Sticky Ends Research Articles

An Indian diagnostic laboratory case report on mosaic chromosome 18

<p class="abstract">Distal 18q deletion syndrome, and ring chromosome 18 are structural abnormalities involving chromosome 18. Distal or terminal deletion event is characterized by deletion of a region from the terminal end of a chromosome, while in ring chromosome, the telomeric ends of both the arms of homologous chromosomes are lost, causing the sticky ends to fuse together to form a ring. Clinical findings vary in each case depending on the type of abnormality, and the region of chromosome affected. This case report focuses on the chromosome 18 abnormality detected in the proband tested with the clinical indication of cleft lip, congenital anomaly, and feeding difficulty. Parental karyotyping to rule out de-novo or abnormality due to inheritance, clinical correlation, genetic counseling and high resolution microarray was recommended.</p>

Treatment of Wilms’ nephroblastoma cancer cells via EGFR targeting of dactinomycin loaded DNA-nanowires

Dactinomycin (DCTM) is a highly cytotoxic hydrophobic drug requiring robust nanomaterials for uniformed water dispersion and safe delivery to tumor site avoiding exposure to healthy cells. DNA triangulation produces sturdier two-dimensional nanostructures through the polymerization of DNA-triangles by sticky ends cohesion in the form of DNA-nanosheets. The curvature of the B-form (right twisted) DNA causes the coiling of the DNA-nanosheets into DNA-nanowires (D-NWs) structures. DNA-triangles scaffolded by the short circular templates (84-NT) are stiffer in topology giving rise to compact D-NWs for DCTM loading, and cellular delivery. The PAGE gel analysis was performed to assess the polymerization of the DNA-triangles to observe restricted electrophoretic mobility, and attainment of a single sharp band. The morphology and compactness of the D-NWs were confirmed by the AFM analysis and confocal imaging. Epidermal growth factor (EGF) functionalization of the D-NWs was performed through amide chemistry using amino-modified DNA strands reacting with the carboxylic group of EGF for EGFR targeting. EGFR is highly expressed on NB-OK-1 Wilms’ tumor nephroblastoma cancer cells. DCTM loading onto D-NWs was carried out through intercalation between the base pairs of GC rich DNA duplex by physical mixing/incubation, and was confirmed through the UV peak shift analysis and confocal imaging. Cell internalizations and the cytotoxic effects were monitored via confocal imaging, MTT assay, and flow cytometry. AFM images of the synthesized D-NWs showed that polymerization of DNA-triangles was successful with the length ranging from 4 to 6 µm, and width ranging from 80 to 120 nm. EGF functionalization was confirmed through the confocal microscopy after labeling EGF with the FITC hook conjugating dye. The slight UV shift (> 15 nm) confirmed DCTM loading onto D-NWs. Blank D-NWs showed biocompatibility to the cells at different (low to high) concentrations (10 µM to 640 µM). MTT assay revealed that DCTM loaded D-NWs showed a dose-dependent (0.25–128 nM) decrease in cell viability. EGF functionalized D-NWs effectively targeted the EGFR rich NB-OK-1 cancer cells compared to the control HEK293/D75 cells lacking EGFR (receptors). By these results, we can expect similar site-specific targeted treatment if administered systemically.

DNA bioelectric field: a futuristic bioelectric marker of cancer, aging and death – A working hypothesis

