Antiparallel Chains Research Articles

Elucidating the enduring transformations in cellulose-based carbon nanofibers through prolonged isothermal treatment

This study investigates the conversion of highly acetylated sugarcane bagasse into high-modulus carbon nanofibers (CnNFs) with exceptional electrical conductivity. By electrospinning the bagasse into nanofibers with diameters ranging from 80 nm to 800 nm, a cost-effective CnNFs precursor is obtained. The study reveals the transformation of the cellulose crystalline structure into a stable antiparallel chain arrangement of cellulose II following prolonged isothermal treatment, leading to a remarkable 50 % increase in CnNFs recovery with carbon contents ranging from 80 % to 90 %. This surpasses the performance of any other reported biomass precursors. Furthermore, graphitization-induced shrinkage of CnNFs diameter results in significant growth of specific surface area and pore volume in the resulting samples. This, along with a highly ordered nanostructure and high crystallinity degree, contributes to an impressive tensile modulus of 9.592 GPa, surpassing that of most petroleum-based CnNFs documented in the literature. Additionally, the prolonged isothermal treatment influences the d002 value (measured at 0.414 nm) and CnNFs degree of crystallinity, leading to an enhancement in electrical conductivity. However, the study observes no size effect advantages on mechanical properties and electrical conductivity, possibly attributed to the potential presence of point defects in the ultrathin CnNFs. Overall, this research opens a promising and cost-effective pathway for converting sugarcane biomasses into high-modulus carbon nanofibers with outstanding electrical conductivity. These findings hold significant implications for the development of sustainable and high-performance materials for various applications, including electronics, energy storage, and composite reinforcement.

Polymer amide as a source of the cosmic 6.2 μm emission and absorption

ABSTRACT Cosmic infrared emission and absorption spectra often carry a well-defined and invariant 6.2 $\mu \rm m$ band that has been proposed to emanate from very small dust grains that may carry polyaromatic hydrocarbons. Hemoglycin, a well-defined polymer of glycine that also contains iron, has been found in meteorites of the primordial CV3 class and therefore originated in the solar protoplanetary disc. Here, we suggest that the polymer hemoglycin should also be considered as a source of the cosmic 6.2 $\mu{\rm m}$ emission and absorption. In quantum calculations, the principal amide I infrared absorption band of hemoglycin is centred, before splitting, at 6.0 $\mu\rm m$. Multiple hemoglycin polymers interact to split amide I into the strong (a-) band in the region of 6.2 $\mu\rm m$ and the much weaker (a+) band in the region of 5.8 $\mu\rm m$. Experimentally, these two components are seen in extracts of the Sutter’s Mill meteorite and in stromatolite ooid. The two 11-mer glycine antiparallel chains of hemoglycin have an exact structural analogue in antiparallel poly-l-lysine beta sheet crystals which in the laboratory have an (a-) absorption peak at 6.21 $\mu\rm m$. This wavelength coincidence, the demonstrated propensity of hemoglycin 4.9 nm rods to form accreting lattice structures, and its proven existence in the solar protoplanetary disc suggest that the cosmic 6.2 $\mu\rm m$ emission and absorption could be from small grains that are hemoglycin lattices or shell-like vesicles carrying internal organic molecules of various types. Calculated hemoglycin ultraviolet absorptions associated with iron in the molecule match the observed ultraviolet extinction feature at nominal 2175 Å.

