Synthesis of double‐hydrophilic block copolymers via combination of oxyanion‐initiated polymerization and polymer reaction for fabricating magnetic target gene carrier

In this work, we have synthesized a polycation and a polyanion via a combination of oxyanion‐initiated polymerization and polymer reaction, and then developed a novel approach to prepare a controlled magnetic target gene carrier with magnetic Fe₃O₄ nanoparticles as core and poly(ethylene glycol) (PEG) segment as corona via layer‐by‐layer (LbL) assembly and shell‐crosslinking. Magnetic nanoparticles (MNPs) were first modified by poly[2‐(dimethylamino)ethyl methacrylate] (PDMAEMA) via radical polymerization. The resulting MNPs were used to compact deoxyribonucleic acid (DNA) through LbL assembly, involving four steps: ( 1 ) the binding of DNA to the polycation PDMAEMA on the surface of MNPs; ( 2 ) the produced particles in Step 1 with negative charge interacting with additional polycation ethoxy group end‐capped PDMAEMA (EtO‐PDMAEMA) homopolymer, leading to a positive charge surface; ( 3 ) using carboxyl group (‐COO^‐) of poly(methacrylic acid) (PMAA) in a diblock copolymer (MePEG2000‐b‐PMAA_SH) as polyanion, which has partial mercapto groups (‐SH) in PMAA segment, to interact with the particles produced in Step 2; ( 4 ) the shell of the composite nanoparticle was crosslinked by oxidizing the ‐SH groups of the MePEG2000‐b‐PMAA_SH to form disulfide linkage (S? S). All the processes of LbL assembly were investigated by agarose gel retardation assay and zeta potential measurements. The in vitro cytotoxicity analysis proves that polyions/DNA MNPs have excellent properties and potential applications as gene carriers. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011     

Nucleic Acid Driven DNA Machineries Synthesizing Mg2+‐Dependent DNAzymes: An Interplay between DNA Sensing and Logic‐Gate Operations

Polymerase/nicking enzymes and nucleic‐acid scaffolds are implemented as DNA machines for the development of amplified DNA‐detection schemes, and for the design of logic gates. The analyte nucleic acid target acts, also, as input for the logic gates. In the presence of two DNA targets, acting as inputs, and appropriate DNA scaffolds, the polymerase‐induced replication of the scaffolds, followed by the nicking of the replication products, are activated, leading to the autonomous synthesis of the Mg²⁺‐dependent DNAzyme or the Mg²⁺‐dependent DNAzyme subunits. These biocatalysts cleave a fluorophore/quencher‐functionalized nucleic‐acid substrate, thus providing fluorescence signals for the sensing events or outputs for the logic gates. The systems are used to develop OR, AND, and Controlled‐AND gates, and the DNA‐analyte targets represent two nucleic acid sequences of the smallpox viral genome.     

Bioelectronic Interface Connecting Reversible Logic Gates Based on Enzyme and DNA Reactions

It is believed that connecting biomolecular computation elements in complex networks of communicating molecules may eventually lead to a biocomputer that can be used for diagnostics and/or the cure of physiological and genetic disorders. Here, a bioelectronic interface based on biomolecule‐modified electrodes has been designed to bridge reversible enzymatic logic gates with reversible DNA‐based logic gates. The enzyme‐based Fredkin gate with three input and three output signals was connected to the DNA‐based Feynman gate with two input and two output signals—both representing logically reversible computing elements. In the reversible Fredkin gate, the routing of two data signals between two output channels was controlled by the control signal (third channel). The two data output signals generated by the Fredkin gate were directed toward two electrochemical flow cells, responding to the output signals by releasing DNA molecules that serve as the input signals for the next Feynman logic gate based on the DNA reacting cascade, producing, in turn, two final output signals. The Feynman gate operated as the controlled NOT gate (CNOT), where one of the input channels controlled a NOT operation on another channel. Both logic gates represented a highly sophisticated combination of input‐controlled signal‐routing logic operations, resulting in redirecting chemical signals in different channels and performing orchestrated computing processes. The biomolecular reaction cascade responsible for the signal processing was realized by moving the solution from one reacting cell to another, including the reacting flow cells and electrochemical flow cells, which were organized in a specific network mimicking electronic computing circuitries. The designed system represents the first example of high complexity biocomputing processes integrating enzyme and DNA reactions and performing logically reversible signal processing.     