Telomeres are associated with the ends of DNA double strands. The lengths of the telomeres are controlled by the telomerase enzyme. The shortening of the telomeres is known to relate to aging. In cancers, telomere lengths are abnormally short. Telomeres could act as buffers shielding the part of DNA coding for the proteins. For cancer cells, germ cells and stem cells the length of the telomeres is not varying. There is an analogy with microtubules, which are highly dynamical and carry a longitudinal electric field, whose strength correlates with the microtubule length. Could sticky ends generate a longitudinal field along DNA double strand with strength determined by the lengths of the sticky ends? In the standard picture the flux of the longitudinal electric field would be proportional to the difference of the negative charges associated with the sticky ends. In TGD framework, DNA strands are accompanied by the dark analog of DNA with codons realized as 3-proton units at magnetic flux tubes parallel to DNA strands and neutralizing the negative charge of ordinary DNA except at the sticky ends. This allows considering the possibility that opposite sticky ends carry opposite charges generating a longitudinal electric field along the magnetic flux tube associated with the system. DNA/Telomere bioelectric field could serve as a novel bioelectric marker to be used for prognostic and diagnostic purposes in researches of cancer, aging, surgery grafts and rejuvenation. We propsed that DNA bioelectric field can be used as a futuristic bioelectric marker of cancer, aging and death.

Sensitive detection of p53 DNA based on spatially confined fluorescence resonance energy transfer and multivalent assembly of branched DNA.

A key challenge for the discrete distribution-based Förster resonance energy transfer system (D-FRET) is the reduced intensity and stability of signal probes in complex biological matrices. Here, we present a spatially confined FRET (SC-FRET) probe with a stable structure and strong signal output. It consists of multivalent FRET pairs labeled with FAM or TAMRA. In this assay, p53 DNA was chosen as a model hairpin probe (HP), and two kinds of branched DNA probes (ssDNA-FAM, ssDNA-TAMRA) were involved. Under the action of p53 DNA, the unfolded HP acts as a primer to initiate polymerization extension of KFP polymerase and cleavage of Nb.BbvCI endonuclease, which produces plenty of ssDNA (primer-DNA). The branched DNA is designed to have the same binding core and different sticky ends, the core part of which can self-assemble to form X-shaped branched DNA (X-FAM or X-TAMRA), and the sticky ends of which are complementary to the primer-DNA. Therefore, the primer-DNAs released during the polymerization cleavage process will combine a large number of X-FAM and X-TAMRA in a limited space through complementary base pairing. Fluorescence was transferred from FAM to TAMRA, and a strong FRET response was generated by the locational effects. The proposed SC-FRET system based on the multivalent assembly of branched DNA exhibited a strong FRET response with an LOD of 0.01394 pM. Importantly, it also showed a high-contrast and stable FRET response in HeLa cells. Its superior biological stability is attributed to the large steric hindrance of the compact and rigid frame of the SC-FRET probe, which helps prevent intracellular degradation and provides a powerful tool for biomedical research.

The flexibility-based modulation of DNA nanostar phase separation.

Phase separation of biomolecules plays key roles in physiological compartmentalization as well as pathological aggregation. A deeper understanding of biomolecular phase separation requires dissection of a relation between intermolecular interactions and resulting phase behaviors. DNA nanostars, multivalent DNA assemblies of which sticky ends define attractive interactions, represent an ideal system to probe this fundamental relation governing phase separation processes. Here, we use DNA nanostars to systematically study how structural flexibility exhibited by interacting species impacts their phase behaviors. We design multiple nanostars with a varying degree of flexibility using single-stranded gaps of different lengths in the arm of each nanostar unit. We find that structural flexibility drastically alters the phase diagram of DNA nanostars in such a way that the phase separation of more flexible structures is strongly inhibited. This result is not due to self-inhibition from the loss of valency but rather ascribed to a generic flexibility-driven change in the thermodynamics of the system. Our work provides not only potential regulatory mechanisms cells may exploit to dynamically control intracellular phase separation but also a route to build synthetic systems of which assembly can be controlled in a signal dependent manner.

Demonstration of elementary functions via DNA algorithmic self-assembly.

