Double Helix Research Articles

Dynamics of Soliton Collision in DNA Double Helix

Dynamics of Soliton Collision in DNA Double Helix

Long-Axial-Range Double-Helix Point Spread Functions for 3D Volumetric Super-Resolution Imaging.

Single-molecule localization microscopy (SMLM) is a powerful tool for observing structures beyond the diffraction limit of light. Combining SMLM with engineered point spread functions (PSFs) enables 3D imaging over an extended axial range, as has been demonstrated for super-resolution imaging of various cellular structures. However, super-resolving structures in 3D in thick samples, such as whole mammalian cells, remains challenging as it typically requires acquisition and postprocessing stitching of multiple slices to cover the entire sample volume or more complex analysis of the data. Here, we demonstrate how the imaging and analysis workflows can be simplified by 3D single-molecule super-resolution imaging with long-axial-range double-helix (DH)-PSFs. First, we experimentally benchmark the localization precisions of short- and long-axial-range DH-PSFs at different signal-to-background ratios by imaging fluorescent beads. The performance of the DH-PSFs in terms of achievable resolution and imaging speed was then quantified for 3D single-molecule super-resolution imaging of mammalian cells by DNA-PAINT imaging of nuclear lamina protein lamin B1 in U-2 OS cells. Furthermore, we demonstrate how the use of a deep-learning-based algorithm allows the localization of dense emitters, drastically improving the achievable imaging speed and resolution. Our data demonstrate that using long-axial-range DH-PSFs offers stitching-free, 3D super-resolution imaging of whole mammalian cells, simplifying the experimental and analysis procedures for obtaining volumetric nanoscale structural information.

Structural basis of transcriptional regulation by UrtR in response to uric acid.

Uric acid (UA)-responsive transcriptional regulators (UrtRs), which belong to the multiple antibiotic resistance regulator (MarR) superfamily, transcriptionally coordinate virulence and metabolism in bacteria by modulating interactions with operator DNA in response to UA. To elucidate the transcriptional regulatory mechanism of UrtR, we structurally analyzed UrtR proteins, including PecS, MftR, and HucR, alone and in complex with UA or DNA. UrtR contains a dimerization domain (DD) and a winged helix-turn-helix domain (wHTHD) and forms a homodimer primarily via the DD, as observed for other MarR superfamily proteins. However, UrtRs are characterized by a unique N-terminal α-helix, which contributes to dimerization and UA recognition. In the absence of UA, the UrtR dimer symmetrically binds to the operator double-stranded DNA (dsDNA) by inserting its α4 recognition helix and β-stranded wing within the wHTHD into the major and minor grooves of dsDNA, respectively. Upon exposure to UA, UrtR accommodates UA in the intersubunit pocket between the DD and wHTHD. UA binding induces a conformational change in the major groove-binding core element of the UrtR wHTHD, generating a DNA binding-incompatible structure. This local allosteric mechanism of UrtR completely differs from that generally observed in other MarR superfamily members, in which the entire wHTHD undergoes effector-responsive global shifts.

Gentle Skepticism to the Degeneracy Nature of “First Genetic Code UUU”

