Double Helix Formation Research Articles

Favored CH-π interaction between enzymatically modified high amylose starch and resveratrol improves digestion resistance

Starch-stilbene polyphenol complexes, a novel form of resistant starch (RS), have received considerable attention due to their potential health benefits. To enhance the functionality of this type of complex, we examined the interactions between resveratrol (RA) and high-amylose starch with different molecular weights, achieved through enzymatic modification followed by high-pressure homogenization (HPH). We examined how these interactions affect the digestibility and ordered structures of the complexes. Our findings reveal that, notwithstanding the inhibition of double helix and B-type crystalline structure formation, RA-starch complexation markedly boosted single helix content, V-type crystalline structure formation, and aggregate structure density. These effects contributed notably to increased RS content. Interestingly, the formation of the V6-type crystalline structure within the complexes was primarily facilitated by the CH-π interaction between the aromatic rings of RA and the C–H of starch, rather than conventional hydrogen bonding and electrostatic forces. The strength of the CH-π interaction increased with higher amylose content and lower molecular weight of the starch, achievable through a 12-h pullulanase hydrolysis followed by a 2-h α-amylase hydrolysis. The resulting HPH-Pα2-RA complexes exhibited remarkable levels of the V-type crystalline structure and RS content, reaching up to 25.45% and 57.37%, respectively. Overall, this study offers valuable insights into the design of starch-polyphenols complexes with a high RS content.

Artwork


 
 
 As a learner, I’ve always been curious about the world around me, including a keen interest in how organisms function at a cellular level. This curiosity led to me developing a passion for the sciences. Not only that but as a curious individual I have always felt drawn to the sciences, a field where questions are always encouraged, hence the title of piece being “But, why?”. My passion for understanding the world at a cellular level made me want to study CPPS for my undergrad. Now, being in the second year of my degree I not only enjoy my classes but also appreciate the shift in perspective they have caused in how I view the world around me. This art piece is dedicated to the change in perspective I have experienced. Through my art piece, I try to use biological figures in imitation of the natural world to show that the things we learn are everywhere around us. For example, the DNA bridge is indicative of our genetic material being the backbone of who we are at the molecular level. Below the DNA bridge, I included the initials R.E.F as an homage to Rosalind E. Franklin whom I first learned about in grade 11 about not having received credit for her work in revealing the double helix formation of DNA. I drew the DNA so that it is unwinding closer to the end to show how there is still so much we have yet to discover and understand regarding its many complexities. I also included a body of water since it is crucial to many forms of life, and inside of it, I drew outlines of duplicating cells. Next to the water, is a phospholipid bilayer, something that has come up in my studies since high school as something simple yet crucial. The bacteriophages creeping towards the left are meant to contrast the bright and joyful imagery, to show how in sciences we learn about the interesting ways in which our bodies and environments are able to fend off potential dangers. However, these dangers are also important in the balance of life and the natural environment. The greenery framing the art piece is meant to represent the extracellular matrix, the various proteins that hold cells together. I tried to imitate this through my painting as crosslinked greenery. In the bottom right corner, I’ve also drawn myself looking up from reading a textbook as a way to show what it’s like to learn about such fascinating things and how it directly shifts my world view. Lastly, I drew this piece with a clear vanishing point as a metaphorical way of showing that our knowledge of the world and the study of science has gone through a journey and though our knowledge may have “dates of discovery” and points at which we began the studies of certain things, there is still no clear end to learning and everything we discover only leads to more questions which is definitely my favourite part about learning in my degree. Similar to the endless journey of the sciences, I look forward to where my own journey in this field will go.
 