DNA‐Based Adaptive Plasmonic Logic Gates

Self‐assembled plasmonic logic gates that read DNA molecules as input and return plasmonic chiroptical signals as outputs are reported. Such logic gates are achieved on a DNA‐based platform that logically regulate the conformation of a chiral plasmonic nanostructure, upon specific input DNA strands and internal computing units. With systematical designs, a complete set of Boolean logical gates are realized. Intriguingly, the logic gates could be endowed with adaptiveness, so they can autonomously alter their logics when the environment changes. As a demonstration, a logic gate that performs AND function at body temperature while OR function at cold storage temperature is constructed. In addition, the plasmonic chiroptical output has three distinctive states, which makes a three‐state molecular logic gate readily achievable on this platform. Such DNA‐based plasmonic logic gates are envisioned to execute more complex tasks giving these unique characteristics.     

HPW/PDMAEMA‐b‐PMAA/ZIF‐8 Ternary Lamellar Composite and the Photocatalytic Degradation of Methylene Blue

PDMAEMA‐b‐PMAA block copolymers were prepared by the sequential RAFT polymerization of DMAEMA and tBMA, followed by hydrolysis. Phosphotungstic acid (HPW) was anchored to the PDMAEMA blocks through electrostatic interactions and the as‐obtained HPW/PDMAEMA‐b‐PMAA was added to the synthesis of ZIF‐8. During the formation of ZIF‐8, the PMAA blocks coordinated to the Zn²⁺ ions through their carboxy groups, along with the HPW groups that were anchored to the PDMAEMA blocks. In this way, the block copolymer could consolidate the interactions between HPW and ZIF‐8 and prevent the leakage of HPW. Finally, the HPW/PDMAEMA‐b‐PMAA/ZIF‐8 ternary lamellar composite was obtained and the structure of the HPW/PDMAEMA‐b‐PMAA/ZIF‐8 hybrid material was characterized by using powder X‐ray diffraction (PXRD), X‐ray photoelectron spectroscopy (XPS), and scanning electron microscopy (SEM). As a photocatalyst, the HPW/PDMAEMA‐b‐PMAA/ZIF‐8 ternary lamellar composite showed excellent photoactivity for the degradation of methylene blue (MB). The rate of degradation of MB was 0.0240 min^?1, which was 7.5‐times higher than that of commercially available P25 (0.0032 min^?1). In the presence of H₂O₂, the kinetic degradation parameters of the composite reached 0.0634 min^?1, which was about 19.8‐times higher than that of P25.     

Metal‐Ion‐Triggered Exonuclease III Activity for the Construction of DNA Colorimetric Logic Gates

The logic system is obtained by using a series of double‐stranded (ds) DNA templates with mismatched base pairs (T–T or C–C) and ion‐modulated exonuclease III (Exo III) activity, in which the Exo III cofactors, Hg²⁺ and Ag⁺ ions, are used as inputs for the activation of the respective scission of Exo III based on the formation of T–Hg²⁺–T or C–Ag⁺–C base pairs. Additionally, two kinds of signal probes are utilized to transduce the logic operations. One is the two split G‐rich DNA strands that are used to design the OR, AND, INHIBIT, and XOR gates, whereas the other is the self‐assembled split G‐quadruplex structure to construct NOR, NAND, IMPLICATION, and XNOR operations based on DNA hybridization and strand displacement. In the presence of hemin, the split G‐quadruplex biocatalyzes the formation of a colored product, which is an output signal for the different logic gates. Thus, we have constructed a complete set of colorimetric DNA logic gates based on the Exo III and split G‐quadruplex for the first time. In addition, we are able to effortlessly recognize the logic output signals by the naked eye and their simplicity and cost‐effective design is the most apparent feature for the logic gates developed in this work.     

