Double Helix Research Articles

Effects of chlorogenic acid on the physicochemical properties, 3D printing characteristics, and anti-digestive properties of sweet potato starch.

This study investigated the effects of different concentrations chlorogenic acid (CA) (0.5 %-2.0 %) on the printing accuracy, micro-structure, rheological properties, thermodynamic properties, texture, digestion characteristics, and other indicators of sweet potato starch (SPS). Results showed that the printed SPS products with 0.5 % CA exhibited the best structural recovery properties and printing accuracy, with a thixotropic recovery rate of 98.37 %. The addition of CA significantly increased the gelatinization enthalpy of SPS and free water content, The SPS gel with 2.0 % CA exhibited the poorest water-binding ability with a free water content of 3.49 %. SPS with higher levels of CA displayed less lamellar structure denser network structure, and more thickened pore walls. The printed SPS product with 2.0 % CA had the lowest hardness (173.64 g), elasticity (0.74), adhesiveness (89.24), and chewiness (65.93). The content of double helix structure in SPS with 0.5 %-1.5 % CA was significantly lower than that in the starch without CA. All the addition proportions of CA significantly increased the relative crystallinity of SPS, and the SPS with 2 % CA had the highest relative crystallinity (19.96 %). Additionally, CA significantly enhanced the antioxidant ability of printed SPS products. All the levels of CA significantly reduced the RDS content and increased the RS content in the printed SPS products. The RS content in SPS with 2.0 % CA increased by 25.44 %, compared with SPS alone. Therefore, this study provides a theoretical basis for the development of polyphenol-enriched 3D-printed SPS diets for the populations with hyperglycemia and obesity.

Physicochemical, structural properties, and in vitro digestibility of starches isolated from Amorphophallus konjac K. Koch and Amorphophallus dunnii: A comparison study.

This study compared the physicochemical and structural properties, and in vitro digestibility of Amorphophallus konjac K. Koch starch (AKS) and Amorphophallus dunnii starch (ADS), by using potato starch (PS) as a control. ADS exhibited larger granule sizes, which led to higher transparency, swelling power (SP), and water solubility than AKS. Both AKS and ADS exhibited A-type crystalline patterns; however, ADS demonstrated higher relative crystallinity, gelatinization transition temperatures, and enthalpies of gelatinization, which may be due to higher 1047/1022 and more double helix contents. Regarding rheological and pasting properties, ADS exhibited greater viscosity than that of AKS, likely due to larger particle size and higher SP. In vitro digestion analysis revealed that >50 % of each starch type consisted of rapidly digestible starch. Notably, ADS contained the highest amount of resistant starch among the three types. The estimated glycemic index (eGI) values of AKS and ADS were 65.54 ± 0.54 and 63.28 ± 0.36, respectively, indicating that both starch types belong to the medium GI food category, though AKS was significantly higher than ADS. These findings suggest that konjac starch serves as a beneficial dietary carbohydrate alternative. AKS may be suited for fast-digesting food formulas for individuals with digestive impairment, whereas ADS could be advantageous for those managing diabetes.

Binding of Homeodomain Proteins to DNA with Hoogsteen Base Pair.

In DNA double helices, Hoogsteen (HG) base pairing is an alternative mode of Watson-Crick (WC) base pairing. HG bp has a different hydrogen bonding pattern than WC bp. We investigate here the binding energy of homeodomain proteins with a HG-DNA duplex, where DNA adopts a HG bp in its sequence. We observe that the presence of the HG bp increases the binding energy of both the specific and nonspecific homeodomain proteins compared to WC-DNA bps. The neutral mutation in the N-terminal basic arm of the nonspecific protein significantly changes the binding energy between nonspecific protein and HG-DNA only, while the acidic mutation significantly changes the binding energy of both the specific and nonspecific proteins with HG-DNA. The significant variation in the binding energy of the homeodomains within distinct DNA-protein complexes can be ascribed to the differences in the number of intermolecular contacts between DNA bases and protein residues. Our conformational thermodynamics calculations based on the fluctuation of microscopic conformational variables at the interface show that with increasing conformational stability and order at the interface, the binding of the homeodomain protein gets stronger.

A Novel Aggregation-Induced Emission-Based Electrochemiluminescence Aptamer Sensor Utilizing Red-Emissive Sulfur Quantum Dots for Rapid and Sensitive Malathion Detection.