Target-oriented cellular automata with computation are the primary challenge in the field of DNA algorithmic self-assembly in connection with specific rules. We investigate the feasibility of using the principle of cellular automata for mathematical subjects by using specific logic gates that can be implemented into DNA building blocks. Here, we connect the following five representative elementary functions: (i) enumeration of multiples of 2, 3, and 4 (demonstrated via R094, R062, and R190 in 3-input/1-output logic rules); (ii) the remainder of 0 and 1 (R132); (iii) powers of 2 (R129); (iv) ceiling function for n/2 and n/4 (R152 and R144); and (v) analogous pattern of annihilation (R184) to DNA algorithmic patterns formed by specific rules. After designing the abstract building blocks and simulating the generation of algorithmic lattices, we conducted an experiment as follows: designing of DNA tiles with specific sticky ends, construction of DNA lattices via a two-step annealing method, and verification of expected algorithmic patterns on a given DNA lattice using an atomic force microscope (AFM). We observed representative patterns, such as horizontal and diagonal stripes and embedded triangles, on the given algorithmic lattices. The average error rates of individual rules are in the range of 8.8% (R184) to 11.9% (R062), and the average error rate for all the rules was 10.6%. Interpretation of elementary functions demonstrated through DNA algorithmic patterns could be extended to more complicated functions, which may lead to new insights for achieving the final answers of functions with experimentally obtained patterns.

Reconfigurable Transitions between One- and Two-Dimensional Structures with Bifunctional DNA-Coated Janus Colloids.

Coating colloidal particles with DNA provides one of the most versatile and powerful methods for controlling colloidal self-assembly. Previous studies have shown how combining DNA coatings with DNA strand displacement allows one to design phase transitions between different three-dimensional crystal structures. Here we show that by using DNA coatings with bifunctional colloidal Janus particles, we can realize reconfigurable thermally reversible transitions between one- and two-dimensional self-assembled colloidal structures. We introduce a colloidal system in which DNA-coated asymmetric Janus particles can reversibly switch their Janus balance in response to temperature, resulting in the reconfiguration of assembling structures between colloidal chains and bilayers. Each face of the Janus particles is coated with different self-complementary DNA strands. Toehold strand displacement is employed to selectively activate or deactivate the sticky ends on the smaller face, which enables Janus particles to selectively assemble through either the smaller or larger face. This strategy could be useful for constructing complex systems that could be reconfigured to assemble into different structures in different environments.

Ordered Nanofibers Fabricated from Hierarchical Self-Assembling Processes of Designed α-Helical Peptides.

Peptide self-assembly is fast evolving into a powerful method for the development of bio-inspired nanomaterials with great potential for many applications, but it remains challenging to control the self-assembling processes and nanostrucutres because of the intricate interplay of various non-covalent interactions. A group of 28-residue α-helical peptides is designed including NN, NK, and HH that display distinct hierarchical events. The key of the design lies in the incorporation of two asparagine (Asn) or histidine (His) residues at the a positions of the second and fourth heptads, which allow one sequence to pack into homodimers with sticky ends through specific interhelical Asn-Asn or metal complexation interactions, followed by their longitudinal association into ordered nanofibers. This is in contrast to classical self-assembling helical peptide systems consisting of two complementary peptides. The collaborative roles played by the four main non-covalent interactions, including hydrogen-bonding, hydrophobic interactions, electrostatic interactions, and metal ion coordination, are well demonstrated during the hierarchical self-assembling processes of these peptides. Different nanostructures, for example, long and short nanofibers, thin and thick fibers, uniform metal ion-entrapped nanofibers, and polydisperse globular stacks, can be prepared by harnessing these interactions at different levels of hierarchy.

A Self‐Assembled Rhombohedral DNA Crystal Scaffold with Tunable Cavity Sizes and High‐Resolution Structural Detail

AbstractDNA is an ideal molecule for the construction of 3D crystals with tunable properties owing to its high programmability based on canonical Watson–Crick base pairing, with crystal assembly in all three dimensions facilitated by immobile Holliday junctions and sticky end cohesion. Despite the promise of these systems, only a handful of unique crystal scaffolds have been reported. Herein, we describe a new crystal system with a repeating sequence that mediates the assembly of a 3D scaffold via a series of Holliday junctions linked together with complementary sticky ends. By using an optimized junction sequence, we could determine a high‐resolution (2.7 Å) structure containing R3 crystal symmetry, with a slight subsequent improvement (2.6 Å) using a modified sticky‐end sequence. The immobile Holliday junction sequence allowed us to produce crystals that provided unprecedented atomic detail. In addition, we expanded the crystal cavities by 50 % by adding an additional helical turn between junctions, and we solved the structure to 4.5 Å resolution by molecular replacement.