 

Dispersion-driven formation of chiral twisted PAH double helices

Dispersion-driven formation of chiral twisted PAH double helices

Characterization of different high amylose starch granules. Part I: Multi-scale structures and relationships to thermal properties

The multi-scale structure and thermal properties of eight widely different types of high-amylose starches (HASs) having amylose contents (AC) in the range of 34.4%–97.3% originating from maize, wheat, barley, and potato were analyzed to unveil possible relationships among different levels of structures and thermal properties. The starches were found to cluster in four groups: (I) two HASs from maize, Gelose50 and Gelose80, with high gelatinization enthalpy (△H) and low onset (T0) and peak (Tp) gelatinization temperatures, (II) two HASs from potato and wheat, with medium and high △H and extremely low T0 and Tp, (III) two HASs from maize, NAFU50 and NAFU60, with medium △H and medium T0 and Tp, (IV) two HASs from maize and barley, Hylon VII and AOBS, with low △H but high T0 and Tp. The degree of molecular branching and the extent of the granule V-type crystalline polymorph were the critical factors determining their thermal properties, while botanical source and AC were not found important. HASs from wheat and barley showed relatively low lamellar and crystalline order, which was related to high content of amylopectin or AM-like chains with degree of polymerization (DP) 6–12 and long amylose chains, both of which can contribute to prevent the formation of double helices. Our data pinpoint the importance of amylopectin short chains, amylose long chains, and degree of branching on HAS starch granule structural order and thermal stability, which are potentially useful in boosting the development of HAS-based products and be beneficial for developing new HAS crops.

Modulation of the tetrameric I-motif folding of C-rich Tetrahymena telomeric sequences by hexitol nucleic acid (HNA) modifications

I-motifs are non-canonical DNA structures consisting of two parallel strands held together by hemiprotonated cytosine-cytosine+ base pairs, which intercalate to form a ordered column of stacked base pairs. This unique structure covers potential relevance in various fields, including gene regulation and biotechnological applications. A unique structural feature of I-motifs (iM), is the presence of sugar-sugar interactions through their extremely narrow minor grooves. Consistently, oligonucleotides containing pentose derivatives such as ribose, 2′-deoxyribose, arabinose, and 2′-deoxy-2′-fluoroarabinose highlighted a very different attitude to fold into iM. On the other hand, there is significant attention focused on exploring sugar-modifications that can increase nucleic acids resistance to nuclease degradation, a crucial requirement for therapeutic applications.An interesting example, not addressed in the iM field yet, is represented by hexitol nucleic acid (HNA), a metabolically stable six-membered ring analogue compatible with A-like double helix formation. Herein, we selected two DNA C-rich Tetrahymena telomeric sequences whose tetrameric iMs were already resolved by NMR and we investigated the iM folding of related HNA and RNA oligonucleotides by circular dichroism, differential scanning calorimetry and NMR. The comparison of their behaviours vs the DNA counterparts provided interesting insights into the influence of the sugar on iM folding. In particular, ribose and hexitol prevented iM formation. However, by clustering the hexitol-containing residues at the 3′-end, it was possible to modulate the distribution of the different topological species described for the DNA iMs. These data open new avenues for the exploitation of sugar modifications for I-motif characterization and applications.

Molecular origin of the two-step mechanism of gellan aggregation

Among hydrocolloids, gellan is one of the most studied polysaccharides due to its ability to form mechanically stable gels. Despite its long-standing use, the gellan aggregation mechanism is still not understood because of the lack of atomistic information. Here, we fill this gap by developing a new gellan force field. Our simulations offer the first microscopic overview of gellan aggregation, detecting the coil to single-helix transition at dilute conditions and the formation of higher-order aggregates at high concentration through a two-step process: first, the formation of double helices and then their assembly into superstructures. For both steps, we also assess the role of monovalent and divalent cations, complementing simulations with rheology and atomic force microscopy experiments and highlighting the leading role of divalent cations. These results pave the way for future use of gellan-based systems in a variety of applications, from food science to art restoration.

Insights into the textural properties and starch digestibility on rice noodles as affected by the addition of maize starch and rice starch

The effects of maize starch (MS) and rice starch (RS) addition on rice noodle quality were investigated, aiming to develop high-quality noodles with both desirable textural properties and low starch digestibility. The results showed that the MS had more short branch chains and higher branch density when compared to RS, and the final viscosity and gel strength of rice paste decreased with its addition. The textural properties between rice noodles with less than 20% MS and without MS did not differ significantly, while the network structure of rice noodles with more MS was significantly weakened due to the steric hindrance of short branch chains. The addition of RS increased the texture quality of rice noodles. Moreover, their addition reduced the estimated glycemic index of rice noodles, because more starch promoted the arrangement of starch chains and formed ordered double helix. The MS with more short chains was conducive to the formation of double helix to reduce digestion rate, and the RS with more long chains formed stabler gel and crystal structures to reduce digestible starch content. Therefore, MS and RS addition had potential to produce rice noodles with high comprehensive quality, and MS content should be controlled below 20%.