RNA as a component of scrapie fibrils

Recently, electron cryo-microscopy (cryo-EM) maps of fibrils from the brains of mice and hamsters with five infectious scrapie strains have been published and deposited in the electron microscopy data bank (EMDB). As noted by the primary authors, the fibrils contain a second component other than protein. The aim of the present study was to identify the nature of this second component in the published maps using an in silico approach. Extra densities (EDs) containing this component were continuous, straight, axial, at right angles to protein rungs and within hydrogen-bonding distance of protein, consistent with a structural role. EDs co-located with strips of basic residues, notably lysines, and formed a conspicuous cladding over parts of the N-terminal lobe of the protein. A Y-shaped polymer consistent with RNA was found, in places forming a single chain and at one location forming a duplex, comprising two antiparallel chains, and raising the intriguing possibility of replicative behaviour. To reflect the monotonous nature of the protein interface, it is suggested that the RNA may be a short tandem repeat. Fibrils from brains of patients with Alzheimer’s disease, Parkinson’s disease, amyotrophic lateral sclerosis and other neurodegenerations also contain EDs and may be of a similar aetiology.

N-(4-Eth-oxy-phen-yl)-3-oxobutanamide.

The title compound, C12H15NO3, crystallizes with Z' = 2 in space group Pca21 with the two independent mol-ecules having almost the same conformation, differing mostly at the end of the butanamide chain. A local inversion center near 1/8, 3/4, z relates the two mol-ecules, as is common for structures in this space group with Z' = 2. The mol-ecule crystallizes as the keto tautomer, and the β-diketone moieties are twisted out of planarity, with O-C⋯C-O pseudo torsion angles of -74.4 (5) and -83.9 (5)°. The N-H group of each independent mol-ecule donates an inter-molecular hydrogen bond to an amide carbonyl oxygen atom by positive or negative translations along the b axis, thus forming anti-parallel chains propagating in the [010] direction.

Dynamics of 24 Self-Assembling H-(RADA)<sub>4</sub>-OH Peptides Complexed in Bi-Layered Structure with Layers in <i>syn</i> and <i>anti</i> Orientation

H-(RADA)4-OH peptide in water tends to form biolgels at physiological conditions. Thusly made scaffold is formed of fibrils resulted from peptides self-assembling. Fibrils have two external hydrophilic layers, while hydrophobic one is situated between of them. Bio gels by the H-(RADA)4-OH peptides are considered to be a prominent source for designed extra cellular matrix aimed to cell cultures of different types. Little is known about detailed structure the filament structure and β-sheets peptide composition. We have designed and studied molecular dynamics of bi-layered protofilament structures with β-sheets formed of parallel or anti-parallel peptide chains. Method of molecular dynamics was used to study H-(RADA)4-OH peptide complexes at 80 and 300 K. While the most stable peptide complex was found to consist of anti-parallel peptides, had the lowest free energy and the least deviation of atom coordinates, yet another stable structure of the peptide complex was identified as 24-mer of parallel peptides with two β-sheets placed in syn orientation. These results underlined the importance of factors, directing the initial stages of the H-(RADA)4-OH peptide self-assembling in solution.

Raman Metabolomics of Candida auris Clades: Profiling and Barcode Identification.

This study targets on-site/real-time taxonomic identification and metabolic profiling of seven different Candida auris clades/subclades by means of Raman spectroscopy and imaging. Representative Raman spectra from different Candida auris samples were systematically deconvoluted by means of a customized machine-learning algorithm linked to a Raman database in order to decode structural differences at the molecular scale. Raman analyses of metabolites revealed clear differences in cell walls and membrane structure among clades/subclades. Such differences are key in maintaining the integrity and physical strength of the cell walls in the dynamic response to external stress and drugs. It was found that Candida cells use the glucan structure of the extracellular matrix, the degree of α-chitin crystallinity, and the concentration of hydrogen bonds between its antiparallel chains to tailor cell walls’ flexibility. Besides being an effective ploy in survivorship by providing stiff shields in the α–1,3–glucan polymorph, the α–1,3–glycosidic linkages are also water-insoluble, thus forming a rigid and hydrophobic scaffold surrounded by a matrix of pliable and hydrated β–glucans. Raman analysis revealed a variety of strategies by different clades to balance stiffness, hydrophobicity, and impermeability in their cell walls. The selected strategies lead to differences in resistance toward specific environmental stresses of cationic/osmotic, oxidative, and nitrosative origins. A statistical validation based on principal component analysis was found only partially capable of distinguishing among Raman spectra of clades and subclades. Raman barcoding based on an algorithm converting spectrally deconvoluted Raman sub-bands into barcodes allowed for circumventing any speciation deficiency. Empowered by barcoding bioinformatics, Raman analyses, which are fast and require no sample preparation, allow on-site speciation and real-time selection of appropriate treatments.

