Probing the Structure and in Silico Stability of Cargo Loaded DNA Icosahedron using MD Simulations

Platonic solids such as polyhedra based on DNA have been deployed for multifarious applications such as RNAi delivery, biological targeting and bioimaging. All of these applications hinge on the capability of DNA polyhedra for molecular display with high spatial precision. Therefore high resolution structural models of such polyhedra are critical to widen their applications in both materials and biology. Here, we present an atomistic model of a well-characterized DNA icosahedron, with demonstrated versatile functionalities in biological systems. We study the structure and dynamics of this DNA icosahedron using fully atomistic molecular dynamics simulation in explicit water and ions. The major modes of internal motion have been identified using principal component analysis. We provide a quantitative estimate of the radius of gyration (Rg), solvent accessible surface area (SASA) and volume of the icosahedron which is essential to estimate its maximal cargo carrying capacity. Importantly, our simulation of gold nanoparticles (AuNP) encapsulated within DNA icosahedra revealed enhanced stability of the AuNP loaded DNA icosahedra compared to empty icosahedra. This is consistent with experimental results that show high yields of cargo-encapsulated DNA icosahedra that have led to its diverse applications for precision targeting. These studies reveal that the stabilizing interactions between the cargo and the DNA scaffold powerfully positions DNA polyhedra as targetable nanocapsules for payload delivery. These insights can be exploited for precise molecular display for diverse biological applications.Comment: 46 pages, 16 Figures and 3 Tables, Accepted for publication in Nanoscal

Structure of cholest-5-en-3β-oxy-5-bromopentane by single-crystal X-ray diffraction at 130 K

Cholest-5-en-3β-oxy-5-bromopentane (1) and cholest-5-en-3β-oxy-11-bromoundecane (2), key precursors for the synthesis of novel cationic amphiphiles based on cholesterol, have been synthesized and characterized by 1H-NMR spectroscopy and X-ray crystallography. Thermal disorder and effect of length of the bromoalkyl segment on the crystal structure have been investigated. Possible molecular level explanation of the unusual alternating s-trans-gauche conformation of the bromopentyl side chain of (1) has been presented

A DNA nanomachine that maps spatial and temporal pH changes inside living cells

DNA nanomachines are synthetic assemblies that switch between defined molecular conformations upon stimulation by external triggers. Previously, the performance of DNA devices has been limited to in vitro applications. Here we report the construction of a DNA nanomachine called the I-switch, which is triggered by protons and functions as a pH sensor based on fluorescence resonance energy transfer (FRET) inside living cells. It is an efficient reporter of pH from pH 5.5 to 6.8, with a high dynamic range between pH 5.8 and 7. To demonstrate its ability to function inside living cells we use the I-switch to map spatial and temporal pH changes associated with endosome maturation. The performance of our DNA nanodevices inside living systems illustrates the potential of DNA scaffolds responsive to more complex triggers in sensing, diagnostics and targeted therapies in living systems

Quantitative Mapping of Endosomal DNA Processing by Single Molecule Counting

Extracellular DNA is engulfed by innate immune cells and digested by endosomal DNase II to generate an immune response. Quantitative information on endosomal stage‐specific cargo processing is a critical parameter to predict and model the innate immune response. Biochemical assays quantify endosomal processing but lack organelle‐specific information, while fluorescence microscopy has provided the latter without the former. Herein, we report a single molecule counting method based on fluorescence imaging that quantitatively maps endosomal processing of cargo DNA in innate immune cells with organelle‐specific resolution. Our studies reveal that endosomal DNA degradation occurs mainly in lysosomes and is negligible in late endosomes. This method can be used to study cargo processing in diverse endocytic pathways and measure stage‐specific activity of processing factors in endosomes.Eine bildgebende Fluoreszenzmethode zur quantitativen Kartierung der endosomalen Prozessierung von Fracht‐DNA in Zellen des angeborenen Immunsystems mit Organellen‐spezifischer Auflösung (organellar single‐molecule, high‐resolution localization and counting; oSHiRLoC) wurde entwickelt. Mithilfe dieser Methode wurde gezeigt, dass die endosomale DNA‐Zersetzung hauptsächlich in Lysosomen erfolgt und in späten Endosomen zu vernachlässigen ist.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/148254/1/ange201811746_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/148254/2/ange201811746.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/148254/3/ange201811746-sup-0001-misc_information.pd

Structural DNA nanotechnology: from bases to bricks, from structure to function.

