% of the initial capacitance can still be retained. In terms of dynamic bending, it is found that the cyclic voltammetry curves show periodically fluctuations simultaneously with the bending frequency and the intensity of fluctuation increases with higher bending frequency, while the dynamic capacitance is almost not affected. With extraordinary mechanical flexibility and excellent electrochemical stability, the high performance PDWS is considered to be a promising power source for wearable electronics. Figure 1

A closer look at the parallel RNA double helix poly(rA)

A closer look at the parallel RNA double helix poly(rA)

Crystal structure of a poly(rA) staggered zipper at acidic pH: evidence that adenine N1 protonation mediates parallel double helix formation

We have solved at 1.07 Å resolution the X-ray crystal structure of a polyriboadenylic acid (poly(rA)) parallel and continuous double helix. Fifty-nine years ago, double helices of poly(rA) were first proposed to form at acidic pH. Here, we show that 7-mer oligo(rA), i.e. rA7, hybridizes and overlaps in all registers at pH 3.5 to form stacked double helices that span the crystal. Under these conditions, rA7 forms well-ordered crystals, whereas rA6 forms fragile crystalline-like structures, and rA5, rA8 and rA11 fail to crystallize. Our findings support studies from ∼50 years ago: one showed using spectroscopic methods that duplex formation at pH 4.5 largely starts with rA7 and begins to plateau with rA8; another proposed a so-called ‘staggered zipper’ model in which oligo(rA) strands overlap in multiple registers to extend the helical duplex. While never shown, protonation of adenines at position N1 has been hypothesized to be critical for helix formation. Bond angles in our structure suggest that N1 is protonated on the adenines of every other rAMP−rAMP helix base pair. Our data offer new insights into poly(rA) duplex formation that may be useful in developing a pH sensor.

The Influence of Lipid Bilayer Physicochemical Properties on Gramicidin A Conformer Preferences

The conformational preferences adopted by gramicidin A (GA) dimers inserted into phospholipid bilayers are reported as a function of the bilayer cholesterol content, temperature, and incubation time. Through use of vesicle capture-freeze drying methodology, GA dimers were captured in lipid bilayers and the conformational preferences of the complex were analyzed using ion mobility-mass spectrometry. Perturbations that affect the physicochemical interactions in the lipid bilayer such as cholesterol incorporation, temperature, and incubation time directly alter the conformer preferences of the complex. Regardless of bilayer cholesterol concentration, the antiparallel double helix (ADH) conformation was observed to be most abundant for GA dimers in bilayers composed of lipids with 12 to 22 carbon acyl chains. Incorporation of cholesterol into lipid bilayers yields increased bilayer thickness and rigidity, and an increased abundance of parallel double helix (PDH) and single-stranded head-to-head (SSHH) dimers were observed. Bilayers prepared using 1,2-dilauroyl-sn-glycero-3-phosphocholine, a lipid with 12 carbon acyl chains, yielded a nascent conformer that decreased in abundance as a function of bilayer cholesterol content. High resolution ion mobility-mass spectrometry data revealed two peaks in the ADH region suggesting that ADH populations are composed of two distinct conformers. The conformer preferences of GA dimers from 1,2-distearoyl-sn-glycero-3-phosphocholine bilayers were significantly different for samples incubated at 4°C vs. 60°C; increased cholesterol content yielded more PDH and SSHH at 60°C. The addition of cholesterol as well as incubating samples of 1,2-distearoyl-sn-glycero-3-phosphocholine at 60°C for 24–72 h yielded an increase in PDH and SSHH abundance.

Supercapacitors: Flexible Wire-Shaped Supercapacitors in Parallel Double Helix Configuration with Stable Electrochemical Properties under Static/Dynamic Bending (Small 8/2016)

Supercapacitors: Flexible Wire-Shaped Supercapacitors in Parallel Double Helix Configuration with Stable Electrochemical Properties under Static/Dynamic Bending (Small 8/2016)

Flexible Wire-Shaped Supercapacitors in Parallel Double Helix Configuration with Stable Electrochemical Properties under Static/Dynamic Bending.

Wire-shaped flexible supercapacitors (SCs) have aroused much attention due to their small size, light weight, high flexibility, and deformability. However, the previously reported wire-shaped SCs usually involve complex assembly processes, encounter potential structural instabilities, and the influence of dynamic bending on the electrochemical stability of wire-shaped SCs is also not clear. Here, a parallel double helix wire-shaped supercapacitor (PDWS) protocol has been developed with two symmetric titanium@MnO2 fiber electrodes winded on a flexible nylon fiber by a simple and reliable process. The PDWSs show an operate voltage of 0.8 V, a high capacitance of 15.6 mF cm(-2) and an energy density of 1.4 µWh cm(-2) . Due to rational structure design, the PDWSs demonstrate excellent mechanical and electrochemical stability under both static and dynamic deformations. Over 3500 bending cycles, 88.0% of the initial capacitance can still be retained. In terms of dynamic bending, it is found that the cyclic voltammetry curves show periodically fluctuations simultaneously with the bending frequency and the intensity of fluctuation increases with higher bending frequency, while the dynamic capacitance is almost not affected. With extraordinary mechanical flexibility and excellent electrochemical stability, the high performance PDWS is considered to be a promising power source for wearable electronics.