Molecular dynamics simulations and X-ray scattering show the κ-carrageenan disorder-to-order transition to be the formation of double-helices

Recent molecular dynamics simulations, verified experimentally by solution-state x-ray scattering experiments, have found that κ-carrageenan chains contain helical secondary structure, akin to that found in the solid-state, even in aqueous solution. Furthermore, upon the addition of ions to single chains the simulations found no evidence that any conformational transitions take place. These findings challenge the long-held assumption that the so-called disorder-to-order transition in carrageenan systems involves a uni-molecular ‘coil-to-helix transition’. Herein, the results of further molecular dynamics simulations undertaken using pairs of κ-carrageenan chains in 0.1 M NaI solutions are reported, and are validated experimentally using state-of-the-art solution-state WAXS experiments. From initially separated chains double-helices are shown to form, leading the authors to propose ‘two single helices-to-stabilized double-helix’ as a description of the molecular events taking place during the disorder-to-order transition.

Effect of Pullulanase Debranching Time Combined with Autoclaving on the Structural, Physicochemical Properties, and In Vitro Digestibility of Purple Sweet Potato Starch

The effects of pullulanase debranching combined with autoclaving (PDA) at various debranching times (0 h, 5 h, 10 h, 15 h, 20 h, and 25 h) and 121 °C/20 min of autoclave treatment on the structural and physicochemical characteristics of purple sweet potato (Jinshu No.17) starch were investigated. The results indicated that the native starch (NS) was polygonal, round, and bell-shaped with smooth surfaces. After debranching treatment, the surface of the starch samples became rough and irregular. The molecular weight became smaller after treatments. X-ray diffraction C-type pattern was transformed into a B-type structure in treated samples with increased relative crystallinity. 13C NMR indicated an increased propensity for double helix formation and new shift at C1, 3, 5 region compared to NS. The apparent amylose content was 21.53% in the NS. As the swelling power decreased, the percentage of soluble solids increased and different thermal properties were observed. A higher yield of the resistant starch (RS) was observed in all treated starch except PDA 25 h. The findings of our study reveal that a combination of pullulanase debranching time (15 h) and autoclaving (121 °C for 20 min) is a great technique that can be used to produce a higher amount of resistant starch in the Jinshu No.17 starch.

Hydrogen-bond-driven supramolecular helical assembly of a coumarin-substituted phthalonitrile derivative: synthesis and in vitro anticancer activity against colorectal adenocarcinoma.

Phthalonitrile derivatives are generally reported to crystallize in space groups P21/c and P1 in the literature. In this study, 7-hydroxy-4,8-dimethyl-3-pentylcoumarin (2) and its phthalonitrile derivative (2d) were crystallized; 2d crystallized in the rare trigonal space group R3. In the phthalonitrile derivative (2d), weak C-H...O hydrogen-bonding interactions promoted the formation of supramolecular double helices, and these supramolecular P and M double helices came together to form a honeycomb-like architectural motif involving one-dimensional tubular channels. In silico molecular-docking studies were performed to support the experimental processes and the results agree with each other. In vitro studies of compounds 2 and 2d were performed in LoVo colorectal adenocarcinoma and CCD18Co healthy human cell lines using flow cytometry. For compounds 2 and 2d, there was a statistically significant increase (p < 0.001) in both early and late apoptosis with respect to the control in a dose-dependent manner.