Single crystal structure of 3-(2-(3-acetylphenyl)hydrazono)pentane-2,4-dione and molecular docking study with CYP450 members for anticancer molecular screening

Coupling of acetyl acetone with diazotized 3-aminoacetophenone was carried out to give the compound 3. The compound was characterized by IR, 1HNMR, MS and elemental analysis. The X-ray analysis of 3 revels its planar nature with torsion angles between phenyl ring and acetyl group C2–C3–C7–O1 and C2–C3–C7–C8 of 177.8(3)° and −0.9(4)°, respectively. Small deviations from planarity are evident also by torsion angles N1–N2–C9–C10 and N2–C9–C12–O3 of 176.6(2)° and 2.9(4)°, while the N2–C9–C10–O2 torsion angle with the value of −165.2(3)° deviates from planarity. Hydrogen-bonded chain formed through C5–H5⋯O2 is connected with the adjacent antiparallel chain through C11–H11B···π interaction between the methyl group of the acetyl substituent and phenyl ring forming a double-layered chain. N1–N2 shows presence of single bond, showing it to be a hydrazone. Molecular docking study of the title compound with six members from CYP450 family shows encouraging activity.

Permittivity order modulation by intrinsic dielectric coupling

The room-temperature permittivity is reduced by one order of magnitude in a wide frequency range during each step, when the stoichiometric proportion of Cu in CaCu3Ti4O12 is decreased from 3 to 2 and then to 1. The frequency-independent reduction can be applied down to 140 K. Such an almost frequency- and temperature-independent decrease in the permittivity magnitude order suggests the existence of intrinsic dielectric coupling between binary dielectric polarization species, by which the less polaron-like 3d electrons from B-site copper ions more strongly depress the permittivity contribution from one-dimensional, anti-parallel, mutually independent, and finite length dipole chains of thermally activated off-center displacements of A-site titanium ions.

Non-intertwined strands of plasmid DNA contradict the Watson and Crick model of DNA structure

According to Watson and Crick (W/C) model of DNA structure, a DNA molecule consists of two antiparallel polynucleotide chains, intertwined with each other. Although W/C model is accepted widely, some researchers have raised questions against it and proposed alternative structures for DNA. In the present study, we examined W/C model using plasmid DNA. It was hypothesized that two strands of plasmid will remain intertwined (and not separate from each other) under denaturing conditions if it follows W/C model. To test this, plasmid DNA was denatured using sodium hydroxide (NaOH) and analyzed by agarose gel electrophoresis. It was observed that addition of 0.5 N NaOH to pUC19 or pBR322 plasmids resulted in a new form of DNA having higher electrophoretic mobility in agarose gel. Higher electrophoretic mobility DNA (HmDNA) in NaOH-denatured pUC19 was digestible with S1 nuclease, but not with HindIII and ‘exonuclease I + alkaline phosphatase’. These results demonstrated that HmDNA is single-stranded circular DNA, formed due to separation of two strands of NaOH-denatured plasmid. Single-stranded and circular nature of HmDNA was corroborated by its comparable electrophoretic mobility with purified top and bottom strands of plasmid DNA. Next, we examined whether HmDNA can re-anneal into the native plasmid. Interestingly, when subjected to renaturing conditions, HmDNA from NaOH-denatured pUC19 re-annealed to form native pUC19 plasmid, which was digestible with HindIII and induced ampicillin resistance in Escherichia coli. These findings demonstrated the reversible separation of two strands of plasmid DNA and contradicted the W/C model of DNA structure.