A Self-Assembled Rhombohedral DNA Crystal Scaffold with Tunable Cavity Sizes and High-Resolution Structural Detail.

DNA is an ideal molecule for the construction of 3D crystals with tunable properties owing to its high programmability based on canonical Watson-Crick base pairing, with crystal assembly in all three dimensions facilitated by immobile Holliday junctions and sticky end cohesion. Despite the promise of these systems, only a handful of unique crystal scaffolds have been reported. Herein, we describe a new crystal system with a repeating sequence that mediates the assembly of a 3D scaffold via a series of Holliday junctions linked together with complementary sticky ends. By using an optimized junction sequence, we could determine a high-resolution (2.7 Å) structure containing R3 crystal symmetry, with a slight subsequent improvement (2.6 Å) using a modified sticky-end sequence. The immobile Holliday junction sequence allowed us to produce crystals that provided unprecedented atomic detail. In addition, we expanded the crystal cavities by 50 % by adding an additional helical turn between junctions, and we solved the structure to 4.5 Å resolution by molecular replacement.

Targeting folate receptors (α1) to internalize the bleomycin loaded DNA-nanotubes into prostate cancer xenograft CWR22R cells

DNA-nanotechnology based on DNA scaffolding technique is an established approach to formulate water-miscible nano-structural frameworks. We have designed the hydrophilic DNA-nanotubes (D-NTs) as a (water-soluble) vehicle to encapsulate a water-insoluble DNA-intercalating anticancer drug. Bleomycin (BM) is a model hydrophobic anticancer drug used in this study capable to bind with the D-NTs to formulate BM loaded D-NTs. This BM@D-NTs system was evaluated for the improvement of the in vitro anti-cancer effects on the resistant prostate cancer xenograft CWR22R cells, over-expressed with the folate receptors/alpha (FRα). D-NTs were functionalized with the FRα-targeting antibodies to interact with the FRα (receptors) highly expressed on the resistant prostate cancer xenograft CWR22R cells. D-NTs not only increased the aqueous miscibility/dispersibility of BM but also enhanced the therapeutic efficiency as a targeted (site-specific) drug delivery system. D-NTs synthesis was achieved by sticky ends cohesions of DNA triangular tiles. DNA triangles were self-assembled from a freshly circularized short scaffold chain (84-NT) by annealing with the various staple strands. The polymerization of the triangular tiles gave rise to DNA-nanosheet lattices which underwent morphological transition guided by the twists in the DNA duplexes. This DNA double helix curvature caused self-coiling of the DNA 2D nano-sheets to condense into D-NTs morphology. Native-Page gel experiment showed decreased electrophoretic mobility down the gel confirming the successful execution of the polymerized lattices via sticky ends cohesion of the DNA-triangles. The final morphology and self-coiling of 2D DNA nano-sheets were confirmed through atomic force microscopy (AFM) showed the successful synthesis of D-NTs having diameter 3 to 5 μm and length 200 to 600 nm. BM was loaded onto D-NTs via incubation of hydro-alcoholic solution of the BM with the aqueous solution of D-NTs followed by the evaporation of alcohol and intercalation of the BM onto D-NTs. The intercalation of BM onto D-NTs was confirmed by UV-shift analysis. The targeted cytotoxicity of the BM@D-NTs for the CWR22R (resistant prostate cancer xenograft) cells was confirmed through MTT assay and the flow cytometry compared to the highly compatible empty D-NTs. Confocal microscopy revealed the time-dependent transfection of BM@D-NTs into CWR22R cells compared to the control cell line.