Bifurcated Halogen Bond-Driven Supramolecular Double Helices from 1,2-Dihalotetrafluorobenzene and 2,2′-Bi(1,8-naphthyridine)

The unique enantiomeric pairs of double helices have been found in the structure of the cocrystal between 1,2-diiodotetrafluorobenzene and 2,2′-bi(1,8-naphthyridine). The formation of the supramolecular double helices is driven by the strong bifurcated iodine bonds which can force the herringbone packing arrangement of the molecules 2,2′-bi(1,8-naphthyridine) into a face-to-face π···π stacking pattern. In contrast, the cocrystal between 1,2-dibromotetrafluorobenzene (or 1,2-dichlorotetrafluorobenzene) and 2,2′-bi(1,8-naphthyridine) was not obtained under the same conditions. The interaction energies of the bifurcated halogen bonds and π···π stacking interactions were computed with the reliable dispersion-corrected density functional theory. The computational results show that the bifurcated iodine bond is much stronger than the bifurcated bromine bond and bifurcated chlorine bond, and it is the much stronger bifurcated iodine bond that makes the cocrystal of 1,2-diiodotetrafluorobenzene and 2,2′-bi(1,8-naphthyridine) much easier to be synthesized.

Forming a Double-Helix Phase of Single Polymer Chains by the Cooperation between Local Structure and Nonlocal Attraction.

Double-helix structures, such as DNA, are formed in nature to realize many unique functions. Inspired by this, researchers are pursuing strategies to design such structures from polymers. A key question is whether the double helix can be formed from the self-folding of a single polymer chain without specific interactions. Here, using Langevin dynamics simulation and theoretical analysis, we find that a stable double-helix phase can be achieved by the self-folding of single semiflexible polymers as a result of the cooperation between local structure and nonlocal attraction. The critical temperature of double-helix formation approximately follows T^{cri}∼ln(k_{θ}) and T^{cri}∼ln(k_{τ}), where k_{θ} and k_{τ} are the polymer bending and torsion stiffness, respectively. Furthermore, the double helix can exhibit major and minor grooves due to symmetric break for better packing. Our results provide a novel guide to the experimental design of the double helix.

Thermal Input/Concentration Output Systems Processed by Chemical Reactions of Helicene Oligomers

This article describes thermal input/concentration output systems processed by chemical reactions. Various sophisticated thermal inputs can be converted into concentration outputs through the double-helix formation of helicene oligomers exhibiting thermal hysteresis. The inputs include high or low temperature, cooling or heating state, slow or fast cooling state, heating state, and cooling history. The chemical basis for the properties of the chemical reactions includes the reversibility out of chemical equilibrium, sigmoidal relationship and kinetics, bistability involving metastable states, positive feedback by self-catalytic chemical reactions, competitive chemical reactions, and fine tunability for parallel processing. The interfacing of concentration outputs in other systems is considered, and biological cells are considered to have been utilizing such input/output systems processed by chemical reactions.

Exploitation of a Half-Conjugate Polydentate Salamo-Salen Hybrid Ligand and Its Two Phenoxide-Bridged Heterohexanuclear 3d-s Double-Helical Cluster Complexes.

A half-conjugate polydentate Salamo-Salen hybrid ligand, H5L, containing two unique N2O2 pockets was first designed so that these metal ions in the complexes appear in different coordination modes. Two heterohexanuclear 3d-s double-helical cluster complexes, [Zn4Ca2L2(μ1-OAc)2(EtOH)2]·2EtOH (1; EtOH = ethanol) and [Zn4Sr2L2(μ2-OAc)2(MeOH)2]·2CH2Cl2 (2; MeOH = methanol), are reported that are formed through the reaction of H5L with zinc(II) and calcium(II) acetate or strontium(II) acetate, respectively. IR spectral analysis of the two complexes showed the existence of monodentate- and bidentate-coordinated acetate ions. The fluorescence properties of the ligand and its two heterohexanuclear complexes were explored in MeOH and water solutions, separately. In addition, theoretical calculations (density functional theory, interaction region indicator, and bond order) were performed to further understand the formation of a single-molecular double helix and the electron distribution characteristics of the two complexes.

Decoding the Structural Dynamics and Conformational Alternations of DNA Secondary Structures by Single-Molecule FRET Microspectroscopy.