This study reports our discoveries about the serious defects of the genetic topic “UUU’s degeneracy”, as • Matthaei-Nirenberg poly-U experiment in 1961 never mentioned the degeneracy nature of first genetic code UUU. • Ochoa’s experimental conclusion “3U:phe, 2U1C:phe” was lack of the chemical transforming process between “20 groups of 3 nucleotides (or 20 species of amino acids)” and “64 linear nucleotide triplets( or 64 times of amino acids frequency), the mathematical transformation of three consecutive nucleotides on Watson-Crick model of DNA from 64 linear triplets to 20 triangles (in Gamow’s observation of diamond code) could never be the chemical relations to make “20 species of amino acids” repeated to “64 times of amino acids” , and Ochoa’s UUU was neither a group of three U, nor linear triplet UUU. • Many concepts involved in UUU’s degeneracy seriously violates Matthaei-Nirenberg poly-U experiment in 1961. • In mathematics, the parameters array of (1:1, 1:1, 1:1, 1:1, 1:3, 1:3, 1:3, 1:3, 1:3, 1:3, 1:3, 1:3, 1:3, 1:3, 1:3, 1:3, 1:6, 1:6, 1:6, 1:6) is not only the “degeneracy value” of each triplet, but also the “expansion value” of each amino acid, therefore, each amino acid can be chosen to correspond any value of triplets in Gamow - Crick “coding” proposals. • Wobble Hypothesis only changes anticodon and doesn’t change the species of amino acids on tRNA. • In chemistry, Poly-(U,C) producing poly-phe in non-Nirenberg experiments serious violates Poly-U producing poly-phe in Matthaie-Nirenberg experiments. • No biochemists find the model protein in which the phenylalanine has only 2 shares, nor the total proportion among different amino acids are as “(1:1:2 :2,:2 :2:2 :2 :2 :2:2 :3:4 :4:4:4:4:6:6:6) “, and in which the model nucleic acid has 64 triplet (each triplet codon displays once in the model nucleic acids). In the end, we suggest to cancel the concept of UUU’s degeneracy, i.e.: “UUU degenerate to UUC” cannot be established in biochemical sciences.

Crystal structure of the HMGA AT-hook 1 domain bound to the minor groove of AT-rich DNA and inhibition by antikinetoplastid drugs

High mobility group (HMG) proteins are intrinsically disordered nuclear non-histone chromosomal proteins that play an essential role in many biological processes by regulating the expression of numerous genes in eukaryote cells. HMGA proteins contain three DNA binding motifs, the “AT-hooks”, that bind preferentially to AT-rich sequences in the minor groove of B-form DNA. Understanding the interactions of AT-hook domains with DNA is very relevant from a medical point of view because HMGA proteins are involved in different conditions including cancer and parasitic diseases. We present here the first crystal structure (1.40 Å resolution) of the HMGA AT-hook 1 domain, bound to the minor groove of AT-rich DNA. In contrast to AT-hook 3 which bends DNA and shows a larger minor groove widening, AT-hook 1 binds neighbouring DNA molecules and displays moderate widening of DNA upon binding. The binding affinity and thermodynamics of binding were studied in solution with surface plasmon resonance (SPR)-biosensor and isothermal titration calorimetry (ITC) experiments. AT-hook 1 forms an entropy-driven 2:1 complex with (TTAA)2-containing DNA with relatively slow kinetics of association/dissociation. We show that N-phenylbenzamide-derived antikinetoplastid compounds (1–3) bind strongly and specifically to the minor groove of AT-DNA and compete with AT-hook 1 for binding. The central core of the molecule is the basis for the observed sequence selectivity of these compounds. These findings provide clues regarding a possible mode of action of DNA minor groove binding compounds that are relevant to major neglected tropical diseases such as leishmaniasis and trypanosomiasis.

From Double-Stranded Helicates to Abiotic Double Helical Supramolecular Assemblies.

The folding of oligomeric strands is the method that nature has selected to generate ordered assemblies presenting spectacular functions. In the purpose to mimic these biomacro-molecules and extend their properties and functions, chemists make important efforts to prepare artificial secondary, tertiary, and even quarternary structures based on folded abiotic backbones. A large variety of oligomers and polymers, encoded with chemical informations, were designed, synthesized and characterized, and the establishment of non-covalent interactions lead to complex and functional supramolecular architectures resulting from a spontaneous self-assembly process. The association of comple-mentary molecular strands into double helical structures is a common structural pattern of nucleic acids and proteins, so the synthesis of bio-inspired double helices has emerged as an important subject. In recent years, a number of synthetic oligo-mers have been reported to form stable double helices and it was shown that the equilibrium between single and double helices can be controlled via different stimuli like the modification of the solvent or the temperature. This kind of structure presents highly interesting functions, such as molecular recognition within the cavity of double helices, and some other potential applications will emerge in the future.