Rapid, effective, and cost-effective methods for large-scale screening of pesticide residues in the environment and agricultural products are important for assessing potential environmental risks and safeguarding human health. Here, we constructed a novel aggregation-induced emission (AIE) electrochemical aptamer (Apt) sensor based on red-emissive sulfur quantum dots (SQDs), which aimed at the rapid screening and quantitative detection of malathion. SQDs were prepared using a two-step oxidation method with good electrochemiluminescence (ECL) optical properties. These SQDs were modified onto the electrode surface to serve as ECL luminophores. Subsequently, Apt was introduced and modified to form a double-helix structure with the complementary chain (cDNA). The ECL signal was reduced because the biomolecules had poor electrical conductivity and inefficient electron transfer. When the target malathion was added, the double helix structure was unraveled, the malathion Apt fell off the electrode surface, and the ECL signal was restored. The linear range of detection was 1.0 × 10-13-1.0 × 10-8 mol·L-1, and the detection limit was 0.219 fM. The successful preparation of the sensor not only develops the ECL optical properties of SQDs but also expands the application of SQDs in ECL sensing.

Insights into interaction of quaternary ammonium salt cationic surfactants with different branched-chain lengths and DNA: Multi-spectral analysis, viscosity method, and gel electrophoresis.

In this study, the interactions between three quaternary ammonium salt (QAS) cationic surfactants with different branched-chain lengths (TMBAC, TEBAC, and TBBAC) and DNA are investigated by UV-vis absorption, fluorescence and CD spectroscopy, viscosity method, and gel electrophoresis. Berberine hydrochloride (BR) is utilized as a fluorescent probe. The three interaction modes and strengths are compared. The effects of surfactant concentrations, ratio of DNA and BR, and ionic strength on the interaction are estimated. DNA conformational changes are explored. The results indicate that three surfactants can interact with DNA through electrostatic interaction rather than groove and intercalation binding. The interaction results in DNA double helix compression. Also, interaction strength is TBBAC-DNA > TEBAC-DNA > TMBAC-DNA due to different branched-chain lengths. Moreover, fluorescence quenching extent is more obvious at 10.0:1.0 mol ratio (DNA: BR). The fluorescence quenching of three surfactant-DNA-BR systems is static. Three binding models are equal, and three interaction processes are spontaneous. The binding force of TBBAC-DNA is electrostatic, while that of TMBAC-DNA and TEBAC-DNA is Van der Waals forces and hydrogen bonding. Besides, DNA conformation keeps the B-form. It is expected to offer insights into the interaction of QAS cationic surfactants with different branched-chain lengths and DNA.

Calcium Alginate Encapsulation of Rice Starch, Instead of a Physical Mixture of Both, Regulates the Fermentation Rate and Production of Acetate

ABSTRACTCalcium alginate–encapsulated rice starch (AES) could be potentially applied as a rice analog with a significantly improved amount of resistant starch, while its effects on gut microbiota remain less clear. To this end, structural characteristics of AES and their impact on gut microbiota, fermentation rate, and short‐chain fatty acid (SCFA) production were examined using an in vitro batch fermentation method. Cooked AES showed a significantly higher amount of intermolecular interactions (∼46 times), short‐range double helices, and degree of crystallinity compared to the simple mixture of rice starch and calcium alginate (Mix), resulting in a more homogenous and densely packed network microstructure. As a result, AES, instead of Mix, showed a significantly slower gas production rate (∼17%), while relatively higher production of SCFAs, especially the ratio of acetate. Bifidobacterium pesudocatenulatum was possibly responsible for the higher production of acetate in AES. Collectively, these results show that AES has the potential to be used as a slowly fermentable carbohydrate, favoring the production of acetate in the human colon.

Efficient and Rapid Enrichment of Extracellular Vesicles Using DNA Nanotechnology-Enabled Synthetic Nano-Glue.