ABSTRACT The two fields of structural DNA nanotechnology and functional nucleic acids have been independently coevolving, with the former seeking to arrange and bring about movement of nucleic acid modules precisely and with control in space and the latter producing modules with incredible diversity in effective recognition and function. Here, we track the key developments in structural DNA nanotechnology that reveal a current trend that is seeing the integration of functional nucleic acid modules into their architectures to access a range of new functions. This contribution will seek to provide a perspective for the field of structural DNA nanotechnology where the integration of such functional modules on precisely controlled architectures can uncover phenomena of interest to physical chemists. D NA has proven to be a powerful material for construction on the nanoscale on the basis of the following properties: (i) the availability of automated synthetic methods and continually dropping costs, (ii) chemical robustness that confers stability on the resultant architectures and their subsequent ability to be functional under a variety of environmental conditions, (iii) the uniformly rodlike nature of the DNA double helix irrespective of its primary sequence, (iv) the specificity of Watson-Crick base pairing, which functions as an easily engineerable, site-specific, molecular-scale glue applicable to any DNA double helix, (v) the periodic nature of the DNA double helix and the predictable nature of sequence-specific thermal stability, both of which predispose it to computational methods to design and fabricate superarchitectures, (vi) the availability of well-characterized biochemical and molecular biological methods to cut, copy, and covalently link B-DNA double helices sequencespecifically, which allows manipulation of the construction material, (vii) the modular nature of the DNA scaffold that allows fabrication of architectures that are complex in terms of both structure and function when multiple modules are appended to each other, and (viii) single-stranded DNA sequences, called functional nucleic acids, which can fold and offer three-dimensional cavities suited to bind with great specificity a range of molecular entities with diverse function. In 1982, Ned Seeman proposed that DNA, which until then had been thought of as a linear polymer, could be used to make branched architectures by using stable artificial junctions with helical DNA limbs radiating from a central node. 1 These structures were analogous to metastable naturally occurring DNA motifs, such as the replication fork and Holliday junction. "It appears to be possible to generate covalently joined...networks of nucleic acids which are periodic in connectivity and perhaps in space." 1 This marked the origin of structural DNA nanotechnology that seeks to create defined architectures on the nanoscale using sequences of DNA that self-assemble into rigid rods that are, in turn, connected to form superarchitectures of precise dimensions. In 1999, it was shown that DNA could switch between two forms (the B-form and the Z-form), and this motion could be transduced along a DNA architecture, making it undergo a twisting motion. 2 Thus began a complementary aspect of structural DNA nanotechnology, of bringing about defined molecular-scale movements of DNA architectures triggered by the addition of input stimuli that are chemical, photonic, thermal, or electrical in nature. Functional nucleic acids are obtained from a test tube evolution method called SELEX independently conceptualized by the Szostak and Gold groups. 3,4 It uses molecular biology tools to pick out from a library of ∼10 15 different DNA (or RNA) sequences, a subset of sequences based on a given selection criterion and amplify them. 5 When subjected to the same selection criterion repeatedly with progressively higher stringencies, it is possible to progressively enrich from the library, a pool of DNA (or RNA) sequences with a specific functionality. If the selection criterion is the recognition of a target molecule, then selected single-stranded DNA (ssDNA) sequences are capable of binding to the target with high specificity and affinity. Thus, SELEX has yielded DNA sequences that can bind a huge variety of chemical entities ranging from small molecules to proteins, peptides, transition-stat

A mechanism of lysosomal calcium entry

Lysosomal calcium (Ca2+) release is critical to cell signaling and is mediated by well-known lysosomal Ca2+ channels. Yet, how lysosomes refill their Ca2+ remains hitherto undescribed. Here, from an RNA interference screen in Caenorhabditis elegans, we identify an evolutionarily conserved gene, lci-1, that facilitates lysosomal Ca2+ entry in C. elegans and mammalian cells. We found that its human homolog TMEM165, previously designated as a Ca2+/H+ exchanger, imports Ca2+ pH dependently into lysosomes. Using two-ion mapping and electrophysiology, we show that TMEM165, hereafter referred to as human LCI, acts as a proton-activated, lysosomal Ca2+ importer. Defects in lysosomal Ca2+ channels cause several neurodegenerative diseases, and knowledge of lysosomal Ca2+ importers may provide previously unidentified avenues to explore the physiology of Ca2+ channels