Non-intertwined strands of plasmid DNA contradicts the Watson and Crick model of DNA structure

According to Watson and Crick (W/C) model of DNA structure, a DNA molecule consists of two antiparallel polynucleotide chains, intertwined with each other. Although W/C model is accepted widely, some researchers have raised questions against it and proposed alternative structures for DNA. In the present study, we examined W/C model using plasmid DNA. It was hypothesized that two strands of plasmid will remain intertwined (and not separate from each other) under denaturing conditions if it follows W/C model. To test this, plasmid DNA was denatured using sodium hydroxide (NaOH) and analyzed by agarose gel electrophoresis. It was observed that addition of NaOH to pUC19 and pBR322 plasmids resulted in a new form of DNA having higher electrophoretic mobility in agarose gel. Higher electrophoretic mobility DNA (HmDNA) in NaOH-denatured pUC19 was digestible with S1 nuclease, but not with HindIII and ‘exonuclease I + alkaline phosphatase’. These results demonstrated that HmDNA is single-stranded circular DNA, formed due to separation of two strands of NaOH-denatured plasmid. Single-stranded and circular nature of HmDNA was corroborated by its comparable electrophoretic mobility with purified top and bottom strands of plasmid DNA. Next, we examined whether HmDNA can re-anneal into the native plasmid. Interestingly, when HmDNA from NaOH-denatured pUC19 was subjected to renaturing conditions, it formed native pUC19 plasmid, which was digestible with HindIII and induced ampicillin resistance in Escherichia coli cells. These findings demonstrated the reversible separation of two strands of plasmid DNA and contradicted the W/C model of DNA structure.

Recent Progress in Preparation and Application of Nano‐Chitin Materials

Chitin is a kind of natural macromolecule material which was first discovered in mushrooms and was widely found in the shells of crustaceans and arthropods, the cell walls of fungi (yeast and mold) and algae, and the mollusks. The original chitin in nature usually has an antiparallel molecular chain alignment forming nanofibers connected by inter‐ and intramolecular hydrogen bonds. These microfibers consist of nanofibers about 2‐5 nm in diameter, and about 300 nm long, embedded by protein matrices. Due to their unique dimensional, optical, mechanical, and other characteristics, the preparation of nano‐chitin materials is an important subject. It is possible to extract nano‐chitins from their sources with various methods, including acid hydrolysis, mechanical disintegration, TEMPO‐mediated oxidation, electrospinning, and others. In this article, the latest progress in recent years in the preparation and applications of nano‐chitin were reviewed. The morphology of the nano‐chitins obtained from the above methods was presented. The advantages and disadvantages of each method were analyzed. An overview of applications of nano‐chitins was discussed, including biomedicine, food applications, water treatment, green electronic materials, enzyme immobilization carriers, cotton textile materials, cosmetics, and others.

Self-Assembly of Linear and Cyclic Polylactide Stereoblock Copolymers with a Parallel and Antiparallel Chain Arrangement Distinguishing Their Directions on a Water Surface.

The self-assembly of molecules into a well-ordered structure is one of the most important processes in fabricating sophisticated materials. Here, we show that polymer chains can be self-assembled, distinguishing their direction (parallel or antiparallel), and could be a new useful scaffold for self-assembly in a controlled direction. The system that was used was a stereocomplex (SC) formation of linear and cyclic polylactide (PLA) stereoblock copolymers with a parallel and antiparallel chain arrangement in a Langmuir monolayer. The linear and cyclic stereoblock copolymers with a parallel arrangement formed a well-ordered lamellar SC in the first and second layers upon compression, but the linear and cyclic stereoblock copolymers with an antiparallel arrangement did not form a first-layer lamella and instead formed only the second-layer lamella. These results were only rationally explained by assuming that the enantiomeric PLA chains selectively assembled in a parallel direction, not in an antiparallel direction, in the SC. A simple polymer chain could be self-assembled, distinguishing the direction without a specific interaction group in it.