Swift and efficient enrichment and isolation of extracellular vesicles (EVs) are crucial for enhancing precise disease diagnostics and therapeutic strategies, as well as elucidating the complex biological roles of EVs. Conventional methods of isolating EVs are often marred by lengthy and laborious processes. In this study, we introduce an innovative approach to enrich and isolate EVs by leveraging the capabilities of DNA nanotechnology. We have developed a novel multivalent cholesterol-modified paranemic crossover DNA (PX-DNA-chol) construct, which is a four-stranded DNA structure containing adjacent double helices intertwined with their local helix axes parallel and serves as an effective synthetic nano-glue. This construct promotes the rapid coalescence of nanoscale EVs into clusters of micrometer scale, thereby streamlining their enrichment. Utilizing a conventional low-speed centrifuge, this intriguing methodology achieves a rapid concentration of EVs within minutes, bypassing the laborious and high-speed centrifugation steps typically required. The quality of EVs isolated by our technique is comparable to that obtained through ultracentrifugation methods. Given these advancements, our PX-DNA-chol-facilitated EVs enrichment protocol is poised to advance the field of EVs research, providing a robust and accessible tool for in-depth studies of EVs.

Double-Helix Electrode Ion Funnel: A New Ion Funnel Design with an Extended Mass Range.

The development of an atmospheric pressure interface (API) with a high ion transfer efficiency and wide mass range is advantageous for the performance improvement of mass spectrometry (MS) instruments. In this work, a novel ion guide, namely, the double-helix electrode ion funnel (DHE-IF), has been developed to enhance the ion transmission over a wide mass range in the rough vacuum region. The DHE-IF consists of two funnel-shaped helix electrodes. There are almost no potential "traps" along the central axis of DHE-IF due to the continuous double-helix electrode structure compared to the stacked ring ion funnel. The electrode design of the DHE-IF assembly was guided by ion trajectory simulations. After being fabricated, DHE-IF was integrated into an ESI-TOF-MS platform for tests. A conventional stacked ring ion funnel (IF) was also tested for comparison. The experimental results showed that DHE-IF extended the transmission window of the IF and improved the efficiency of the simultaneous transferring of low and medium m/z ions. In addition, the intensities of caffeine ions (m/z = 195) and reserpine ions (m/z = 609) were enhanced by more than 50% and 10%, respectively. These values were compared with the results obtained by the IF. The DHE-IF is expected to be widely used as an ion import device in MS instruments, which is due to its improved performance and advantages in, e.g., integration and power supply design.

Carbonless DNA.

Carbonless DNA was designed by replacing all carbon atoms in the standard DNA building blocks with boron and nitrogen, ensuring isoelectronicity. Electronic structure quantum chemistry methods (DFT(ωB97XD)/aug-cc-pVDZ) were employed to study both the individual building blocks and the larger carbon-free DNA fragments. The reliability of the results was validated by comparing selected structures and binding energies using more accurate methods such as MP2, CCSD, and SAPT2+3(CCD)δMP2. Carbonless analogs of DNA components, including cytosine, thymine, guanine, adenine, and deoxyribose, were investigated, showing strong resemblance to the carbon-based versions in terms of spatial structure, polarity, and molecular interaction capabilities. Complementary base pairs of the carbonless analogs exhibited a similar number and length of hydrogen bonds as those found in their carbon-containing counterparts, with binding energies for A-T and G-C analogs remaining comparable. Carbonless DNA fragments containing two and six base pairs were studied, revealing double-helix structures analogous to natural DNA. Structural parameters such as fragment size, hydrogen bond lengths, and rise per base pair were consistent with those observed in unmodified DNA. Docking simulations with a 12 base pair fragment and netropsin as a ligand indicated a slight shift in binding preference for the carbonless DNA through the minor groove, with an approximate 25% increase in binding affinity compared to natural DNA.

Divergent evolution of opposite base specificity and single-stranded DNA activity in animal and plant AP endonucleases.

Apurinic/apyrimidinic (AP) endonucleases are key enzymes responsible for the repair of base-less nucleotides generated by spontaneous hydrolysis or as DNA repair intermediates. APE1, the major human AP endonuclease, is a druggable target in cancer and its biological function has been extensively studied. However, the molecular features responsible for its substrate specificity are poorly understood. We show here that, in contrast to APE1, its Arabidopsis ortholog ARP (apurinic endonuclease-redox protein) exhibits orphan base-dependent activity on double-stranded DNA and very poor AP cleavage capacity on single-stranded DNA (ssDNA). We found that these differences are largely a consequence of the variation at two DNA intercalating amino acids that have undergone divergent changes in the metazoan and plant lineages. Swapping the identity of the residue invading the minor groove is sufficient to switch the orphan base specificities of APE1 and ARP. The affinity for ssDNA is largely determined by the major groove invading residue, and swapping its identity switches the ability of APE1 and ARP to cleave AP sites in ssDNA. Importantly, we show that the critical residue for ssDNA cleavage is crucial for mammalian APE1 function in antibody class switch recombination, suggesting an evolutionary advantage for ssDNA activity. These findings provide new molecular insights into the evolution of AP endonucleases.

