Regulation of DNA Strand Displacement Using an Allosteric DNA Toehold

Toehold-mediated DNA strand displacement is the fundamental basis for the construction and operation of diverse DNA devices, including circuits, machines, sensors, and reconfigurable structures. Controllable activation and regulation of toeholds are critical to construct devices with multistep, autonomous, and complex behaviors. A handful of unique toehold activation mechanisms, including toehold-exchange, associative toehold, and remote toehold, have been developed and are often combined to achieve desired strand displacement behaviors and functions. Here we report an allosteric DNA toehold (A-toehold) design that allows the flexible regulation of DNA strand displacement by splitting an input strand into an A-toehold and branch migration domain. Because of its simplicity, the A-toehold mechanism can be a useful addition to the current toolbox of DNA strand displacement techniques. We demonstrated that A-toehold enabled a number of interesting functions that were previously shown using more sophisticated DNA strand displacement systems, including (1) continuously tuning the rate of strand displacement, (2) dynamic control of strand displacement reactions, and (3) selective activation of multiple strand displacement reactions. Moreover, by combining A-toehold and toehold-exchange mechanisms, we have successfully constructed a noncovalent DNA catalysis network that resembles an allosteric enzyme

PEP Search in MyCompoundID: Detection and Identification of Dipeptides and Tripeptides Using Dimethyl Labeling and Hydrophilic Interaction Liquid Chromatography Tandem Mass Spectrometry

Small peptides, such as dipeptides and tripeptides, are naturally present in many biological samples (e.g., human biofluids and cell extracts). They have attracted great attention in many research fields because of their important biological functions as well as potential roles as disease biomarkers. Tandem mass spectrometry (MS/MS) can be used to profile these small peptides. However, the type and number of fragment ions generated in MS/MS are often limited for unambiguous identification. Herein we report a novel database-search strategy based on the use of MS/MS spectra of both unlabeled and dimethyl labeled peptides to identify and confirm amino acid sequences of di/tripeptides that are separated using hydrophilic interaction (HILIC) liquid chromatography (LC). To facilitate the di/tripeptide identification, a database consisting of all the predicted MS/MS spectra from 400 dipeptides and 8000 tripeptides was created, and a search tool, PEP Search, was developed and housed at the MyCompoundID website (www.mycompoundid.org/PEP). To evaluate the identification specificity of this method, we used acid hydrolysis to degrade a standard protein, cytochrome c, to produce many di/tripeptides with known sequences for LC/MS/MS. The resultant MS/MS spectra were searched against the database to generate a list of matches which were compared to the known sequences. We correctly identified the di/tripeptides in the protein hydrolysate. We then applied this method to detect and identify di/tripeptides naturally present in human urine samples with high confidence. We envisage the use of this method as a complementary tool to various LC/MS techniques currently available for small molecule or metabolome profiling with an added benefit of covering all di/tripeptide chemical space

Geometric stability and adsorption property of hydroxyl group on graphene sheets

<div><p></p><p>The stable geometrics and adsorption behaviors of hydroxyl (OH) groups on graphene sheets are investigated using the first-principles calculations. The single hydroxyl adatom has small adsorption energy and diffusion barrier on pristine graphene. The binding strength of the hydroxyl group increases with the coverage, and the aggregations of the hydroxyl groups reduce the structural bucking of graphene sheet. On the graphene with single vacancy (SV-graphene), the large trapping zones mean the adsorbed OH would be easily trapped at the vacancy site. The hydroxyl groups prefer to aggregate on graphene surfaces and form the water molecule, leaving the epoxy group on pristine graphene or oxygen dopant in SV-graphene, which is used to constitute the structural model of oxidized graphene. These results would provide us a useful reference to understand the atomic structure and adsorption property of functional groups on graphene sheets.</p></div

The adsorption behaviours of Pt adatom on pristine and defective bilayer graphene

<p>The structural stability and electronic property of metal Pt atom anchors on two typical substrates (including the pristine and defective bilayer graphene, PBG and DBG) are studied using the first-principles calculations. For the PBG sheets, the Pt atom at the bridge site of bottom layer has only one stable adsorption, which is more stable than other sites of the top layer. For the DBG sheets, the doped Pt below defective site has the larger adsorption energy than that of the upper one. Compared to the isolated graphene films, the Pt(111) substrate-supported graphene systems have effect on the adsorption energies of Pt adatom to some extent, but it does not affect the most preferable configurations. Moreover, the diffusion pathways and energy barriers of Pt adatom on PBG and DBG substrates are comparatively investigated. For the DBG sheets, the Pt dopant has smaller diffusion barrier on upper layer than that of the intercalation process through the defective site. Therefore, the Pt dopant prefers to diffuse on the top layer and then forms the metal impurity. This work provides valuable information on understanding the formation process and intercalation mechanism of metal adatom on graphene sheets.</p

Enzyme-Powered Three-Dimensional DNA Nanomachine for DNA Walking, Payload Release, and Biosensing

Herein, we report a DNA nanomachine, built from a DNA-functionalized gold nanoparticle (DNA–AuNP), which moves a DNA walker along a three-dimensional (3-D) DNA–AuNP track and executes the task of releasing payloads. The movement of the DNA walker is powered by a nicking endonuclease that cleaves specific DNA substrates on the track. During the movement, each DNA walker cleaves multiple substrates, resulting in the rapid release of payloads (predesigned DNA sequences and their conjugates). The 3-D DNA nanomachine is highly efficient due to the high local effective concentrations of all DNA components that have been co-conjugated on the same AuNP. Moreover, the activity of the 3-D DNA nanomachine can be controlled by introducing a protecting DNA probe that can hybridize to or dehybridize from the DNA walker in a target-specific manner. This property allows us to tailor the DNA nanomachine into a DNA nanosensor that is able to achieve rapid, isothermal, and homogeneous signal amplification for specific nucleic acids in both buffer and a complicated biomatrix