Switchable electrode controlled by Boolean logic gates using enzymes as input signals

Application of Boolean logic operations performed by enzymes to control electrochemical systems is presented. Indium–tin oxide (ITO) electrodes with the surface modified with poly-4-vinyl pyridine (P4VP) brush were synthesized and used as switchable electrochemical systems. The switch ON and OFF of the electrode activity were achieved by pH changes generated in situ by biocatalytic reactions in the presence of enzymes used as input signals. Two logic gates operating as AND/OR Boolean functions were designed using invertase and glucose oxidase or esterase and glucose oxidase as input signals, respectively. The electrode surface coated with a shrunk P4VP polymer at neutral pH values was not electrochemically active because of the blocking effect of the polymer film. The positive outputs of the logic operations yielded a pH drop to acidic conditions, resulting in the protonation and swelling of the P4VP polymer allowing penetration of a soluble redox probe to the conducting support, thus switching the electrode activity ON. The electrode interface was reset to the initial OFF state, with the inhibited electrochemical reaction, upon in situ pH increase generated by another enzymatic reaction in the presence of urease. Logically processed biochemical inputs of various enzymes allowed reversible activation–inactivation of the electrochemical reaction.     

Switchable Biosensor Controlled by Biocatalytic Process

The poly(dimethylamino methacrylate) (PDMAEMA) brush‐modified indium tin oxide (ITO) electrode was used to test the switch properties of interfacial activity caused by bioelectrochemical signals. The swelling of the polymer brushes increased when the medium’s pH changed from alkaline to acid after glucose was added to the system. A pH change generated in situ by means of biocatalytic reactions enabled bioelectrocatalytic interface’s reversible activation.     

Synthesis and micellization of PSt‐PNIPAM‐PDMAEMA hetero‐arm star polymer with double thermo‐responsibility

A hetero‐arm star polymer, polystyrene‐poly(N‐isopropylacrylamide)‐ poly(2‐(dimethylamino)ethylmethacrylate) (PSt‐PNIPAM‐PDMAEMA), was synthesized by “clicking” the alkyne group at the junction of PSt‐b‐PNIPAM diblock copolymer onto the azide end‐group of PDMAEMA homopolymer via 1,3‐dipolar cycloaddition. The resultant polymer was characterized by gel permeation chromatography, proton nuclear magnetic resonance spectroscopy and Fourier transform infrared spectroscopy. PSt‐PNIPAM‐PDMAEMA micelles with PSt block as core and PNIPAM and PDMAEMA blocks as shell were formed when adding the copolymer solution in THF into 10 folds of water. Lower critical solution temperature (LCST) of PNIPAM and PDMAEMA homopolymer is 32 °C for PNIPAM and 40 to 50 °C for PDMAEMA, respectively. Upon continuous heating through their LCSTs, PSt‐PNIPAM‐PDMAEMA core‐shell micelles exhibited two‐stage thermally induced collapse. The first‐stage collapse, from 20 to 34 °C, is ascribed to the shrinkage of PNIPAM chains; and the second‐stage collapse, from 38 to 50 °C, is due to the shrinkage of PDMAEMA chains. Dynamic light scattering was used to confirm the double phase transitions. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 786–796, 2009     

DNA Triplexes‐Guided Assembly of G‐Quadruplexes for Constructing Label‐free Fluorescent Logic Gates

Assembly of G‐quadruplexes guided by DNA triplexes in a controlled manner is achieved for the first time. The folding of triplex sequences in acidic conditions brings two separated guanine‐rich sequences together and subsequently a G‐quadruplex structure is formed in the presence of K⁺. Based on this novel platform, label‐free fluorescent logic gates, such as AND, INHIBIT, and NOR, are constructed with ions as input and the fluorescence of a G‐quadruplex‐specific fluorescent probe NMM as output.     