Rectangular DNA structure allows for one-dimensional random walk functionality

Binding four strands with four sticky ends leads a DNA lattice to randomly deliver information to one of two sides.

Construction of one-dimensional random walk lattices using DNA algorithmic self-assembly

Algorithmic DNA lattices are constructed using pre-defined rules such as COPY, NOT, and XOR, where patterns are predicted based on initial values. However, the experimental implementation of an unpredictable random walk pattern (which is the implementation of a random rule, i.e., equally probable to move toward either the left or right in 1D systems) in DNA has not been reported yet. Here, we construct DNA lattices with DNA rule tiles implemented using the random rule. Patterns are visualized by atomic force microscopy. Finally, we discussed the average displacement, mean-square displacement, and number of displacement occurrences of experimental as well as simulated 1D random walk. The encoded information in sticky ends of DNA rule tiles demonstrates the feasibility of universal computation through DNA algorithmic self-assembly, which could be extremely beneficial in future computations.

Detection of ATP from “fluorescence” to “enhanced fluorescence” based on metal-enhanced fluorescence triggered by aptamer nanoswitch

Herein, we demonstrate a novel approach to detect intracellular adenosine triphosphate (ATP) from “fluorescence” to “enhanced fluorescence” by metal-enhanced fluorescence (MEF), which is an activatable means to amplify fluorescence signal. In the meantime, hybridization chain reaction (HCR) is employed to aggregate DNA on the substrate of MEF, and the length of generated DNA strands is controllable. ATP target molecules specifically bind to aptamer, which is designed as the recognition part of the nanoswitch, and the sticky ends are released. Then, HCR is triggered, bringing Cy7 modified on H1 and H2 close to the surface of gold nanobipyramids (AuNBPs) substrate. The fluorescence signal is amplified with the ATP concentration increasing owing to MEF. Thus, the strategy based on structure-switching aptamer triggering metal-enhanced fluorescence (SATMEF) for Cy7 is designed to detect ATP via “enhanced fluorescence” signals, and the maximum fluorescence enhancement by the approach of SATMEF reaches 5.63-fold. We applied this DNA nanoswitch for quantitative analysis to ATP, and the results show that the intensity of enhanced Cy7 fluorescence is positively correlated with the ATP concentration in the range of 0.2−10 μM, with a detection limit of 35 nM. We believe that the SATMEF for quantitative detection by signal from “fluorescence” to “enhanced fluorescence” provides a new approach for those fluorophores which are superior but difficult to be quenched to construct DNA nanoswitches.

Combinatorial-Entropy-Driven Aggregation in DNA-Grafted Nanoparticles.

We use computer simulations and experiments to study the interactions between nanoparticles (NPs) grafted with self-complementary DNA strands. Each strand ends with a sticky palindromic single-stranded sequence, allowing it to associate equally favorably with strands grafted on the same particle or on different NPs. Surprisingly we find an attractive interaction between a pair of NPs, and we demonstrate that at low temperature it arises purely from a combinatorial-entropy contribution. We evaluate theoretically and verify numerically this entropic contribution originating from the number of distinct bonding patterns associated with intra- and interparticle binding. This entropic attraction becomes more favorable with decreasing inter-NP distance because more sticky ends can participate in making this choice.

Determinants of cyclization-decyclization kinetics of short DNA with sticky ends.

Cyclization of DNA with sticky ends is commonly used to measure DNA bendability as a function of length and sequence, but how its kinetics depend on the rotational positioning of the sticky ends around the helical axis is less clear. Here, we measured cyclization (looping) and decyclization (unlooping) rates (kloop and kunloop) of DNA with sticky ends over three helical periods (100-130 bp) using single-molecule fluorescence resonance energy transfer (FRET). kloop showed a nontrivial undulation as a function of DNA length whereas kunloop showed a clear oscillation with a period close to the helical turn of DNA (∼10.5 bp). The oscillation of kunloop was almost completely suppressed in the presence of gaps around the sticky ends. We explain these findings by modeling double-helical DNA as a twisted wormlike chain with a finite width, intrinsic curvature, and stacking interaction between the end base pairs. We also discuss technical issues for converting the FRET-based cyclization/decyclization rates to an equilibrium quantity known as the J factor that is widely used to characterize DNA bending mechanics.

