scholarly journals Continuous nonenzymatic cross-replication of DNA strands with in situ activated DNA oligonucleotides

2019 ◽  
Vol 10 (22) ◽  
pp. 5807-5814 ◽  
Author(s):  
Evgeniia Edeleva ◽  
Annalena Salditt ◽  
Julian Stamp ◽  
Philipp Schwintek ◽  
Job Boekhoven ◽  
...  

A nonenzymatic DNA cross-replicator uses temperature cycling to overcome product inhibition and thus survives exponential dilution conditions.

MRS Bulletin ◽  
1994 ◽  
Vol 19 (6) ◽  
pp. 22-25 ◽  
Author(s):  
U. Dahmen

Static electron microscopy provides views of microstructures frozen in time. For many problems, such snapshots give a clear picture of the material's characteristics after a particular processing step, but for other problems it is the evolution of the microstructure itself, its mechanisms and kinetics, that are important to understand. For this class of problem, in situ electron microscopy is an indispensable tool because it can provide real-time dynamic observations of processes, showing, for example, where dislocations nucleate, how a particle grows, by what mechanism and how fast an interface migrates. The major limitation to such experiments is that foils must be extremely thin to be electron transparent. The proximity of the free surfaces can have a strong effect on the dynamic equilibrium. For that reason, high-voltage electron microscopes are particularly useful for in situ TEM experiments. The greater penetration depth of high energy electrons makes it possible to observe processes in foils that are thick enough to avoid the dominant influence of the surfaces.This article will describe some experiments in which the dynamic behavior of precipitates in a simple alloy system was examined during in situ temperature cycling in order to understand the effect of bicrystal anisotropy on the characteristics of interface motion.


Author(s):  
Theo Calais ◽  
Thileepan Stalin ◽  
Vincent S. Joseph ◽  
Pablo Valdivia y Alvarado

Abstract Structures and mechanisms in soft robotics are primarily based on chemically versatile species such as hydrogels, polymers, or elastomers, thus offering great potential for the design of adaptive core properties. In particular, tunable rigidity is highly desirable to enable control of soft grippers or for advanced robot locomotion. However, most of the strategies explored so far rely on mechanisms, such as phase transitions or shape memory effects, that require heavy external hardware or have a limited range of tunable rigidity. In this work, we propose a novel strategy inspired by the sea cucumber dermis mechanism. High aspect ratio carbon nanotubes (CNTs) are reversibly interconnected by DNA oligonucleotides within a polyacrylamide (PAAm) hydrogel. The combination of the excellent mechanical properties of CNTs and the reversible hybridization of DNA strands into a stable double-helicoidal structure allowed the reversible tunability of mechanical properties over one order of magnitude (from ∼100 Pa to ∼1 kPa) within minutes by increasing the temperature beyond the melting temperature of DNA strands (∼50 °C). First, the functionalization strategy of CNTs with DNA strands is described and characterized. The aggregation of CNTs driven by the DNA hybridization is then demonstrated. The mechanical properties of hydrogels functionalized with CNTs are finally analyzed using rheology measurements.


Author(s):  
S. Hinderberger ◽  
S. Q. Xiao ◽  
K. H. Westmacott ◽  
U. Dahmen

Ge precipitates in Al are known to form in a rich variety of shapes and orientation relationships. In this work it is shown that initial non-equilibrium shapes such as plates, laths, needles and tetrahedra can be induced to change to the equilibrium shape of an octahedron by proper temperature cycling. Analysis of this effect in bulk samples was complemented by direct observations of its mechanisms during in-situ temperature cycling.A bulk sample of an Al-1.8at%Ge alloy was solid solution annealed at 420°C for 2h, quenched in ice water, pre-aged at room temperature for 72h and then annealed for 5h at 250°C. Subsequently, part of the sample was repeatedly cycled between 250°C and 360°C. TEM specimens were prepared from both the cycled and non-cycled bulk sample by conventional electropolishing and examined in a JEOL 200CX electron microscope. The in-situ temperature cycling was carried out in a Kratos 1.5 MeV HVEM equipped with a double tilt heating stage.