Fluorescence Logic‐Signal‐Based Multiplex Detection of Nucleases with the Assembly of a Cationic Conjugated Polymer and Branched DNA

An energy‐transfer cascade is generated from a cationic conjugated polymer (PFP) and negatively charged, Y‐shaped DNA labeled with three dyes at its termini (fluorescein (Fl), Tex Red, and Cy5). Multistep fluorescence resonance energy transfer regulates the fluorescence intensities of PFP and the dyes. Different types of logic gates can be operated by observing the emission wavelengths of different dyes with multiplex nucleases as inputs.

     

Connectable DNA Logic Gates: OR and XOR Logics

Modern computer processors are based on semiconductor logic gates connected to each other in complex circuits. This study contributes to the development of a new class of connectable logic gates made of DNA in which the transfer of oligonucleotide fragments as input/output signals occurs upon hybridization of DNA sequences. The DNA strands responsible for a logic function form associates containing immobile DNA four‐way junction structures when the signal is high and dissociate into separate strands when the signal is low. A basic set of logic gates (NOT, AND, and OR) was designed. Two NOT gates, two AND gates, and an OR gate were connected in a network that corresponds to an XOR logic function. The design of the logic gates presented here may contribute to the development of the first biocompatible molecular computer.     

An Amphiphilic Polymer‐ and Carbon Nanotube‐Modified Indium Tin Oxide Electrode for Sensitive Electrochemical DNA Detection with Low Nonspecific Binding

We herein report an amphiphilic polymer‐, carboxylated multiwalled carbon nanotube (CNT)‐, silane polymer‐, and streptavidin‐modified indium tin oxide (ITO) electrode that allows low nonspecific binding and efficient immobilization of DNA, along with good electrocatalytic activities and low background‐current levels. The low nonspecific binding results from the well‐covering of the CNT and ITO surface with the amphiphilic polymer and silane polymer, as well as the poly(ethylene glycol) groups of the polymers. The streptavidin for DNA immobilization is covalently attached to the carboxylic acid groups of the amphiphilic polymer and CNT. A low surface coverage of CNT on the ITO electrode provides the good electrocatalytic activities and low background‐current levels. The fabricated electrode enables us to achieve a detection limit of 100 pM in DNA detection.     

Simple and Sensitive Electrochemical DNA Detection of Primer Generation‐Rolling Circle Amplification

A new electrochemical sequence‐specific DNA detection platform based on primer generation‐rolling circle amplification (PG‐RCA), methylene blue (MB) redox indicator, and indium tin oxide (ITO) electrode is reported. In the presence of a specific target sequence, PG‐RCA, an isothermal DNA amplification technique, produced large amounts of amplicons in an exponential manner. In addition to the standard components, the reaction mixture contained MB, which bound with the PG‐RCA amplicons. End‐point electrochemical measurement by differential pulse voltammetry (DPV) was performed using ITO electrode. The amplicon‐bound MB resulted in a lower DPV signal than free MB due to a smaller diffusion coefficient as well as electrostatic repulsion between the negatively charged amplicon‐bound MB and ITO electrode. With simple assay design (recognition probe) and instrumentation (operating temperature at 37 °C and ITO electrode without the need for probe immobilization), this detection platform is well suited for point‐of‐care and on‐site testing. Real‐time measurement was also achieved by pretreating the ITO electrode with bovine serum albumin.     