Kinetics of Proximity-Induced Intramolecular DNA Strand Displacement

Proximity-induced intramolecular DNA strand displacement (PiDSD) is one of the key mechanisms involved in many DNA-mediated proximity assays and protein-responsive DNA devices. However, the kinetic profile of PiDSD has never been systematically examined before. Herein, we report a systematic study to explore the kinetics of PiDSD by combining the uses of three DNA strand displacement techniques, including a binding-induced DNA strand displacement to generate PiDSD, an intermolecular DNA strand-exchange strategy to measure a set of key kinetic parameters for PiDSD, and a toehold-mediated DNA strand displacement to generate fluorescence signals for the real-time monitoring of PiDSD. By using this approach, we have successfully revealed the kinetic profiles of PiDSD, determined the enhanced local effective concentrations of DNA probes that are involved in PiDSD, and identified a number of key factors that influence the kinetics of PiDSD. Our study on PiDSD establishes knowledge and strategies that can be used to guide the design and operation of various DNA-mediated proximity assays and protein-triggered DNA devices

Universal Strategy To Engineer Catalytic DNA Hairpin Assemblies for Protein Analysis

Nucleic acids can be programmed into enzyme-free catalytic DNA circuits (CDCs) to carry out various functions ranging from DNA computing to signal amplifications for biosensing. Catalytic hairpin assembly (CHA), the accelerated hybridization between two DNA hairpins catalyzed by a DNA input, is one of the most widely studied and used CDCs for amplified detection of nucleic acids and small molecules. So far, it is still challenging to expand CHAs to proteins largely due to the lack of a universal strategy to construct protein-responsive CHAs. To address this challenge, we demonstrate that a rationally designed protein–DNA binding complex can be used as an effective catalyst to accelerate CHA reactions. On the basis of this principle, we developed specific CHAs for a number of important protein biomarkers, including human α-thrombin, human prostate specific antigen, and human epidermal growth factor receptor 2. Upon establishing this panel of protein-responsive CHAs, we further explore their potential applications to the detection of specific protein biomarkers from human serum samples and cancer cells

CO oxidation over BC₃ nanosheet: a theoretical study

<p>Metal-free catalysts have attracted more attention due to their highly active in catalytic oxidation reactions. The electronic structure and catalytic property of BC₃ sheet are investigated by using first-principles calculations. It is found that the BC₃ sheet as the active surface can effectively regulate the adsorptive stability of reactive gases. Besides, the possible reaction processes for CO oxidation on the BC₃ sheet are comparably analysed through different reaction mechanisms, which include the Eley–Rideal (ER), Langmuir–Hinshelwood (LH) and termolecular Eley–Rideal (TER). In the CO oxidation reactions, the decomposition of O₂ molecule as the starting state (0.40 eV) is an energetically more favourable process than those of other processes, the Eley–Rideal (ER) reactions (2O_ads+2CO→CO₂) are more prone to take place with lower energy barriers (< 0.20 eV) on the BC₃ sheet. These results provide an important guidance on exploring the highly efficiency metal-free catalyst for CO oxidation.</p

Mechanism and Origin of Et₂Al(OEt)-Induced Chemoselectivity of Nickel-Catalyzed Three-Component Coupling of One Diketene and Two Alkynes

Density functional theory (DFT) calculations have been performed to unravel the mechanism of Lewis-acid-induced Ni­(cod)₂-catalyzed selective coupling reactions of one diketene and two alkynes. Complex mixtures (unsymmetrical phenylacetic acid <b>P1</b>, symmetrical phenylacetic acid <b>P2</b> and (3E)-4-ethyl-5-methylene-3-heptenoic acid <b>P3</b>) were obtained in the absence of Et₂Al­(OEt). <b>P1</b> formation involves C­(sp²)-O oxidative addition of diketene, twice alkyne insertion, intramolecular CC insertion, acidolysis, and β-H elimination. For <b>P2/P3</b> formation, the common key issue related to the CC double bond cleavage of the substrate diketene was explored and found that it was accomplished via a four-membered-ring-closure/four-membered-ring-opening process. And then, <b>P2</b> was produced via the second alkyne insertion while <b>P3</b> was accessed by a stoichiometric reaction with HCl. The Et₂Al­(OEt)-induced chemoselectivity was also probed. It is found that the Ni–O (from Al reagent) bonding facilitates the second alkyne insertion, and the Al–O (from carboxylate) bonding weakens the four-membered ring-closure step, which consequently leads to the formation of <b>P1</b> exclusively. Additionally, HCl plays a promoting role as a cocatalyst in producing <b>P1</b> and <b>P2</b>. The theoretical results not only well rationalize the experimental observations but provide insights into the mechanism of the Ni-catalyzed multicomponent coupling reactions

Antagomir-93 inhibits tumor growth <i>in vivo</i>.

<p>After transfection of SGC-7901 cells with antagomir-93 or antagomir-NC for 24h, cells were subcutaneously injected into the Left subaxillary of nude mice. (E) Representative images of excised xenograft tumors from nude mice. (A) The growth curve of tumors in nude mice. (B) Tumor weight. (C) Tumor levels of miR-93 measured by Quantitative RT-PCR. (D and F) TIMP2 miRNA expression and proteins levels measured in tumor tissues. (G) TIMP2 proteins levels in xenograft tumors determined by immunohistochemical staining. *P<0.05, **P<0.01, (magnification × 200).</p