Chiral Nanostructures from Artificial Helical Polymers: Recent Advances in Synthesis, Regulation, and Functions.

Helical structures such as right-handed double helix for DNA and left-handed α-helix for proteins in biological systems are inherently chiral. Importantly, chirality at the nanoscopic level plays a vital role in their macroscopic chiral functionalities. In order to mimic the structures and functions of natural chiral nanoarchitectures, a variety of chiral nanostructures obtained from artificial helical polymers are prepared, which can be directly observed by atomic force microscopy (AFM), scanning tunneling microscopy (STM), scanning electron microscopy (SEM), and transmission electron microscopy (TEM). This review mainly focuses on the formation of chiral nanostructures and the morphology regulation triggered by polymer chain length, concentration, solvent, temperature, photoirradiation, and chemical additives. In addition, the distinct chiral functions including chiral recognition, circularly polarized luminescence, drug release, cell imaging, and antibiosis are also discussed.

Photoresponsive Helical Foldamers: Conformational Control Through Double Helix Formation and Light-Induced Protonation.

Helical foldamers constitute particularly relevant targets in the field of host-guest chemistry, be that as hosts or substrates. In this context, the strategies reported so far to control the dimensions and shape of foldamers mainly involve modifications of the skeleton through covalent synthesis. Herein, we prepared an oligopyridine dicarboxamide foldamer substituted by photo-active tetraphenylethylene units (TPE). We demonstrate that it is possible to toggle the length of a helical foldamer by two means. First, the elongation of foldamers can be tuned by adjusting the concentration, as demonstrated by DOSY NMR spectroscopy and X-ray diffraction analyses on both the single and the double helix structures. Secondly, and in a more original manner, a photo-induced protonation process triggered by TPE units promotes a novel pathway to unfold helical foldamers, leading to dramatic conformational and spectroscopic changes.

Identification and characterization of shifted G•U wobble pairs resulting from alternative protonation of RNA.

RNA can serve as an enzyme, small molecule sensor, and vaccine, and it may have been a conduit for the origin of life. Despite these profound functions, RNA is thought to have quite limited molecular diversity. A pressing question, therefore, is whether RNA can adopt novel molecular states that enhance its function. Covalent modifications of RNA have been demonstrated to augment biological function, but much less is known about non-covalent alterations such as novel protonated or tautomeric forms. Conventionally, a G•U wobble has the U shifted into the major groove. We used a cheminformatic approach to identify four structural families of shifted G•U wobbles in which the G instead resides in the major groove of RNA, which requires alternative tautomeric states of either base, or an anionic state of the U. We provide experimental support for these shifted G•U wobbles via the potent, and unconventional, in vivo reactivity of the U with dimethylsulfate (DMS) in three organisms. These shifted wobbles may play important functional roles and could serve as drug targets. Our cheminformatics approach is general and can be applied to identify alternative protonation states in other RNA motifs, as well as in DNA and proteins.

Low background electrochemical sensor based on HCR towards acute myocardial infarction-specific miRNA detection.