Into the Groove: A Multitechnique Insight into the DNA–Vemurafenib Interaction

This study explores the interaction between Vemurafenib (VEM), a potent BRAF inhibitor, and calf thymus DNA (ctDNA) using a comprehensive array of biophysical and computational techniques. The primary objective is to understand the potential off-target effects of VEM on DNA, given its established role in melanoma therapy targeting the BRAF V600E mutation. The investigation employed methods such as ultraviolet–visible absorption spectroscopy, steady-state fluorescence, circular dichroism, isothermal titration calorimetry, and advanced molecular dynamics simulations. The results indicate that VEM interacts with DNA primarily through a minor groove-binding mechanism, causing minimal structural disruption to the DNA double helix. Viscosity measurements and melting temperature analyses further confirmed this non-intercalative mode of binding. Calorimetry data revealed an exothermic, thermodynamically favorable interaction between VEM and ctDNA, driven by both enthalpic and entropic factors. Finally, computer simulations identified the most probable binding site and mode of VEM within the minor groove of the nucleic acid, providing a molecular basis for the experimental findings.

Supramolecular structure and in vitro digestive properties of plasma-treated corn starches varying in amylose content

The effects of plasma treatment on the multi-scale structure and in vitro digestibility of maize starch with different amylose contents were systematically evaluated. The results demonstrated that all maize starches' molecular weights (MW) decreased when treated with plasma, among which the MW of waxy maize starch displayed the largest reduction. Plasma treatment led to an increase in the thickness of the semi-crystalline lamellae and double helix proportions of waxy and normal maize starches. However, high-amylose maize starch presented a less ordered structure by plasma treatment. Additionally, larger pores and channels were observed on the surface of plasma-treated waxy and normal maize starch granules. Moreover, deposits were displayed on the surface of high-amylose maize starch granules. These changes increased the in vitro digestibility and hydrolysis rate of three starches after plasma treatment. Notably, plasma treatment caused diverse alterations in the structure and functionality of maize starch varying in amylose content, leading to maize starch with better digestibility, therefore being used as an ingredient for functional foods.

Evolution of Peptidomimetics-Based Chiral Assemblies of β-Sheet, α-Helix, and Double Helix Involving Chalcogen Bonds.

Developing chiral assemblies that mimic biological secondary structures, e.g., protein β-sheet, α-helix, and DNA double helix, is a captivating goal in supramolecular chemistry. Here, we create a family of biomimetic chiral assemblies from alanine-based peptidomimetics, wherein the incorporation of N-terminal 2,1,3-benzoselenadiazole groups enables the rarely utilized chalcogen bonding as the adhesive interaction. While the alanine-based acylhydrazine molecule 1L was designed as a building unit with an extended conformation, simple derivatization of 1L affords folded unilateral N-amidothiourea 2L with one β-turn and bilateral N-amidothiourea 3L with two β-turns. This derivatization leads to the evolution of molecular assemblies from β-sheet organization (1L) to single helix (α-helix mimic, 2L) and ultimately to double helix (3L), illustrating an evolutionary route relating the structures and superstructures. In the case of the double helix formed by 3L, an unexpected cis-form that brings the two β-turns into one side was observed, stabilized via the π···π interaction between two N-terminal 2,1,3-benzoselenadiazole groups. This conformation allows double-crossed N-Se···S═C chalcogen bonds to support a DNA-like P-double helix featuring intrastrand noncovalent interactions and interstrand covalent linkages, surviving in both the solid state and in dilute acetonitrile solution phase.

Structural Aspects, Binding Interactions, Biological Activity of Co(II)‐ and Ni(II)‐N′‐(2‐fluorobenzoyl)benzo[d]thiazole‐2‐carbohydrazide Chelatess