In addition to the canonical double helix form, DNA is known to be extrapolated into several other secondary structural patterns involving themselves in inter- and intramolecular type hydrogen bonding. The secondary structures of nucleic acids go through several stages of multiple, complex, and interconvertible heterogeneous conformations. The journey of DNA through these conformers has significant importance and has been monitored thoroughly to establish qualitative and quantitative information about the transition between the unfolded, folded, misfolded, and partially folded states. During this structural interconversion, there always exist specific populations of intermediates, which are short-lived or sometimes even do not accumulate within a heterogeneous population and are challenging to characterize using conventional ensemble techniques. The single-molecule FRET(sm-FRET) microspectroscopic method has the advantages to overcome these limitations and monitors biological phenomena transpiring at a measurable high rate and balanced stochastically over time. Thus, tracing the time trajectory of a particular molecule enables direct measurement of the rate constant of each transition step, including the intermediates that are hidden in the ensemble level due to their low concentrations. This review is focused on the advantages of the employment of single-molecule Forster’s resonance energy transfer (sm-FRET), which is worthwhile to access the dynamic architecture and structural transition of various secondary structures that DNA adopts, without letting the donor of one molecule to cross-talk with the acceptor of any other. We have emphasized the studies performed to explore the states of folding and unfolding of several nucleic acid secondary structures, for example, the DNA hairpin, Holliday junction, G-quadruplex, and i-motif.

Temperature-insensitive silicone composites as ballistic witness materials: the impact of water content on the thermophysical properties.

In this work, different formulations of a room-temperature silicone composite backing material (SCBM) composed of polydimethylsiloxane (PDMS), fumed silica and corn starch were investigated using different characterization techniques, i.e., differential scanning calorimetry, thermogravimetry analysis, X-ray diffraction (XRD) and small-angle X-ray scattering, as a function of controlled relative humidity. At ambient relative humidities in the range of about 20-80%, the equilibrium water content in the SCBM ranges from approximately 4-10%, which is predominantly absorbed by the corn starch. This amount of water content has been shown to have minimal effect on thermal transition temperatures (melting and glass transition) of the SCBMs. The enthalpy of melting increases with increasing relative humidity, which reflects the heterogeneous semicrystalline structure of starch granules and the role of moisture in facilitating the formation of amylopectin double helices mainly in the imperfect crystalline regions. The thermal degradation of SCBM exhibits three major mass loss steps that correspond to dehydration, decomposition of corn starch and decomposition of PDMS. The XRD patterns reveal a characteristic diffuse peak for amorphous PDMS and an A-type crystallinity for the corn starch. The XRD results show no observable changes in the crystal type and crystallinity as a function of moisture content. Results from this work help clarify the fundamental structure-property relationships in SCBMs, which are important for future development of documentary standards, especially the handling and storage specifications of next-generation ballistic witness materials for body armor testing.

Thermal Hysteresis Involving Reversible Self-Catalytic Reactions.

Hysteresis is ubiquitous in nature and biology. It appears in ferromagnetism, ferroelectrism, traffic congestion, river sedimentation, electronics, thermoresponses, cell division, differentiation, and apoptosis. Hysteresis phenomena are beyond equilibrium and involve nonlinear, bistable, time delay, and memory events, which are described in input/output profiles by different outputs during continuous decreases and increases in input intensity. Although hysteresis profiles in these phenomena appear similar, the mechanisms underlying them are complex, and their basic understanding is desired. In this Account, I describe thermal hysteresis caused by molecules dispersed in dilute solutions containing optically active helicene oligomers, which form homo- and heterodouble helices, the cooling and heating processes of which cause different structural changes with regard to their relative concentrations. Reversible self-catalytic reactions are involved in the formation of a double helix, which catalyzes its own formation. The reactions accelerate as they progress, in contrast to ordinary reactions, which exhibit monotonic retardation as they progress. Thermal hysteresis involving reversible self-catalytic reactions exhibits notable phenomena, when various cooling/heating inputs are applied during the reaction; these phenomena are shown herein with profiles of experimental results of Δε outputs obtained by circular dichroism (CD) plotted against temperature inputs. Thermal hysteresis is discussed in terms of (1) two states of the homodouble helix and a random coil involving one reversible self-catalytic reaction and (2) three states of enantiomeric heterodouble helices and a random coil involving two reversible self-catalytic reactions. Repeated cooling and heating processes provide the same stable thermal hysteresis loops, when the initial and final high-temperature states are under equilibrium, and nonloop and unstable thermal hysteresis appears when whole the systems are beyond equilibrium. Diverse thermal hysteresis loops are obtained under different temperature change conditions for different oligomers. The mechanism of thermal hysteresis involves different macroscopic mechanisms at a fixed temperature, when the relative concentrations of substrates/products and the reaction direction differ. Microscopic mechanisms, which are shown by energy diagrams, are fixed at a temperature irrespective of cooling or heating. A comparison of thermal hysteresis loops and equilibrium curves provides distances to the metastable states on the loops from equilibrium, and reactions occur from the metastable states toward equilibrium. Notable phenomena described herein include bistability, high sensitivity to small concentration changes, equilibrium crossing, three-state one-directional structural change caused by a single heating procedure, reaction shortcuts, the memory effect on thermal history, figure-eight thermal hysteresis, chemical oscillation, stable and unstable thermal hysteresis, double-helix formation only under heating, and chiral symmetry breaking.