Tissue-specific targeting of DNA nanodevices in a multicellular living organism

Nucleic acid nanodevices present great potential as agents for logic-based therapeutic intervention as well as in basic biology. Often, however, the disease targets that need corrective action are localized in specific organs and thus realizing the full potential of DNA nanodevices also requires ways to target them to specific cell-types in vivo. Here we show that by exploiting either endogenous or synthetic receptor-ligand interactions and by leveraging the biological barriers presented by the organism, we can target extraneously introduced DNA nanodevices to specific cell types in C. elegans, with sub-cellular precision. The amenability of DNA nanostructures to tissue-specific targeting in vivo significantly expands their utility in biomedical applications and discovery biology

The PNA–DNA hybrid I-motif: implications for sugar–sugar contacts in i-motif tetramerization

We have created a hybrid i-motif composed of two DNA and two peptide nucleic acid (PNA) strands from an equimolar mixture of a C-rich DNA and analogous PNA sequence. Nano-electrospray ionization mass spectrometry confirmed the formation of a tetrameric species, composed of PNA–DNA heteroduplexes. Thermal denaturation and CD experiments revealed that the structure was held together by C-H(+)-C base pairs. High resolution NMR spectroscopy confirmed that PNA and DNA form a unique complex comprising five C-H(+)-C base pairs per heteroduplex. The imino protons are protected from D(2)O exchange suggesting intercalation of the heteroduplexes as seen in DNA(4) i-motifs. FRET established the relative DNA and PNA strand polarities in the hybrid. The DNA strands were arranged antiparallel with respect to one another. The same topology was observed for PNA strands. Fluorescence quenching revealed that both PNA–DNA parallel heteroduplexes are intercalated, such that both DNA strands occupy one of the narrow grooves. H1′–H1′ NOEs show that both heteroduplexes are fully intercalated and that both DNA strands are disposed towards a narrow groove, invoking sugar–sugar interactions as seen in DNA(4) i-motifs. The hybrid i-motif shows enhanced thermal stability, intermediate pH dependence and forms at relatively low concentrations making it an ideal nanoscale structural element for pH-based molecular switches. It also serves as a good model system to assess the contribution of sugar–sugar contacts in i-motif tetramerization

Do Gestational Obesity and Gestational Diabetes Have an Independent Effect on Neonatal Adiposity? Results of Mediation Analysis from a Cohort Study in South India.

PURPOSE: Neonates born to mothers with obesity or gestational diabetes mellitus (GDM) have an increased chance of various metabolic disorders later in life. In India, it is unclear whether maternal obesity or GDM is related to offspring adiposity. We aimed to understand the independent effect of maternal obesity and GDM with neonatal adiposity and whether GDM has a mediating effect between maternal obesity and neonatal adiposity. METHODS: We recruited a cohort of 1120 women (between April 2016 and February 2019) from the public hospitals in Bangalore, India, who voluntarily agreed to participate and provided written informed consent. The primary outcome was neonatal adiposity, defined as the sum of skinfold thickness >85th percentile. Exposure included maternal obesity, defined as >90th percentile of skinfold thickness. GDM, the potential mediator, was classified using the World Health Organization criteria by oral glucose tolerance test. Binary logistic regression was applied to test the effect of maternal obesity and GDM on neonatal adiposity, adjusting for potential confounders. We used Paramed command in STATA version 14 for analyzing mediating effects. RESULTS: We found that maternal obesity (odds ratio (OR)=2.16, 95% CI 1.46, 3.18) and GDM (OR=2.21, 95% CI1.38, 3.52) have an independent effect on neonatal adiposity. GDM significantly mediates 25.2% of the total effect between maternal obesity and neonatal adiposity, (natural direct effect OR = 1.16 95% CI 1.04, 1.30) with significant direct effect of maternal obesity (natural direct effect OR = 1.90 95% CI 1.16, 3.10) and significant total effect (OR=2.20 95% CI 1.35, 3.58). CONCLUSION: We showed that maternal obesity and GDM are independently associated with offspring adiposity. Also, GDM mediates the association of maternal obesity on adiposity in children. Interventions focused on obesity prevention in women, and effective screening and management of GDM may contribute to reducing childhood obesity in India