ABSTRACTN′‐(2‐Fluorobenzoyl)benzo[d]thiazole‐2‐carbohydrazide (OFBBTCH, HL) and its chelates with Co(II) and Ni(II) have been synthesized and characterized by elemental analysis, liquid chromatography‐mass spectrometry (LC–MS), Fourier transform infrared spectroscopy (FT‐IR), ultra‐violet visible (UV–vis), nuclear magnetic resonance (NMR) spectroscopy, thermogravimetric analysis (TGA), and powder X‐ray diffraction. The conductance measurements reveal that the chelates are non‐electrolytic, and the spectral analysis indicates octahedral geometry of the chelates. The kinetic and thermodynamic parameters were obtained by Coats–Redfern relations, which shows positive Gibbs's free energy and negative entropy for both chelates. The equilibrium studies carried out by pH‐metry revealed the dissociation constant (pKa) of OFBBTCH as 8.13 and the formation of 1:1 and 1:2 Co(II)‐L and Ni(II)‐L complexes in solution. The CT‐DNA binding studies carried out by electron absorption, fluorescence quenching, steady state emissions and viscosity studies revealed hyperchromism and groove binding for HL and chelates. The Kb values calculated from electron absorption studies are 2.4 × 106, 4 × 106, and 9 × 106 M−1, from the fluorescence quenching studies Ksv values are 0.1722, 0.278, and 0.748 M−1, and Kapp values are 5.9 × 104, 1.3 × 105, and 2.9 × 105 M−1 for HL, Co(II)‐OFBBTCH and Ni(II)‐OFBBTCH, respectively. Bovine serum albumin (BSA) and human serum albumin (HSA) binding interactions were carried out by electron absorption and fluorescence quenching studies. The light switching properties of the chelates, the hydrolytic and oxidative cleavage of CT‐DNA, and the antioxidant properties were evaluated. Anti‐microbial studies carried out by pour plate method showed high activity for Ni(II)‐OFBBTCH chelate. Cytotoxicity of the compounds was performed for HeLa and MCF cell lines by MTT assay. Molecular docking studies revealed the docking of HL and Co(II)‐HL at the minor groove, and Ni(II)‐HL was docked at the major groove with hydrogen bonding.

Mirror-Image RNA: A Right-Handed Z-Form RNA and Its Ligand Complex

Until now, Z-form RNAs were believed to only adopt a left-handed double-helix structure. In this study, we describe the first observation of a right-handed Z-form RNA in NMR solution formed by L-nucleic acid RNA and present the first resolution of structure of the complex between a right-handed Z-form RNA and a curaxin ligand. These results provide a platform for the design of topology specific to Z-form-targeting compounds and are valuable for the development of new potent anticancer drugs.

Controlling the Depth of Hybridization Chain Reaction by Extended Dangling Ends and Its Analytical Applications.

Hybridization chain reaction (HCR) is a powerful enzyme-free nucleic acid amplification strategy. Triggered by an initiator strand, it yields nicked double helices analogous to alternating copolymers. However, there is no effective way to regulate the HCR reaction, and the most apparent phenomenon is the uncontrollable polymerization of product after introducing an initiator. Here we explore controlling the depth of the HCR reaction by extended dangling ends on hairpin monomers and report that sequence length, nucleotide composition, and secondary structure can alter HCR polymerization and can be utilized for the desired regulation. Interaction dynamics between initiator and hairpin monomers simulated by oxDNA are in good accordance with experimental results. Such a controlling effect can be utilized for new analytical applications that HCR cannot previously achieve, such as analyzing strand-extension enzymes and identifying short-sequence structures. The finding provides a concise but effective way for controlling the depth of HCR reaction and opens the application scope of HCR to more fields.

Analysis of Low-Frequency Sound Absorption Performance and Optimization of Structural Parameters for Acoustic Metamaterials for Spatial Double Helix Resonators

Low-frequency noise absorbers often require large structural dimensions, constraining their development in practical applications. In order to improve space utilization, an acoustic metamaterial with a spatial double helix, called a spatial double helix resonator (SDHR), is proposed in this paper. An analytical model of the spatial double-helix resonator is established and verified by numerical simulations and impedance tube experiments. By comparing the acoustic absorption coefficients of the spatial double-helix resonator, it is shown that the results of the analytical model, the numerical model, and the experiments are in good agreement, proving the accuracy of the theoretical model. The effects of different structural parameters on the peak sound absorption coefficient and resonance frequency are quantitatively revealed. The impedance variation law of the model is obtained, and the resistance and reactance distributions at the resonance frequency are analyzed. In the optimization model, the Back Propagation (BP) network is used to construct the mapping between the structural parameters and the resonance frequency and sound absorption coefficient, and this is used as the constraints of the equation, which is combined with Wild Horse Optimization (WHO) to establish the BP-WHO optimization model to minimize the volume of the spatial double helix resonator. The results show that, for a given noise frequency, the optimized structural parameters enhance the space utilization without affecting the performance of the space double helix resonator.