Templated Collagen "Double Helices" Maintain Their Structure.

The self-assembly of collagen-mimetic peptides (CMPs) that form sticky-ended triple helices has allowed the production of surprisingly stable artificial collagen fibers and hydrogels. Assembly through sticky ends requires the recognition of a single strand by a templated strand dimer. Although CMPs and their triple helices have been studied extensively, the structure of a strand dimer is unknown. Here, we evaluate the physical characteristics of such dimers, using disulfide-templated (PPG)10 dimers as a model. Such "linked-dimers" retain their collagen-like structure even in the absence of a third strand, but only when their strands are capable of adopting a triple-helical fold. The intrinsic collagen-like structure of templated CMP pairs helps to explain the success of sticky-ended CMP association and changes the conception of new synthetic collagen designs.

Expression of chromogranin A-derived antifungal peptide CGA-N12 in Pichia pastoris

ABSTRACT The human chromogranin A-derived peptide CGA-N12, which is composed of 12 amino acid residues with the sequence ALQGAKERAHQQ, showed strong antifungal activity and the least hemolytic activity in previous studies. However, synthetic peptides are relatively expensive to produce. Recombinant expression of peptides in the host cells, such as bacteria or yeast, can fastly provide cost-efficient products of peptides. Here, we developed an innovative system to produce CGA-N12 peptides in the yeast Pichia pastoris GS115 using genetic engineering technology. In order to directly secret short CGA-N12 peptides into the culture media from GS115 cells and enhance its expression effect, the structure of the CGA-N12 coding sequence was designed to mimic that of native α-factor gene of Saccharomyces cerevisiae. Four long primer pairs with sticky end were used to synthesize CGA-N12 expression sequence which contains four copies of CGA-N12 flanked by a Lys-Arg pair and two Glu-Ala repeating units. Endogenous proteases Kex2 and Ste13 in Golgi apparatus recognize and excise Lys-Arg and Glu-Ala pair to release short CGA-N12 peptides from the tandem repeat sequences, respectively. The CGA-N12 peptides were successfully expressed in Pichia pastoris with a yield of up to 30 mg/L of yeast culture as determined using HPLC. Our study indicated that the strategy employed in this work may be a good way to express small-molecule peptides directly in the Pichia pastoris system.

Supramolecular assembly of DNA-constructed vesicles.

The self-assembly of DNA hybrids possessing tetraphenylethylene sticky ends at both sides into vesicular architectures in aqueous medium is demonstrated. Cryo-electron microscopy reveals the formation of different types of morphologies from the amphiphilic DNA-hybrids. Depending on the conditions, either an extended (sheet-like) or a compact (columnar) alignment of the DNA hybrids is observed. The different modes of DNA arrangement lead to the formation of vesicles appearing either as prolate ellipsoids (type I) or as spheres (type II). The type of packing has a significant effect on the accessibility of the DNA, as evidenced by intercalation and light-harvesting experiments. Only the vesicles exhibiting the sheet-like DNA alignment are accessible for intercalation by ethidium bromide or for the integration of chromophore-labelled DNA via a strand exchange process. The dynamic nature of type I vesicles enables their elaboration into artificial light-harvesting complexes by DNA-guided introduction of Cy3-acceptor chromophores. DNA-constructed vesicles of the kind shown here represent versatile intermediates that are amenable to further modification for tailored nanotechnology applications.

In vitro trackable assembly of RNA-specific nucleocapsids of the respiratory syncytial virus

In vitro trackable assembly of RNA-specific nucleocapsids of the respiratory syncytial virus