Acute myocardial infarction (AMI) accounts for a significant proportion of global fatalities, and early detection is crucial for improving patient outcomes. However, current diagnostic methods often struggle to detect AMI in its early stages. Herein, we present an electrochemical sensor utilizing a fractal gold (FracAu) electrode and hybridization chain reaction (HCR) amplification technology to detect AMI-specific microRNAs (miRNAs). When the target sequence was added, the HCR was triggered, leading to the formation of a long-nicked DNA double helix that efficiently captured a larger quantity of positively charged RuHex molecules, resulting in significant electrochemical signal amplification. More importantly, to avoid false positive signals, exonuclease I (Exo I) was introduced to selectively cleave single-stranded DNA (ssDNA) probes. These ssDNA probes, underwent random hydrolysis from hpDNA probes, could hybridize with helper DNA1 in the absence of the target, initiating the HCR process and producing a false positive signal. The inclusion of Exo I effectively avoided false positive signals and reduced background noise. Under optimized conditions, the fabricated sensor exhibited significant sensitivity and selectivity, showing a broad linear detection range from 10 pM to 10 nM and a low limit of 0.9 fM. The fabricated electrochemical sensor also successfully detected AMI-specific miRNA in real serum samples, underscoring its diagnostic promise. By providing a reliable tool for early detection, the innovative sensor holds significant potential in combating global cardiovascular disease-related mortality rates.

Mechanism of dsDNA binding, enzyme inhibition, antioxidant activities, and molecular docking studies of taxifolin, daidzein, and S-equol.

This study investigated the binding mechanism of taxifolin (TA), daidzein (DA), and S-equol (SQ) flavonoids with fish sperm double helix DNA (dsDNA) under the simulated physiological pH condition using UV-Vis and photoluminescence spectroscopy, as well as viscometric methods. Binding constants (Kb) for the flavonoids to dsDNA were determined as 1.8 × 104 M-1 for SQ, 1.6 × 104 M-1 for DA and 1.7 × 104 M-1 for TA, indicating moderate affinity. The groove binding mode was confirmed by competitive binding studies with ethidium bromide or rhodamine B, UV-Vis spectrophotometry and viscosity evaluation. Additionally, the compounds showed high cholinesterase (ChE) inhibitory activity, with TA being the most potent, particularly against BChE (IC₅₀ = 2.93 μM) and AChE (IC₅₀ = 6.42 μM). Antioxidant activities were also evaluated using DPPH and ABTS assays, with TA showing the lowest IC₅₀ values. Additionally, molecular docking studies were performed to assess the interactions and binding affinities of all compounds with AChE and BChE enzymes. As a result, the studied compounds were found to prefer minor groove binding. This research analyzed the contribution of the structure-activities of natural flavones in terms of their biological properties, which is important for their future application against diseases.

Effect of (-)-epigallocatechin gallate palmitate complexation under mild temperature on the structure and nutritional functions of porous rice starch.

The correlation among the hierarchical structure, physicochemical properties, and nutritional functions of porous rice starch after absorbing and complexing with (-)-epigallocatechin gallate palmitate (P-EGCG) under mild temperatures at different reaction times were investigated. The P-EGCG loading rate (19.6%-28.5%) of porous starch increased after hydrolysis with a mixture of amyloglucosidase and α-amylase for 3 and 6h, respectively. A decrease in the melting enthalpy of the amylopectin double helix and an increase in the melting enthalpy of the V-type helices after complexation was observed with longer reaction times. The retention index of P-EGCG after 6h of incubation was 57.11% following 21 d of storage. These structural changes significantly transformed portions of the rapidly and slowly digestible starches into resistant starch (41.68%-47.84%), accompanied by enhanced thermal stability, antioxidant activity, and enteropathogenic bacteria-inhibiting ability. Therefore, porous rice starch complexed with P-EGCG may provide controlled digestion, antioxidant activity, and potential gut microbiota benefits.

Double helix rotating TENGs driven by ultra-low loading for harvesting high-entropy water flow energy

Water flow energy in rivers and lakes is a huge clean energy source and widely distributed in nature. Its low water velocity makes it difficult for electromagnetic generators to effectively harvest this energy. Therefore, harvesting high-entropy water flow energy is of great significance to the development of distributed power supply and sensing. In this study, we present a double helix rotating triboelectric nanogenerator (DHR-TENG) that can effectively convert the ultra-low water flow energy into electrical energy. DHR-TENG is designed to optimize space utilization and has a reciprocating transmission mechanism to ensure the continuous operation, achieving a surprisingly high charge density of 356.69 μC⋅m-3 and peak power density of 11.66 W⋅m-3. Compared with similar structures reported by predecessors, the maximum elevation is about 242 times and 2 times, respectively. A stable electrical output performance was achieved by DHR-TENG at ultra-low water flow velocity of 0.4∼0.8 m/s, the harvested energy can drive self-powered temperature sensor systems and wireless signal transmission systems. This work not only effectively improves the electrical output performance at ultra-low water flow velocity, but also helps to promote environmental monitoring and provides a feasible method for establishing early warning in the environment.