Single-Shot 3D Imaging Meta-Microscope.

Three-dimensional (3D) imaging enables high-precision and high-resolution axial positioning, which is crucial for biological imaging, semiconductor defect monitoring, and other applications. Conventional implementations rely on bulky optical elements or scanning mechanisms, resulting in low speed and complicated setups. Here, we generate the double-helix (DH) point spread function with an all-dielectric metasurface and thus innovate the 3D imaging microscope (hence dubbed meta-microscope), both in 4f and 2f imaging systems. The 4f-meta-microscope with a numerical aperture of 0.7 achieves an axial localization accuracy below 0.12 μm within a 15.47 μm detection range, while the 2f-DH meta-microscope with a numerical aperture of 0.3 shows a 1.12 μm accuracy within a 227.33 μm range. We also demonstrate single-shot and accurate 3D biological imaging of the mouse kidney tissue and peach anther, providing a comprehensive and efficient approach for 3D bioimaging and other applications through a single-shot 3D meta-microscope.

The third era of genomics is at risk of being dismantled across the global south.

The first era of genomics started with the publication of Watson and Crick's notable work on the description of the DNA double helix in 1953. This era lasted 50 years, until the publication of the human genome in April 2003. The second era is associated with the period between the completion of the human genome and the present day. I argue that, with the discontinuity caused by the COVID-19 pandemic and the spread and increased use of genomics to every corner of the world, we are entering a new, third era of genomics that provides major opportunities to advance the health of humans, animals, and the planet. However, this can only happen if the capacity that has greatly expanded in recent years is maintained and expanded further rather than left to atrophy, particularly across the global south.

Cobaltabis(dicarbollide) Interaction with DNA Resolved at the Atomic Scale.

Boron neutron capture therapy represents a promising avenue for cancer treatment that requires nontoxic drugs with a high boron content efficiently distributed into cancerous cells. The metallacarborane o-cobaltabis(dicarbollide) ([COSAN]-) fulfills these requirements and constitutes an attractive candidate. Nevertheless, the interaction of this promising drug with nucleic acids, the assumed target of the biological damage, is poorly understood since contradictory results are reported in the literature. This work establishes the DNA/[COSAN]- interaction strength, mechanism, and time scale at the atomistic level by using a combination of microsecond-molecular dynamics and hybrid quantum mechanics/molecular mechanics simulations and by quantifying the absolute binding free energy. Results show that the DNA/[COSAN]- interaction is highly dependent on the ionic strength of the medium. A relatively weak DNA major groove binding (ΔGbind= -2.49 kcal/mol) driven mostly by dihydrogen B-H···H-N bonding is observed in the simulations only at a high NaCl concentration, whereas DNA intercalation mode is deemed highly unlikely.

UVSSA facilitates transcription-coupled repair of DNA interstrand crosslinks

DNA interstrand crosslinks (ICLs) are covalent bonds between bases on opposing strands of the DNA helix which prevent DNA melting and subsequent DNA replication or RNA transcription. Here, we show that Ultraviolet Stimulated Scaffold Protein A (UVSSA) is critical for ICL repair in human cells, at least in part via the transcription coupled ICL repair (TC-ICR) pathway. Inactivation of UVSSA sensitizes human cells to ICL-inducing drugs, and delays ICL repair. UVSSA is required for replication-independent repair of a single ICL in a fluorescence-based reporter assay. UVSSA localizes to chromatin following ICL damage, and interacts with transcribing Pol II, CSA, CSB, and TFIIH. Specifically, UVSSA interaction with TFIIH is required for ICL repair and transcription inhibition blocks localization of transcription coupled repair factors to ICL damaged chromatin. Finally, UVSSA expression positively correlates with ICL-based chemotherapy resistance in human cancer cell lines. Our data strongly suggest that UVSSA is a novel ICL repair factor functioning in TC-ICR. These results provide further evidence that TC-ICR is a bona fide ICL repair mechanism that contributes to crosslinker drug resistance independently of replication-coupled ICL repair.

