Multimodal Interactions of Dopamine Hydrochloride with the Groove Region of DNA: A Key Factor in the Enhanced Stability of DNA

DNA tetrahedral nanocages as a promising nanocarrier for dopamine delivery in neurological disorders

Dopamine is a neurotransmitter in the central nervous system that is essential for many bodily and mental processes, and a lack of it can cause Parkinson's disease. DNA tetrahedral (TD) nanocages are promising in bio-nanotechnology, especially as a nanocarrier. TD is highly programmable, biocompatible, and capable of cell differentiation and proliferation. It also has tissue and blood-brain barrier permeability, making it a powerful tool that could overcome potential barriers in treating neurological disorders. In this study, we used DNA TD as a carrier for dopamine to cells and zebrafish embryos. We investigated the mechanism of complexation between TD and dopamine hydrochloride using gel electrophoresis, fluorescence and circular dichroism (CD) spectroscopy, atomic force microscopy (AFM), and molecular dynamic (MD) simulation tools. Further, we demonstrate that these dopamine-loaded DNA TD nanostructures enhanced cellular uptake and differentiation ability in SH-SY5Y neuroblastoma cells. Furthermore, we extended the study to zebrafish embryos as a model organism to examine survival and uptake. The research provides valuable insights into the complexation mechanism and cellular uptake of dopamine-loaded DNA tetrahedral nanostructures, paving the way for further advancements in nanomedicine for Parkinson's disease and other neurological disorders.

Mechanisms of ssDNA aptamer binding to Cd2+ in aqueous solution: A molecular dynamics study

ssDNA aptamers have been increasingly used to detect heavy metal ions as recognition elements due to their high affinity and specificity. However, the specific recognition and binding mechanisms between aptamers and most heavy metals were still unclear, which limits the development of aptamer-based detection methods. In this work, the interaction mechanisms of CD-2-1 aptamers with Cd2+ in aqueous solutions were investigated using molecular dynamic simulations. The most stable complex was found where Cd2+ binding at aptamer's stem-loop junction and preferred at the phosphate backbone or bases. Noteworthily, two binding modes of Cd2+ combining aptamer in aqueous solution were discovered: direct and indirect. In the former mode, Cd2+ directly coordinated O atoms of bases. For the latter, Cd2+ connected to bases with coordinated water molecules as bridges. Electrostatic interaction was found to be the main driving force, and differences of residues role between two binding modes were elucidated. Buffer molecules in aqueous solutions can stabilize aptamer-Cd2+ complex by hydrogen bonds. This study revealed the specific interaction mechanisms of aptamer with Cd2+ at an atomic level, which provided theoretical references for aptamer-based Cd2+ detection methods establishment as well as an efficient technical route of screening potential aptamers for heavy metal ions.

Protonation State of Dopamine Neurotransmitter at the Aqueous Interface: Vibrational Sum Frequency Generation Spectroscopy Study

Dopamine is an important amine-based chemical neurotransmitter whose protonated state plays a crucial role in the recognition process. Understanding the structure and protonated state of dopamine at the aqueous interface is desired as the diffusion as well as binding of dopamine with the receptors take place frequently in the aqueous interface region. Vibrational sum frequency generation (VSFG) study of the OH stretch of water at the air/water interface in the presence of dopamine is performed and compared with its analog, phenylethylamine, and catechol. The VSFG data suggest that, unlike the bulk case, the population of the deprotonated amine group of dopamine is higher at the aqueous interface. This study suggests that the structure of dopamine at the aqueous interface is different from the bulk which may be useful in understanding the recognition process of dopamine in the interfacial region.

Influence of a Polyneurotransmitter on DNA-Mediated Förster-Based Resonance Energy Transfer: A Path Leading to White Light Generation

The physiologically important biomolecule, dopamine (DA), shows strong self-oxidation and aggregation behaviors, which have been controlled and modulated to result in fluorescent polydopamine (F-PDA) nanoparticles. On the other hand, the simultaneous binding of two diverse deoxyribonucleic acid (DNA) binding probes, 4',6-diamidino-2-phenylindole dihydrochloride (DAPI) and ethidium bromide (EtBr), has been elaborately established to follow the Förster-based resonance energy transfer (FRET) pathway. The comparative understanding of this DNA-mediated FRET in three media, phosphate buffer saline (PBS) of pH 7.4, DA, and F-PDA, has concluded that the FRET efficiency in the three media follows the order: PBS > DA > F-PDA. This controlled FRET in the fluorescent F-PDA matrix serves a pivotal role for efficient white light (WL) generation with excellent Commission Internationale de l'Eclairage (CIE) parameters that match well with that of pure WL emission. The obtained WL emission has been shown to be very specific with respect to concentrations of different participating components and the excitation wavelength of the illuminating source. Furthermore, the optical properties of the WL emitting solution have been observed to be retained excellently inside the well-known agarose gel matrix. Finally, the mechanistic pathway behind such a FRET-based WL generation has been established in detail, and to the best of our knowledge, the current study offers the first and only report that discloses the influence of a fluorescent polyneurotransmitter matrix for successful generation of WL emission.