2012 ◽  
Vol 2012 (1) ◽  
pp. 000825-000828
Author(s):  
Michael Ferrara

The increase in sophistication of reliability testing over the past several years is in part driven by the increase in complexity of package architecture it is meant to evaluate. Movement from a pass/ fail centric suite of testing toward a trend of increased design for reliability and potential problem analysis driven testing criteria is evident. A facet of this is the increased emphasis on test to failure approaches for certain package related tests such as drop shock testing. Additionally, there is an increased importance for extracting more meaningful data from standard fixed duration tests such as temperature cycling. In-situ monitored reliability testing for both drop shock and temperature cycling is an effective method for evaluating package technologies from a test to failure and immediate failure feedback perspective.


2012 ◽  
Vol 2012 ◽  
pp. 1-8 ◽  
Author(s):  
Zonggao Shi ◽  
Jeffrey J. Johnson ◽  
M. Sharon Stack

The noncoding RNA designated as microRNA (miRNA) is a large group of small single-stranded regulatory RNA and has generated wide-spread interest in human disease studies. To facilitate delineating the role of microRNAs in cancer pathology, we sought to explore the feasibility of detecting microRNA expression in formalin-fixed paraffin-embedded (FFPE) tissues. Using FFPE materials, we have compared fluorescentin situhybridization (FISH) procedures to detect miR-146a with (a) different synthetic probes: regular custom DNA oligonucleotides versus locked nucleic acid (LNA) incorporated DNA oligonucleotides; (b) different reporters for the probes: biotin versus digoxigenin (DIG); (c) different visualization: traditional versus tyramide signal amplification (TSA) system; (d) different blocking reagents for endogenous peroxidase. Finally, we performed miR-146a FISH on a commercially available oral cancer tissue microarray, which contains 40 cases of oral squamous cell carcinoma (OSCC) and 10 cases of normal epithelia from the human oral cavity. A sample FISH protocol for detecting miR-146a is provided. In summary, we have established reliablein situhybridization procedures for detecting the expression of microRNA in FFPE oral cancer tissues. This method is an important tool for studies on the involvement of microRNA in oral cancer pathology and may have potential prognostic or diagnostic value.


1991 ◽  
Vol 238 ◽  
Author(s):  
P. Lours ◽  
K. H. Westmacott ◽  
U. Dahmen

ABSTRACTGe precipitates in Al-Ge alloys have been observed to undergo a transformation in shape during in-situ temperature cycling in a high voltage electron microscope. Octahedral precipitates with a parallel-cube orientation relationship spheroidized on heating and refaceted to the octahedral shape on cooling. This shape transformation was essentially conservative if the temperature excursions were kept small. These observations are discussed in terms of an interface roughening transformation.


2020 ◽  
Author(s):  
Song Mao ◽  
Zhihua Chang ◽  
Ya Ying Zheng ◽  
Alexander Shekhtman ◽  
Jia Sheng

A new family of hydrazone modified cytidine phosphoramidite building block was synthesized and incorporated into DNA oligonucleotides to construct photoswitchable DNA strands. The <i>E-Z</i> isomerization triggered by the irradiation of blue light with a wavelength of 450 nm was investigated and confirmed by <sup>1</sup>H NMR and HPLC in the contexts of both nucleoside and DNA oligonucleotide. The light activated <i>Z</i> form isomer of this hydrazone-cytidine with a six-member intramolecular hydrogen bond was found to inhibit DNA synthesis in the primer extension model by using <i>Bst</i> DNA polymerase. In addition, the hydrazone modification caused the misincorporation of dATP together with dGTP into the growing DNA strand with similar selectivity, highlighting the potential G to A mutation. This work provides a novel functional DNA building block and an additional molecular tool that have potential chemical biology and bio-medicinal applications to control DNA synthesis and DNA-enzyme interactions using cell friendly blue light irradiation.


Author(s):  
M. Kaysar Rahim ◽  
Jordan Roberts ◽  
Jeffrey C. Suhling ◽  
Richard C. Jaeger ◽  
Pradeep Lall