Crystal structure of tetra-methyl-ammonium 1,1,7,7-tetra-cyano-hepta-2,4,6-trienide.

The title compound, C4H12N+·C11H5N4 -, contains one tetra-methyl-ammonium cation and one 1,1,7,7-tetra-cyano-hepta-2,4,6-trienide anion in the asymmetric unit. The anion is in an all-trans conjugated C=C bonds conformation. Two terminal C(CN)2 di-nitrile moieties are slightly twisted from the polymethine main chain to which they are attached [C(CN)2/C5 dihedral angles = 6.1 (2) and 7.1 (1)°]. The C-C bond distances along the hepta-dienyl chain vary in the narrow range 1.382 (2)-1.394 (2) Å, thus indicating the significant degree of conjugation. In the crystal, the anions are linked into zigzag chains along the [10] direction by C-H⋯N(nitrile) short contacts. The anti-parallel chains stack along the [110] direction with alternating separations between the neighboring anions in stacks of 3.291 and 3.504 Å. The C-H⋯N short contacts and stacking inter-actions combine to link the anions into layers parallel to the (01) plane and separated by columns of tetra-methyl-ammonium cations.

Multicentered hydrogen bonding in 1-[(1-de-oxy-β-d-fructo-pyranos-1-yl)aza-nium-yl]cyclo-pentane-carboxyl-ate ('d-fructose-cyclo-leucine').

The title compound, C12H21NO7, (I), is conformationally unstable; the predominant form present in its solution is the β-pyran-ose form (74.3%), followed by the β- and α-furan-oses (12.1 and 10.2%, respectively), α-pyran-ose (3.4%), and traces of the acyclic carbohydrate tautomer. In the crystalline state, the carbohydrate part of (I) adopts the 2 C 5 β-pyran-ose conformation, and the amino acid portion exists as a zwitterion, with the side chain cyclo-pentane ring assuming the E 9 envelope conformation. All heteroatoms are involved in hydrogen bonding that forms a system of anti-parallel infinite chains of fused R 3 3(6) and R 3 3(8) rings. The mol-ecule features extensive intra-molecular hydrogen bonding, which is uniquely multicentered and involves the carboxyl-ate, ammonium and carbohydrate hy-droxy groups. In contrast, the contribution of inter-molecular O⋯H/H⋯O contacts to the Hirshfeld surface is relatively low (38.4%), as compared to structures of other d-fructose-amino acids. The 1H NMR data suggest a slow rotation around the C1-C2 bond in (I), indicating that the intra-molecular heteroatom contacts survive in aqueous solution of the mol-ecule as well.

Non-intertwined strands of plasmid DNA contradicts the Watson and Crick model of DNA structure

According to Watson and Crick (W/C) model, a DNA molecule consists of two antiparallel polynucleotide chains, intertwined with each other. Although the W/C model is accepted widely, a number of researchers have raised questions against it and proposed alternative structures for DNA. In the present study, the W/C model was examined using plasmid DNA. It was hypothesized that two strands of plasmid DNA will remain intertwined and not separate from each other under denaturing conditions, if it follows the W/C model. To test this, plasmid DNA was denatured using sodium hydroxide (NaOH) and analyzed by gel electrophoresis. It was observed that addition of NaOH to pUC19 and pBR322 plasmids resulted in new form of DNA with higher electrophoretic mobility in agarose gel. DNA corresponding to higher electrophoretic mobility band of pUC19 (hmP19) was single-stranded and circular, indicating the separation of two strands of pUC19 plasmid. Next, we examined whether hmP19 DNA can re-anneal to form native pUC19 plasmid. It was observed that neutralization of NaOH resulted in the appearance of native pUC19 plasmid in denatured DNA. Native pUC19 was also formed by hmP19 DNA extracted from agarose gel and was found to be digestible with Hind III. Ability to confer ampicillin resistance in transformed Escherichia coli demonstrated the functionality of pUC19 plasmid formed by extracted hmP19 DNA. Reversible separation of two strands of plasmid into single-stranded circular DNA shows that DNA strands are not intertwined with each other and contradicts the W/C model of DNA structure.

