A simple and sensitive colorimetric pH meter based on DNA conformational switch and gold nanoparticle aggregation

A simple and rapid colorimetric pH meter has been developed based on the conformational switch of i-motif DNA and non-crosslinking AuNP aggregation, the average accuracy of the nano-meter was found to be +/- 0.04 pH unit across the physiological operating range.

[Ru(bpy)2dppz]2+ electrochemiluminescence switch and its applications for DNA interaction study and label-free ATP aptasensor

[Ru(bpy)2dppz]2+ electrochemiluminescence (ECL) was studied, and it was used to investigate DNA interaction and develop a label-free ATP aptasensor for the first time. ECL of [Ru(bpy)2dppz]2+ is negligible in aqueous solution, and increases approximately 1000 times when [Ru(bpy)2dppz]2+ intercalates into the nucleic acid structure. The ECL switch behavior of [Ru(bpy)2dppz]2+ is ascribed to the intercalation that shields the phenazine nitrogens from the solvent and results in a luminescent excited state. The ECL switch by DNA was applied to investigate the interaction of [Ru(bpy)2dppz]2+ with herring sperm DNA. The calculated equilibrium constant (K) is 1.35 x 10(6) M(-1), and the calculated binding-site size (s) is 0.88 base pair, which is consistent with the reported values.

Flourescent Switch Constructed Based on Hemin-Sensitive Anionic Conjugated Polymer and Its Applications in DNA-Related Sensors

Here, a fluorescent switch is constructed combining hemin, hemin aptamer, and a newly synthesized anionic conjugated polymer (ACP), poly(9,9-bis(6'-phosphate-hexyl) fluorenealt-1,4-phenylene) sodium salt (PFHPNa/PFP). In the "off-state", the fluorescence of PFP is sensitively quenched by hemin, with a high K-sv value of similar to 10(7). While in the "on-state", the formation of the aptamer/hemin complex recovers the fluorescence intensity. The fluorescent switch is sensitive and selective to hemin. To testify the universality and practicality of the fluorescent switch, a series of label-free DNA-related sensing platforms are developed, containing three DNA sensing strategies and one ATP recognition strategy. The fluorescent switch developed is simple, sensitive, and universal, which extends applications of the anionic conjugated polymers.

Methylene blue as an indicator for sensitive electrochemical detection of adenosine based on aptamer switch

In this paper, a simple, label-free and regenerative method was proposed to study the interaction between aptamer and small molecule by using methylene blue (MB+) as an electrochemical indicator. A thiolated capture probe containing twelve bases was firstly self-assembled on gold electrode by gold-sulfur affinity. Aptamer probe containing thirty two bases, which was designed to hybridize with capture DNA sequence and specifically recognize adenosine, was then immobilized on the electrode surface by hybridization reaction. MB+ was abundantly adsorbed on the aptamer probe by the specific interaction between MB+ and guanine base in aptamer probe. MB+-anchored aptamer probe can be forced to dissociate from the sensing interface after adenosine triggered structure switching of the aptamer. The peak current of MB+ linearly decreased with the concentration of adenosine over a range of 2 x 10 (8)- x 10 (6) M with a detection limit of 1 x 10 (8) M. In addition, we examined the selectivity of this electrochemical biosensor for cytidine, uridine and guanosine that belonged to the nucleosides family and possessed 1 similar structure with adenosine.

Small-Molecule Selectively Recognizes Human Telomeric G-Quadruplex DNA and Regulates Its Conformational Switch

Structural complexity is an inherent feature of the human telomeric sequence, and it presents a major challenge for developing ligands of pharmaceutical interest. Recent studies have pointed out that the induction of a quadruplex or change of a quadruplex conformation on binding may be the most powerful method to exert the desired biological effect. In this study, we demonstrate a quadruplex ligand that binds selectively to different forms of the human telomeric G-quadruplex structure and regulates its conformational switch. The results show that not only can oxazine750 selectively induce parallel quadruplex formation from a random coil telomeric oligonucleotide, in the absence of added cations, it also can easily surpass the energy barrier between two structures and change the G-quadruplex conformation in Na+ or K+ solution. The combination of its unique properties, including the size and shape of the G-quadruplex and the small molecule, is proposed as the predominant force for regulating the special structural formation and transitions.

Sensitive detection of protein by an aptamer-based label-free fluorescing molecular switch

We report an aptamer-based method for the sensitive detection of proteins by a label-free fluorescing molecular switch (ethidium bromide), which shows promising potential in making protein assay simple and economical.

Switch-on transient behavior of vanadium phthalocyanine based organic transistors

The authors investigated the switch-on transient properties of p-type vanadium phthalocyanine (VOPc) transistors, which were fabricated by weak epitaxy growth on ordered para-sexiphenyl (p-6P) layer. The overshoot phenomenon of drain current had been observed in the VOPc/p-6P transistors, which was explained by the filling of carriers in traps of organic films. The small overshoot value of about 35% and transient duration time of 2 ms demonstrated the low trap concentration in organic films, which were comparable to the reported hydrogenated amorphous-silicon thin-film transistors. Therefore, the VOPc/p-6P transistors can be applied in active matrix liquid crystal display as switch elements.