Effects of extrusion temperature on structure and physicochemical properties of proso millet starch.

Due to its thermal stability, and high viscosity, proso millet starch has limited practical applications. Extrusion can alter the functional properties of starch by pre-gelatinization, but the specific effects of extrusion temperature on starch behavior are not clear. In this study, proso millet starch was modified using extrusion at varying temperatures (70°C, 90°C, 110°C), and its structure as well as physicochemical properties were evaluated. As the extrusion temperature increased, the starch granules were gelatinized, and the particle size increased significantly. The relative crystallinity of extruded starch decreased and the short-range order was enhanced notably, but the starch still exhibited an A-type structure. Starch chains degraded, migrated, and aggregated, showing an increase in the double helix content, but there was no difference in the single helix structure with temperature. With the increase of extrusion temperature, the amorphous layer of extruded starch thickened. Moreover, the peak viscosity, breakdown viscosity and setback viscosity initially increased and then decreased, the peak temperature and enthalpy change increased. The water absorption index, water solubility and swelling power significantly decreased with increasing temperatures. The freeze-thaw stability and transparency of extruded starch decreased, and showed a downward trend with prolonged time. The above results indicate that extrusion treatment effectively modifies the thermal stability and viscosity of proso millet starch, laying a foundation for applying it different industrial applications.

Autoclaved Starch: Structure and Functionality Relationship in a Matrix With the Same Contribution ofAmylose and Amylopectin.

The rational use of autoclaved starches in food applications is difficult because there is a lack of information on their structure-functionality relationship. The novelty of this research relies on disclosing such an association. Hylon V starch was autoclaved at 105, 120, and 135°C to investigate its crystalline and double-helical features and its relationship with functionality. In autoclaved Hylon V starch, interactions of amylopectin and amylose improved while the crystalline regions decreased. The degree of double helices (DD) decreased after autoclaving at 105°C and the degree of order (DO) increased after treatment at 120 and 135°C. The water solubility index (WSI) (4.63-6.38%) and swelling power (SP) (4.39-7.1 g/g) increased when the temperature increased. On the other hand, water (103.49-225.01%) and oil (61.91-94.53%) holding capacity (WHC and OHC, respectively) increased after autoclaving treatment, although the values decreased with the treatment intensity. The functional properties were affected when the structure changed as a function of the treatment temperatures. PCA analysis showed that WSI and SP of autoclaved Hylon V starch were associated with a high DD, with better compaction, and with stronger amylopectin-amylose interactions. WHC and OHC were associated with better crystallinity, stronger interactions of amylopectin and amylose, and heterogeneous double-helical crystallites. These findings are useful for understanding the structure-functionality relationship of autoclaved Hylon V starch and pave the way for future research regarding the effects of its incorporation on the properties of food matrices such as bread, yogurt, cakes, and pudding.

Fish collagen mediated alteration of wheat starch thermal properties during multi-species co-fermentation.

This study explores the impact of multi-species co-fermentation on the thermal properties of wheat starch, emphasizing the innovative use of fish collagen as an additive. The effects of adding different levels of fish collagen (0%, 3%, 6%, 9%, 12%, and 15%) on the thermal properties of starch were investigated during co-fermentation with Lactobacillus plantarum and Saccharomyces cerevisiae. Utilizing analytical techniques such as X-ray diffraction (XRD) and Fourier transform infrared spectroscopy (FT-IR), we observed a significant increase in the degree of order from 1.32 to 1.55 and a notable decrease in double helix formation from 1.51 to 0.80 (p<0.05). The introduction of collagen induced the aggregation of B-starch granules, forming aggregates approximately 16μm in diameter. Meanwhile, collagen addition shifted the peak thermal impact by +0.91°C and elevated the maximum mass loss rate temperature from 309.33°C to 317.09°C (p<0.05). Furthermore, a decrease in peak viscosity from 4321 cp to 3123 cp and final viscosity from 4143 cp to 3171 cp (p<0.05), along with a 3°C increase in pasting temperature. The results suggest that fish collagen is a potential quality improver for traditional fermented starch-based foods.