Exploring potentially alternative non-canonical DNA duplex structures through simulation

Hopkins proposed an alternative and chirally distinct family of double-stranded DNA (dsDNA) models that have antiparallel chains with 5′→3′ senses opposite to those of the right-handed Watson–Crick (WC) family. Termed configuration II, this family of dsDNA models contains both right-handed (II-R) and left-handed (II-L) forms, with Z-DNA as an example of the latter. Relative interstrand binding energies for six DNA duplex models, two each of configuration I-R (standard WC canonical B-DNA), II-R, and II-L for the duplex d(CGCGAATTCGCG), have been estimated under identical conditions using MM-PBSA analysis from molecular dynamics trajectories using three different AMBER force fields. These simulations support the stereo chemical soundness of configuration II dsDNA forms. Recent force fields (Barcelona Supercomputing Center [BSC] [bsc1] and Olomouc 2015 [OL15]) successfully render stable II-L structures, whereas the previous force field, bsc0, generated stable II-R structures, although with an energy difference between II-R and II-L of ∼30 kcal/mol.Communicated by Ramaswamy H. Sarma

Morphological Control Over Three‐ and Four‐Phase Superstructures in Blends of Asymmetric ABC and BAC Triblock Terpolymers

AbstractThe versatile and simple attainment of complex superstructures through binary blends of asymmetric polyisoprene‐block‐polystyrene‐block‐poly(methyl methacrylate) (ISM) and polystyrene‐block‐polyisoprene‐block‐poly(methyl methacrylate) (SIM) triblock terpolymers is shown. Different well‐ordered core–shell morphologies with three or four microphases as well as interchanged core‐ and shell‐forming blocks are achieved by different spatial superposition during mixing. Superstructures with three microphases are obtained by antiparallel chain orientation, when ISM and SIM chains align in opposite directions. Similarly, the respective PS, PI, and PMMA blocks are in direct superposition and mix into each other. In contrast, with parallel chain orientation, ISM and SIM chains align in the same direction. It gives rise to four microphases because here, both PI blocks do not assemble into one microdomain, but form two isolated microdomains. These observations are attributed to inverse molecular weight ratios between both blends.

Solvent and intermolecular nitrogen coordination dictated formation of self-assembled organostannane-macrocycles based on monomers and coordination polymers with unsymmetrical 5-[(E)-2-(4-pyridyl)-1-diazenyl]-2-hydroxybenzoate ligand: Structural topologies and dimensionality