Thermal cycling accelerated life testing is an established technique for thermo-mechanical evaluation and qualification of electronic packages. Finite element life predictions for thermal cycling configurations are challenging due to several reasons including the complicated temperature/time dependent constitutive relations and failure criteria needed for solders, encapsulants and their interfaces; aging/evolving material behavior for the packaging materials (e.g. solders); difficulties in modeling plating finishes; the complicated geometries of typical electronic assemblies; etc. In addition, in-situ measurements of stresses and strains in assemblies subjected to temperature cycling are difficult because of the extreme environmental conditions and the fact that the primary materials/interfaces of interest (e.g. solder joints, die device surface, wire bonds, etc.) are embedded within the assembly (not at the surface). For these reasons, little is known about the evolution of the stresses, strains, and deformations occurring within sophisticated electronic packaging geometries during thermal cycling. In this work, we have used test chips containing piezoresistive stress sensors to characterize the in-situ die surface stress during long-term thermal cycling of electronic packaging assemblies. Using (111) silicon test chips, the complete three-dimensional stress state (all 6 stress components) was measured at each rosette site by monitoring the resistance changes occurring in the sensors. The packaging configuration studied in this work was flip chip on laminate where 5 × 5 mm perimeter bumped die were assembled on FR-406 substrates. Three different thermal cycling temperature profiles were considered. In each case, the die stresses were initially measured at room temperature after packaging. The packaged assemblies were then subjected to thermal cycling and measurements were made either incrementally or continuously during the environmental exposures. In the incremental measurements, the packages were removed from the chamber after various durations of thermal cycling (e.g. 250, 500, 750, 1000 cycles, etc.), and the sensor resistances were measured at room temperature. In the continuous measurements, the sensor resistances at critical locations on the die device surface (e.g. die center and die corners) were recorded continuously during the thermal cycling exposure. From the resistance data, the stresses at each site were calculated and plotted versus time. The experimental observations show cycle-to-cycle evolution in the stress magnitudes due to material aging effects, stress relaxation and creep phenomena, and development of interfacial damage.


Molecules ◽  
2018 ◽  
Vol 23 (11) ◽  
pp. 2941 ◽  
Author(s):  
Melissa Meng ◽  
Boris Schmidtgall ◽  
Christian Ducho

Deficient stability towards nuclease-mediated degradation is one of the most relevant tasks in the development of oligonucleotide-derived biomedical agents. This hurdle can be overcome through modifications to the native oligonucleotide backbone structure, with the goal of simultaneously retaining the unique hybridization properties of nucleic acids. The nucleosyl amino acid (NAA)-modification is a recently introduced artificial cationic backbone linkage. Partially zwitterionic NAA-modified oligonucleotides had previously shown hybridization with DNA strands with retained base-pairing fidelity. In this study, we report the significantly enhanced stability of NAA-modified oligonucleotides towards 3′- and 5′-exonuclease-mediated degradation as well as in complex biological media such as human plasma and whole cell lysate. This demonstrates the potential versatility of the NAA-motif as a backbone modification for the development of biomedically active oligonucleotide analogues.


2013 ◽  
Vol 10 (8) ◽  
pp. 5639-5649 ◽  
Author(s):  
D. de Beer ◽  
M. Haeckel ◽  
J. Neumann ◽  
G. Wegener ◽  
F. Inagaki ◽  
...  

Abstract. This study focused on biogeochemical processes and microbial activity in sediments of a natural deep-sea CO2 seepage area (Yonaguni Knoll IV hydrothermal system, Japan). The aim was to assess the influence of the geochemical conditions occurring in highly acidic and CO2 saturated sediments on sulfate reduction (SR) and anaerobic methane oxidation (AOM). Porewater chemistry was investigated from retrieved sediment cores and in situ by microsensor profiling. The sites sampled around a sediment-hosted hydrothermal CO2 vent were very heterogeneous in porewater chemistry, indicating a complex leakage pattern. Near the vents, droplets of liquid CO2 were observed emanating from the sediments, and the pH reached approximately 4.5 in a sediment depth > 6 cm, as determined in situ by microsensors. Methane and sulfate co-occurred in most sediment samples from the vicinity of the vents down to a depth of 3 m. However, SR and AOM were restricted to the upper 7–15 cm below seafloor, although neither temperature, low pH, nor the availability of methane and sulfate could be limiting microbial activity. We argue that the extremely high subsurface concentrations of dissolved CO2 (1000–1700 mM), which disrupt the cellular pH homeostasis, and lead to end-product inhibition. This limits life to the surface sediment horizons above the liquid CO2 phase, where less extreme conditions prevail. Our results may have to be taken into consideration in assessing the consequences of deep-sea CO2 sequestration on benthic element cycling and on the local ecosystem state.


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