Poly(L‐lysine)‐Induced Aggregation of Single‐Strand Oligo‐DNA‐Modified Gold Nanoparticles

Single‐strand oligo‐DNA‐modified Au nanoparticles (AuNPs) undergo aggregation in the presence of poly(L ‐lysine) (PLL), which is attributed to the interactions between the oligo‐DNA and PLL. These interactions between the oligo‐DNA and PLL were identified to be electrostatic when the lysine residues of PLL were positively charged and to be hydrogen bonding when the residues were deprotonated. The aggregation was promoted with an increase in the pH value at a pH level lower than the pK_a value of PLL (pK_a≈10.0) due to the gradual deprotonation of the lysine residues and thus suppressed electrostatic interactions between the positively charged lysine residues of PLL and the negatively charged backbone phosphate groups of the oligo‐DNA. At pH levels higher than the pK_a value of PLL, the aggregation was identified to be dominated by the hydrogen bonds between the bases of the oligo‐DNA and the deprotonated lysine residues of PLL. This study prompts the possibility that the spectral, and thus color, change of AuNPs upon aggregation can be used as a probe to follow the interactions between oligo‐DNA and polypeptides.     

Crystallization and stereocomplexation behavior of poly(D‐ and L‐lactide)‐b‐poly(N,N‐dimethylamino‐2‐ethyl methacrylate) block copolymers

The thermal properties, crystallization, and morphology of amphiphilic poly(D ‐lactide)‐b‐poly(N,N‐dimethylamino‐2‐ethyl methacrylate) (PDLA‐b‐PDMAEMA) and poly (L ‐lactide)‐b‐poly(N,N‐dimethylamino‐2‐ethyl methacrylate) (PLLA‐b‐PDMAEMA) copolymers were studied and compared to those of the corresponding poly(lactide) homopolymers. Additionally, stereocomplexation of these copolymers was studied. The crystallization kinetics of the PLA blocks was retarded by the presence of the PDMAEMA block. The studied copolymers were found to be miscible in the melt and the glassy state. The Avrami theory was able to predict the entire crystallization range of the PLA isothermal overall crystallization. The melting points of PLDA/PLLA and PLA/PLA‐b‐PDMAEMA stereocomplexes were higher than those formed by copolymer mixtures. This indicates that the PDMAEMA block is influencing the stability of the stereocomplex structures. For the low molecular weight samples, the stereocomplexes particles exhibited a conventional disk‐shape structure and, for high molecular weight samples, the particles displayed unusual star‐like shape morphology. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 49: 1397–1409, 2011     

In Situ Generated Janus Fabrics for the Rapid and Efficient Separation of Oil from Oil‐in‐Water Emulsions

A cotton fabric was coated with a polymer that contains both poly(dimethyl siloxane) (PDMS) and poly(N,N‐dimethylaminoethyl methacrylate) (PDMAEMA). When the repeat unit number of PDMS is about three‐fold that of PDMAEMA and the fabric is exposed to air, the fabric is superhydrophobic because PDMS in the coating covers the PDMAEMA chains. Upon contact with an oil‐in‐water emulsion, the water‐soluble PDMAEMA rises to the top and the side in contact with the emulsion becomes hydrophilic. The emerged PDMAEMA chains then cause the emulsion droplets to coagulate, and the aggregated oil fills the pores on the superhydrophobic side of the fabric. The oil‐impregnated side remains hydrophobic even upon prolonged contact with water. Thus, a Janus fabric is elegantly generated in situ and sustained. This easy‐to‐prepare Janus fabric rapidly and efficiently separates oil from emulsions and may find practical applications.     

Synthesis,crystalline morphologies,self‐assembly,and properties of H‐shaped amphiphilic dually responsive terpolymers