Potential energy landscape and robustness of a gene regulatory network: Toggle switch

Finding a multidimensional potential landscape is the key for addressing important global issues, such as the robustness of cellular networks. We have uncovered the underlying potential energy landscape of a simple gene regulatory network: a toggle switch. This was realized by explicitly constructing the steady state probability of the gene switch in the protein concentration space in the presence of the intrinsic statistical fluctuations due to the small number of proteins in the cell. We explored the global phase space for the system. We found that the protein synthesis rate and the unbinding rate of proteins to the gene were small relative to the protein degradation rate; the gene switch is monostable with only one stable basin of attraction. When both the protein synthesis rate and the unbinding rate of proteins to the gene are large compared with the protein degradation rate, two global basins of attraction emerge for a toggle switch. These basins correspond to the biologically stable functional states. The potential energy barrier between the two basins determines the time scale of conversion from one to the other. We found as the protein synthesis rate and protein unbinding rate to the gene relative to the protein degradation rate became larger, the potential energy barrier became larger. This also corresponded to systems with less noise or the fluctuations on the protein numbers.

Dynamics and intrinsic statistical fluctuations of a gene switch

We studied a simple gene regulatory network, the toggle switch. Specifically, we examined the means and statistical fluctuations in numbers of proteins. We found that when omega, the ratio of rates of protein-gene unbinding to protein degradation, was between similar to 10(-3) and similar to 10, the fluctuations were much larger than those we would have expected from Poisson statistics. In addition, we examined characteristic time values for system relaxation and found both that they increased with omega and that they have significant phase transition effects, with a secondary time scale appearing near the boundary between bistable and other phases. Last, we discuss the bistability of the toggle switch.

Context and conformation dictate function of a transcription antitermination switch

In bacteriophage, transcription elongation is regulated by the N protein, which binds a nascent mRNA hairpin ( termed boxB) and enables RNA polymerase to read through distal terminators. We have examined the structure, energetics and in vivo function of a number of N boxB complexes derived from in vitro protein selection. Trp18 fully stacks on the RNA loop in the wild-type structure, and can become partially or completely unstacked when the sequence context is changed three or four residues away, resulting in a recognition interface in which the best binding residues depend on the sequence context. Notably, in vivo antitermination activity correlates with the presence of a stacked aromatic residue at position 18, but not with N boxB binding affinity. Our work demonstrates that RNA polymerase responds to subtle conformational changes in cis-acting regulatory complexes and that approximation of components is not sufficient to generate a fully functional transcription switch.

Defoliation, nitrogen, and competition: effects on plant growth and resource allocation of Cleistogenes squarrosa and Artemisia frigida

Two species, Artemisia frigida Willd. (C-3, semishrub, and dominant on overgrazed sites) and Cleistogenes squarrosa (Trin.) Keng (C-4, perennial bunchgrass, and dominant or codominant on moderately grazed sites) were studied to determine the effects of defoliation, nitrogen (N) availability, competition, and their interactions on growth, biomass, and N allocation in a greenhouse experiment. The main treatments were: two nitrogen levels (NO = 0 mg N pot(-1), N1 = 60 mg N pot(-1)), two defoliation intensities (removing 60% of total aboveground biomass and no defoliation), and three competitive replacement series (monocultures of each species and mixtures at 0.5:0.5). Our results were inconsistent with our hypothesis on the adaptive mechanisms of A. frigida regarding the interactive effects of herbivory, N, and competition in determining its dominant position on overgrazed sites. Cleistogenes squarrosa will be replaced by A. frigida on over-grazed sites, although C. squarrosa had higher tolerance to defoliation than did A. frigida. Total biomass and N yield and N-15 recovery of C. squarrosa in mixed culture were consistently lower than in monocultures, whereas those of A. frigida grown in mixtures were consistently higher than in monocultures, suggesting higher competitive ability of A. frigida. Our results suggest that interspecific competitive ability may be of equal or greater importance than herbivory tolerance in determining herbivore-induced species replacement in semi-arid Inner Mongolian steppe. In addition, the dominance of A. frigida on overgrazed sites has been attributed to its ability to shift plant-plant interactions through (lap colonization, root niche differentiation, and higher resistance to water stress.

Sparsely Faceted Arrays: A Mechanism Supporting Parallel Allocation, Communication, and Garbage Collection

Conventional parallel computer architectures do not provide support for non-uniformly distributed objects. In this thesis, I introduce sparsely faceted arrays (SFAs), a new low-level mechanism for naming regions of memory, or facets, on different processors in a distributed, shared memory parallel processing system. Sparsely faceted arrays address the disconnect between the global distributed arrays provided by conventional architectures (e.g. the Cray T3 series), and the requirements of high-level parallel programming methods that wish to use objects that are distributed over only a subset of processing elements. A sparsely faceted array names a virtual globally-distributed array, but actual facets are lazily allocated. By providing simple semantics and making efficient use of memory, SFAs enable efficient implementation of a variety of non-uniformly distributed data structures and related algorithms. I present example applications which use SFAs, and describe and evaluate simple hardware mechanisms for implementing SFAs. Keeping track of which nodes have allocated facets for a particular SFA is an important task that suggests the need for automatic memory management, including garbage collection. To address this need, I first argue that conventional tracing techniques such as mark/sweep and copying GC are inherently unscalable in parallel systems. I then present a parallel memory-management strategy, based on reference-counting, that is capable of garbage collecting sparsely faceted arrays. I also discuss opportunities for hardware support of this garbage collection strategy. I have implemented a high-level hardware/OS simulator featuring hardware support for sparsely faceted arrays and automatic garbage collection. I describe the simulator and outline a few of the numerous details associated with a "real" implementation of SFAs and SFA-aware garbage collection. Simulation results are used throughout this thesis in the evaluation of hardware support mechanisms.