A series of six new organotin(IV) compounds, namely, [nPr3Sn(HL)(MeOH)] 1, [nBu3Sn(HL)]n2, [Bz3Sn(HL)]n3, [Ph3Sn(HL)]n⋅nC6H64, [Ph3Sn(HL)(EtOH)] 5 and [nBu2Sn(L)]n6 were synthesized by reacting appropriate tri- and di-organotin(IV) precursors with the flexible pro-ligand 5-[(E)-2-(4-pyridyl)-1-diazenyl]-2-hydroxybenzoic acid. Their solid-state structures were deduced from single crystal X-ray diffraction data and, in the case of compound 6, also by solid-state 13C and 119Sn NMR spectroscopy. Compounds 1 and 5 are mononuclear as a consequence of methanol/ethanol coordination preventing the propagation of the polymers. The monodentate oxygen atom from the carboxylate group of HL− and the tin-coordinated oxygen atom of alcohol are situated at the axial positions, while Sn-R substituents are at the equatorial sites, defining the distorted trigonal-bipyramidal coordination polyhedron. Both 1 and 5 form one-dimensional (1D) chains created by virtue of O−Hsolv⋯Npy hydrogen bonding interactions, and antiparallel running chains in 1 furnish 34-membered dinuclear macrocyclic rings occupied by SnPr3 groups. Compounds 2–4 feature a one-dimensional coordination polymer facilitated by intermolecular N→Sn bond formation with the pyridyl substituent of LH−. The axially located OOCO and Npy donor atoms and equatorial Sn-R groups give rise to a trigonal-bipyramidal geometry. While similar coordination geometries are observed for 2–4, the tri-n-butyl derivative 2 generates 60-membered macrocyclic rings where four n-butyl groups from two neighboring molecules occupy the cavities. The triphenyltin analogue 4 forms two-dimensional layers with voids filled by benzene solvate molecules, and the sterically demanding tribenzyltin groups in compound 3 result in only relatively weak C−H⋯π, C−H⋯N and van der Waals contacts. On the other hand, compound 6 is a two-dimensional (2D) coordination polymer displaying a distorted pentagonal-bipyramidal geometry around the tin atom where four oxygen atoms of two ligand molecules and the nitrogen atom of a ligand constitute the equatorial plane, while the carbon atoms of the n-butyl groups complete the axial positions. The molecules of 6 self assembled to an interesting dimeric tecton based on a four-membered Sn2O2 ring, generating large 48-membered hexanuclear macrocycles, where the cavities are filled by four di-n-butyl groups from two neighboring molecules. The solution behaviors of compounds 1–5 were judged from the results of the 119Sn NMR spectroscopic characterization.

Double helix formation from non-natural amylose analog polysaccharides

Double helix formation from the non-natural anionic and cationic amylose analog polysaccharides (amylouronic acid and amylosamine, respectively) was achieved through electrostatic interactions. A water-insoluble complex was obtained by simply mixing the two polysaccharides in water. The 1H NMR analysis indicated that the formation of the complexes with an approximately equimolar unit ratio from the two polysaccharides was resulted regardless of feed ratios for mixing. The powder X-ray diffraction (XRD) measurement suggested that the helix had larger sizes both in diameter and pitch compared with well-known amylose double helix. The formation of the double helical structure was also examined by theoretical calculations. The double helix models, differing in a chain polarity and a charge state of the residues, were constructed based on the 6-fold left-handed amylose chain of the A-amylose crystal structure. Molecular dynamics calculations indicated that those with an antiparallel chain polarity retained an intertwined form. The antiparallel double helical model with the free form residues was suggested to be the most likely structure for the non-natural polysaccharides.

Characterization of the binding interactions between EvaGreen dye and dsDNA.

Understanding the dsDNA·EG binding interaction is important because the EvaGreen (EG) dye is increasingly used in real-time quantitative polymerase chain reaction, high resolution melting analysis, and routine quantification of DNA. In this work, a binding isotherm for the interactions of EG with duplex DNA (poly-dA17·poly-dT17) has been determined from the absorption and fluorescence spectra of the EG and dsDNA·EG complex. The isotherm has a sigmoidal shape and can be modeled with the Hill equation, indicating positive cooperativity for the binding interaction. A Scatchard plot of the binding data yields a concave-down curve in agreement with the Hill analysis of the binding isotherm for a positive cooperative binding interaction. Analysis of the Scatchard plot with the modified McGhee and von Hippel model for a finite one-dimensional homogeneous lattice and nonspecific binding of ligands to duplex DNA yields the intrinsic binding constant, the number of lattice sites occluded by a bound ligand, and the cooperativity parameter of 3.6 × 105 M-1, 4.0, and 8.1, respectively. The occluded site size of 4 indicates that moieties of the EG intercalate into the adjacent base pairs of the duplex DNA with a gap of 1 intercalation site between EG binding sites, as expected for a bifunctional molecule. Interestingly, at high [EG]/[base pair], the intercalation is disrupted. A model is proposed based on the fluorescence spectrum where the formation of anti-parallel stacked chains of EGs bound externally to the duplex DNA occur at these high ratios.