Polydopamine aggregation: A novel strategy for power-free readout of loop-mediated isothermal amplification integrated into a paper device for multiplex pathogens detection

Loop-mediated isothermal amplification (LAMP) has been widely used for detecting pathogens. However, power-free and clear visualization of results still remain challenging. In this study, we developed a paper device integrated with power-free DNA detection strategy realized by polydopamine aggregation. In the presence of DNA amplicons, the polymerization of dopamine into aggregated polydopamine was hindered, while in the absence of DNA amplicons, polydopamine aggregation is facilitated. The porosity of the paper enabled the capillary flow of dispersed polydopamine for positive sample, while aggregated polydopamine remained at the bottom of the paper strip due to large size of the aggregates for negative sample. Based on this mechanism, we fabricated a slidable paper device integrating LAMP with dopamine polymerization for the naked-eye detection, operated in a seamless manner. Moreover, the introduced paper device was successfully used to detect DNA extracted from Escherichia coli O157:H7 and SARS-CoV-2 within 25 min, as well as Enterococcus faecium within 35 min. The detection limits of both Escherichia coli O157:H7 and SARS-CoV-2 were 10^-4 ng/μL. The introduced paper device can be used as a simple and sensitive tool for detecting multiple infectious pathogens, making it an ideal tool particularly for resource-limited environment.

Restructuring of Membrane Water and Phospholipids in Direct Interaction of Neurotransmitters with Model Membranes Associated with Synaptic Signaling: Interface-Selective Vibrational Sum Frequency Generation Study

Comprehensive molecular-level understanding of the role of interfacial water and phospholipids associated with synaptic membranes during their direct interaction with neurotransmitters is essential because of their involvement in synaptic signaling. Herein, the interfacial regions of the synaptic membranes mimicking anionic and zwitterionic phospholipids are probed in the presence of dopamine and serotonin neurotransmitters using surface-specific vibrational sum frequency generation technique. Neurotransmitters intrude into the headgroup region of both zwitterionic and anionic lipids by restructuring the interfacial water associated with the phospholipids, although the restructuring mechanism is different for both lipids. Neurotransmitters also decrease the overall ordering of both the phospholipids probably by creating gauche defects. Neurotransmitters restructure the surface water, conformation, and the ordering of the hydrocarbon chains of the zwitterionic and anionic phospholipids associated with synaptic membranes, which could be potentially an important step for synaptic signaling.

Sequence specific hydrogen bond of DNA with denaturants affects its stability: Spectroscopic and simulation studies

BACKGROUND

Several different small molecules have been used to target the DNA helix in order to treat the diseases caused by its mutation. Guanidinium(Gdm⁺) and urea based drugs have been used for the diseases related to central nervous system, also as the anti-inflammatory and chemotherapeutic agent. However, the role of Gdm⁺ and urea in the stabilization/destabilization of DNA is not well understood.

METHODS

Spectroscopic techniques along with molecular dynamics (MD) simulation have been performed on different sequences of DNA in the presence of guanidinium chloride (GdmCl) and urea to decode the binding of denaturants with DNA and the role of hydrogen bond with the different regions of DNA in its stability/destability.

RESULTS AND CONCLUSION

Our study reveals that, Gdm⁺ of GdmCl and urea both intrudes into the groove region of DNA along with the interaction with its phosphate backbone. However, interaction of Gdm⁺ and urea with the nucleobases in the groove region is different. Gdm⁺ forms the intra-strand hydrogen bond with the central region of the both sequences of DNA whereas inter-strand hydrogen bond along with water assisted hydrogen bond takes place in the case of urea. The intra-strand hydrogen bond formation capability of Gdm⁺ with the nucleobases in the minor groove of DNA decreases its groove width which probably causes the stabilization of B-DNA in GdmCl. In contrast, the propensity of the formation of inter-strand hydrogen bond of urea with the nucleobases in the groove region of DNA without affecting the groove width destabilizes B-DNA as compared to GdmCl. This study depicts that the opposite effect of GdmCl and urea on the stability is a general property of B-DNA. However, the extent of stabilization/destabilization of DNA in Gdm⁺ and urea depend on its sequence probably due to the difference in the intra/inter-strand hydrogen bonding with different bases present in both the sequences of DNA.

GENERAL SIGNIFICANCE

The information obtained from this study will be useful for the designing of Gdm⁺ based drug molecule which can target the DNA more specifically and selectively.

Hydrogen bonding of ionic liquids in the groove region of DNA controls the extent of its stabilization: synthesis, spectroscopic and simulation studies

Ionic liquids (ILs) have been extensively used for stabilization and long-term DNA storage. However, molecular level understanding of the role of the hydrogen bond of DNA with ILs in its stabilization is still inadequate. Two ILs, namely, 1,1,3,3-tetramethylguanidinium acetate (TMG) and 2,2-diethyl-1,1,3,3-tetramethylguanidinium acetate (DETMG), have been synthesized, of which TMG has a hydrogen bonding N-H group whereas DETMG does not contain any hydrogen bonding site. It has been found that both TMG and DETMG cations interact in the groove region of DNA; however, their mode of interaction is distinctly different, which causes the stabilization of DNA in the presence of TMG, whereas the effect is opposite in the case of DETMG. It is apparent from the data that only the accommodation of ILs in the groove region is not enough for the stabilization of DNA. MD simulation and spectroscopic studies combinedly indicate that the hydrogen bonding capability of the TMG cation enhances the hydrogen bonding between the Watson-Crick base pairs of DNA, resulting in its stabilization. In contrast, the bigger size as well as the absence of the hydrogen bonding site of the DETMG cation perturbs the minor groove width and base pair step parameters of DNA during its intrusion into the minor groove, which decreases the hydrogen bond between the Watson-Crick base pairs of DNA, leading to destabilization.