Conformational transitions and helical structures of a dipolar chain in external electric fields.

The conformational behavior of a single dipolar chain in a uniform electric field is investigated by molecular dynamics simulations. The dipolar chain is modeled as a backbone bead-on-spring chain of equally charged beads, each connected by a rigid spring with an oppositely charged side bead that can freely rotate around the backbone bead. In the strong coupling regime, when the dipolar chain is in the globular state due to a strong electrostatic correlational attraction, the application of an electric field causes the chain swelling and elongation along the field direction. In the weak coupling regime, a qualitatively new regime is found when the swollen dipolar chain shrinks along the field direction adopting flattened conformations due to the field-induced anisotropy of the chain rigidity and the head-to-tail attraction of the dipoles orienting along the field lines. A novel helical conformation is detected for low-polar media and strong electric fields. An increasing rigidity of the backbone chain leads to some stabilization of the helical conformation and the formation of double and triple helices as well as flat spread springs. Fine tuning of the interplay between dipolar and volume interactions by external electric fields induces re-orientation of rod-like dipolar chains in dilute solutions. The obtained results can provide new ways to control dipolar polymer conformations and design materials with responsive properties.

Deciphering molecular interaction and digestibility in retrogradation of amylopectin gel networks.

The impact of the internal part of aewx amylopectin on the gel network and digestibility during retrogradation was investigated using wx amylopectin as a reference. After β-amylolysis for 60 min (aewx-60), greater shifts in both λmax value and absorbance of iodine binding profiles were observed, accompanied by an increment of short chains (DP 3-5) with reducing the external long chains (DP 17.2). For the amylopectin gels aged 7 days at 4 °C, aewx had greater intermolecular aggregation of double helices to form junction zones, resulting in remarkably higher G', which was significantly greater than that of wx amylopectin or aewx-60. Moreover, aewx amylopectin had a greater RS accompanied by a reduction in RDS after retrogradation. The gel network models of retrograded amylopectins were built to interpret more molecular interactions for aewx than those of wx. The results revealed that aewx amylopectin with a higher proportion of longer external chains prompted the flexibility to align and interact for the formation of double helices and enzyme-resistant structures.

Controlling the chirality and number of strands of helices self-assembled from achiral block copolymers confined inside a nanopore: a simulation study.

Achiral block copolymers can self-assemble into helical structures when confined inside a cylindrical nanopore. However, controlling the chirality and the number of strands of helices is challenging. We present our simulation results of the influence of a chiral patch added to the confining nanopore on the structures and chirality of helices self-assembled from achiral cylinder-forming diblock copolymers under the confinement. Our results indicate that, when the designed patch is of proper geometry, it can induce the formation of helical structures and exhibit good control over their chirality. The bottom surface of the patch can induce the formation of a characteristic local structure near and parallel to it. It is the characteristic local structure that directs the formation of helices and of their chirality consistent with that of the patch. A large patch angle or the top/bottom surface of a weakly selective pore promotes the formation of double-helices compared to single-helices by enlarging the pitch of the helices near the patch or through the entropic attraction of the top surface of the pore to the minority blocks.