Thermodynamics of Forming a Parallel DNA Crossover

The process of genetic recombination involves the formation of branched four-stranded DNA structures known as Holliday junctions. The Holliday junction is known to have an antiparallel orientation of its helices, i.e., the crossover occurs between strands of opposite polarity. Some intermediates in this process are known to involve two crossover sites, and these may involve crossovers between strands of identical polarity. Surprisingly, if a crossover occurs at every possible juxtaposition of backbones between parallel DNA double helices, the molecules form a paranemic structure with two helical domains, known as PX-DNA. Model PX-DNA molecules can be constructed from a variety of DNA molecules with five nucleotide pairs in the minor groove and six, seven or eight nucleotide pairs in the major groove. A topoisomer of the PX motif is the juxtaposed JX1 molecule, wherein one crossover is missing between the two helical domains. The JX1 molecule offers an outstanding baseline molecule with which to compare the PX molecule, so as to measure the thermodynamic cost of forming a crossover in a parallel molecule. We have made these measurements using calorimetric and ultraviolet hypochromicity methods, as well as denaturing gradient gel electrophoretic methods. The results suggest that in relaxed conditions, a system that meets the pairing requirements for PX-DNA would prefer to form the PX motif relative to juxtaposed molecules, particularly for the 6:5 structure.

Specific RNA Self-Assembly with Minimal Paranemic Motifs

The paranemic crossover (PX) is a motif for assembling two nucleic acid molecules using Watson-Crick (WC) basepairing without unfolding preformed secondary structure in the individual molecules. Once formed, the paranemic assembly motif comprises adjacent parallel double helices that crossover at every possible point over the length of the motif. The interaction is reversible as it does not require denaturation of basepairs internal to each interacting molecular unit. Paranemic assembly has been demonstrated for DNA but not for RNA and only for motifs with four or more crossover points and lengths of five or more helical half-turns. Here we report the design of RNA molecules that paranemically assemble with the minimum number of two crossovers spanning the major groove to form paranemic motifs with a length of three half turns (3HT). Dissociation constants (Kd's) were measured for a series of molecules in which the number of basepairs between the crossover points was varied from five to eight basepairs. The paranemic 3HT complex with six basepairs (3HT_6M) was found to be the most stable with Kd = 1 x 10-8 M. The half-time for kinetic exchange of the 3HT_6M complex was determined to be approximately 100 min, from which we calculated association and dissociation rate constants ka = 5.11 x 103 M-1s-1 and kd = 5.11 x 10-5 s-1. RNA paranemic assembly of 3HT and 5HT complexes is blocked by single-base substitutions that disrupt individual intermolecular Watson-Crick basepairs and is restored by compensatory substitutions that restore those basepairs. The 3HT motif appears suitable for specific, programmable, and reversible tecto-RNA self-assembly for constructing artificial RNA molecular machines.

Chiral self-assembly of methyltin(IV)-naproxenates: Combining dative Sn–O bonds, secondary Sn⋯O interactions and C–H⋯O hydrogen bonding to make an inter-helical meander-shaped network and a cross-linked Z-shaped ribbon

Three new chiral organotin(IV) carboxylates, Me 2Sn(nap) 2 ( 1), {[Me 2Sn(nap)] 2O} 2 ( 2) and Me 3Sn(nap) ( 3) (nap = ( S)-(+)-6-methoxy-α-methyl-2-naphthaleneaceto anion) have been synthesized. All of them have been characterized by elemental analysis, multinuclear ( 1H, 13C and 119Sn) NMR and IR spectroscopy. The crystal structures of 1 and 2 have been determined by X-ray diffraction analysis. The bicapped tetrahedral molecules of 1 are linked by C–H⋯O hydrogen bonds into homochiral helices, which are also interconnected by C–H⋯O interactions to form an inter-helical meander-shaped network. The molecule of 2 is a parallel double helix incorporating four chiral tin centers in a Sn 4O 10C 4 ladder type molecular skeleton. The C–H⋯O interactions translate the molecular chirality of 2 throughout the crystal via formation of infinite ribbons. These ribbons in their turn are further cross-linked by C–H⋯O hydrogen bonds. The structural characterization of the complexes 1– 3 in solution has been performed by routine multinuclear 1H, 13C and 119Sn NMR as well as specialized multidimensional ( 1H– 119Sn-gHMQC and 1H-DOSY) experiments. The relevant 2 J 1 H – 119 Sn and 1 J 13 C – 119 Sn coupling constants have been extracted and related to molecular geometries on the basis of the literature data. The measurement of the translational diffusion constants using diffusion ordered spectroscopy allowed the estimation of the spherical hydrodynamic radii of the newly prepared structures.

Crystal Structure of B-Amylose

A fiber specimen of B-amylose was prepared from enzymatically synthesized amylose, which is a purely linear 1,4-linked poly-α-d-glucose. X-ray crystal structure analysis was carried out by using the newly collected intensity data, which was estimated by using imaging plate according to the new procedure. The molecule of B-amylose assumes a left-handed parallel strand double helix, and two double helices pass through a hexagonal unit cell with parameters a = b = 18.52 A, c (fiber axis) = 10.57 A, γ = 120°, and the space group P61C62. A total of 36 water molecules were contained in a unit cell. The conformation of the primary hydroxyl group is gg, and the conformation of the bonds linking two glucose residues, Φ and Ψ, are +84.3 and −135.2°, respectively.