Current-driven mechanical motion of double stranded DNA results in structural instabilities and chiral-induced-spin-selectivity of electron transport.

Chiral-induced-spin-selectivity of electron transport and its interplay with DNA's mechanical motion are explored in a double stranded DNA helix with spin-orbit-coupling. The mechanical degree of freedom is treated as a stochastic classical variable experiencing fluctuations and dissipation induced by the environment as well as force exerted by nonequilibrium, current-carrying electrons. Electronic degrees of freedom are described quantum mechanically using nonequilibrium Green's functions. Nonequilibrium Green's functions are computed along the trajectory for the classical variable taking into account dynamical, velocity dependent corrections. This mixed quantum-classical approach enables calculations of time-dependent spin-resolved currents. We showed that the electronic force may significantly modify the classical potential, which, at sufficient voltage, creates a bistable potential with a considerable effect on electronic transport. The DNA's mechanical motion has a profound effect on spin transport; it results in chiral-induced spin selectivity, increasing spin polarization of the current by 9% and also resulting in temperature-dependent current voltage characteristics. We demonstrate that the current noise measurement provides an accessible experimental means to monitor the emergence of mechanical instability in DNA motion. The spin resolved current noise also provides important dynamical information about the interplay between vibrational and spin degrees of freedom in DNA.

Atomistic simulations of polysaccharide materials for insights into their crystal structure, nanostructure, and dissolution mechanism

AbstractCrystalline polysaccharides are abundant in nature and can be transformed into highly functional materials. However, the molecular basis for the formation of higher-order structures remains unclear. Computer simulation is an advanced tool for modeling macromolecular structures, and the atomistic simulations provide valuable information on the crystalline polysaccharides. Fiber deformation, crystalline transition, and novel nanostructures of cellulose were characterized through molecular dynamics simulations and density functional theory calculations of models of molecular chain sheets extracted from the crystal structure of the cellulose polymorphs. Extended ensemble molecular dynamics simulations were applied to analyze the artificial crystal structure of non-natural amylose analog polysaccharides, revealing the hexagonal packing of double helices through the self-assembly of molecular chains dispersed in aqueous solution. Dissolution simulations of the cellulose and chitin crystalline fibers revealed that the anions of ionic liquids, with their solvation power, played a key role in the cleavage of intermolecular hydrogen bonds in the crystal structure, whereas the cations contributed to irreversible molecular chain dispersion. The good correlation between the actual solubility of polysaccharides and the predicted number of intermolecular hydrogen bonds prompted the development of a platform that combined simulations and machine learning for high-throughput screening of solvents for cellulose and chitin.

First Principle Studies of Electronic Properties, Global Reactivity Descriptors, and Molecular Docking of Olivacine Drug

AbstractOlivacine, a semisynthetic isomer of ellipticine, belongs to the family of natural alkaloids; which possess analgesic, antibacterial, and antipyretic properties. It is a model anticancer drug acting as topoisomerase II inhibitor. The mechanism of action and antineoplastic properties of olivacine are ascribed to its intercalative binding into DNA helices. The present paper reports DFT investigation of the molecular structure, electronic properties, and global reactivity descriptors of the drug. Frontier orbitals (HOMO and LUMO) and MEP surface of the olivacine molecule have been examined. Furthermore, inhibition activity and binding sites of olivacine with kinase protein (PDB Id: 3OG7) have been explored by molecular docking technique. Results have been used to elucidate physico‐chemical aspects and preferred binding patterns of the olivacine drug.