Novel and well‐defined amphiphilic H‐shaped terpolymers poly(L‐lactide)‐block‐(poly(2‐(N,N‐dimethylamino)ethyl methacrylate) ‐block‐)poly(ε‐caprolactone)(‐block‐poly(2‐(N,N‐dimethylamino)ethyl methacrylate)) ‐b‐poly(L‐lactide) (PLLA‐b‐(PDMAEMA‐b‐)PCL(‐b‐PDMAEMA)‐b‐PLLA) were synthesized by the combination of ring‐opening polymerization, atom transfer radical polymerization, and click chemistry. The H‐shaped amphiphilic terpolymers can self‐assemble into spherical nano‐micelles in water. Because of the dually responsive (temperature and pH) properties of PDMAEMA segments, the hydrodynamic radius of the micelles of the H‐shaped terpolymer solution can be adjusted by altering the environmental temperature or pH values. The thermal properties investigation and the crystalline morphology analysis indicate that the branched structure of the H‐shaped terpolymers and the presence of amorphous PDMAEMA segments together led to the obvious decrease of PCL segments and the complete destruction of crystallinity of the PLLA segments in the H‐shaped terpolymers. In addition, the H‐shaped terpolymer film has better hydrophilicity than linear PCL or triblock polymer of PLLA‐b‐(N₃? )PCL(? N₃)‐b‐PLLA, due to the decrease or destruction of the crystallizability of the PCL or PLLA in the H‐shaped terpolymer and the presence of hydrophilic PDMAEMA segments. These unique H‐shaped amphiphilic terpolymers composed of biodegradable and biocompatible PCL and PLLA components and intelligent and biocompatible PDMAEMA component will have the potential applications in biomedical fields. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012     

Label‐Free Photoelectrochemical Detection of Double‐Stranded HIV DNA by Means of a Metallointercalator‐Functionalized Electrogenerated Polymer

The design of photoactive functionalized electrodes for the sensitive transduction of double‐stranded DNA hybridization is reported. Multifunctional complex [Ru(bpy‐pyrrole)₂(dppn)]²⁺ (bpy‐pyrrole=4‐methyl‐4′‐butylpyrrole‐2,2′‐bipyridine, dppn=benzo[i]dipyrido[3,2‐a:2′,3′‐c]phenazine) exhibiting photosensitive, DNA‐intercalating, and electropolymerizable properties was synthesized and characterized. The pyrrole groups undergo oxidative electropolymerization on planar electrodes forming a metallopolymer layer on the electrode. Thanks to the photoelectrochemical and intercalating properties of the immobilized Ru^II complex, the binding of a double‐stranded HIV DNA target was photoelectrochemically detected on planar electrodes. Photocurrent generation through visible irradiation was correlated to the interaction between double‐stranded DNA and the metallointercalator polymer. These interactions were well fitted by using a Langmuir isotherm, which allowed a dissociation constant of 2×10⁶ L mol^?1 to be estimated. The low detection limit of 1 fmol L^?1 and sensitivity of 0.01 units per decade demonstrate excellent suitability of these modified electrodes for detection of duplex DNA.     

Voltammetric Behavior of Osmium‐Labeled DNA at Mercury Meniscus‐Modified Solid Amalgam Electrodes. Detecting DNA Hybridization

The complex of osmium tetroxide with 2,2′‐bipyridine has been utilized as a probe of DNA structure and an electroactive marker of DNA in DNA hybridization sensors. It produces several voltammetric signals, the most negative of them has been observed only at mercury electrodes. This signal is of catalytic nature affording a high sensitivity of DNA determination. The catalytic current due to evolution of hydrogen in voltammetry of DNA modified by complex of osmium tetroxide with 2,2′‐bipyridine (DNA‐Os,bipy) was studied. Solid amalgam electrodes (modified with mercury menisci) of silver (m‐AgSAE), copper (m‐CuSAE), gold, and of combined bismuth and silver, were used as possible substitutes for mercury electrodes. Besides the hanging mercury drop electrode (HMDE), the catalytic current was observed only on m‐AgSAE and m‐CuSAE. Electrodes of gold and bismuth amalgams did not give the catalytic current. The detection limit of DNA‐Os,bipy on HMDE was 0.1 ng mL^?1 (RSD=2.3 %, N=11), and on m‐AgSAE 0.2 ng mL^?1 (RSD=3.1%, N=11). The m‐AgSAE was successfully applied as a detection electrode in double‐surface DNA hybridization experiments offering highly specific discrimination between complementary (target) and nonspecific DNAs, as well as determination of the length of a repetitive DNA sequence. The m‐AgSAE has proved a convenient alternative to the HMDE or carbon electrodes used for similar purposes in previous work.