Mechanism of Proton Relaxation for Enzyme‐Manipulated,Multicomponent Gold–Magnetic Nanoparticle Chains

Longitudinal and transverse relaxation times of multicomponent nanoparticle (NP) chains are investigated for their potential use as multifunctional imaging agents in magnetic resonance imaging (MRI). Gold NPs (ca. 5 nm) are arranged linearly along double‐stranded DNA, creating gold NP chains. After cutting gold NP chains with restriction enzymes (EcoRI or BamHI), multicomponent NP chains are formed through a ligation reaction with enzyme‐cut, superparamagnetic NP chains. We evaluate the changes in relaxation times for different constructs of gold–iron oxide NP chains and gold–cobalt iron oxide NP chains using 300 MHz ¹H NMR. In addition, the mechanism of proton relaxation for multicomponent NP chains is examined. The results indicate that relaxation times are dependent on the one‐dimensional structure and the amount of superparamagnetic NP chains present in the multicomponent constructs. Multicomponent NP chains arranged on double‐stranded DNA provide a feasible method for fabrication of multifunctional imaging agents that improve relaxation times effectively for MRI applications.     

DNA/CdS纳米粒子复合体系的光谱和光电化学性质

在水溶液中以DNA作为模板和稳定剂, 构筑了DNA与CdS纳米粒子复合体系(DNA/CdS NPC), 研究DNA的含量, 单双链等对复合体系光电响应的影响, 并综合TEM, UV-Vis, IR和荧光光谱等对其形貌和光谱性质进行表征. 结果表明, CdS纳米粒子(CdS NPs)与DNA链之间主要通过静电作用结合; DNA模板对CdS NPs的禁带宽度没有影响; 以DNA模板合成的CdS NPs具有较高的表面态密度, 其对CdS NPs的荧光有增强作用, 而对光电流响应有抑制作用, 并且DNA在复合体系中的含量影响荧光增强和光电流减弱的程度. 该复合体系在荧光标记检测和DNA的定量分析方面可能具有应用前景.     

Bioconjugated nanoparticles for DNA protection from cleavage

We have developed a novel method to protect DNA from cleavage using bioconjugated nanoparticles. Positively charged amino-modified silica nanoparticles have been directly prepared using water-in-oil microemulsion. Plasmid DNA can be easily enriched onto the positively charged nanoparticle surface, and the DNA strands are well protected from enzymatic cleavage. When incubated with nuclease enzyme for enzymatic cleavage, free plasmid DNA strands are completely cleaved, while those on the nanoparticle surfaces are intact. Our results clearly demonstrate unique properties of nanomaterials when combined with biomolecules. Our simple bionanotechnology will be highly useful in DNA separation, manipulation, and detection, and possibly in genetic engineering and gene therapy, as plasmid DNA can be protected in cellular environments without any change in its property.     

DNA interaction probed by evanescent wave cavity ring-down absorption spectroscopy via functionalized gold nanoparticles

Evanescent wave cavity ring-down absorption spectroscopy (EW-CRDS) is employed to study interaction and binding kinetics of DNA strands by using gold nanoparticles (Au NPs) as sensitive reporters. These Au NPs are connected to target DNA of study that hybridizes with the complementary DNA fixed on the silica surface. By the absorbance of Au NPs, the interaction between two DNA strands may be examined to yield an adsorption equilibrium constant of 2.2 × 10¹⁰ M⁻¹ using Langmuir fit. The binding efficiency that is affected by ion concentration, buffer pH and temperature is also examined. This approach is then applied to the label-free detection of the DNA mutation diseases using the sandwich hybridization assay. For monitoring a gene associated with sickle-cell anemia, the detection limit and the adsorption equilibrium constant is determined to be 1.2 pM and (3.7 ± 0.8) × 10¹⁰ M⁻¹, distinct difference from the perfectly matched DNA sequence that yields the corresponding 0.5 pM and (1.1 ± 0.2) × 10¹¹ M⁻¹. The EW-CRDS method appears to have great potential for the investigation of the kinetics of a wide range of biological reactions.     

Stability of DNA-linked nanoparticle crystals: effect of number of strands, core size, and rigidity of strand attachment

Three-dimensional ordered lattices of nanoparticles (NPs) linked by DNA have potential applications in novel devices and materials, but most experimental attempts to form crystals result in amorphous packing. Here we use a coarse-grained computational model to address three factors that impact the stability of bcc and fcc crystals formed by DNA-linked NPs : (i) the number of attached strands to the NP surface, (ii) the size of the NP core, and (iii) the rigidity of the strand attachment. We find that allowing mobility in the attachment of DNA strands to the core NP can very slightly increase or decrease melting temperature T(M). Larger changes to T(M) result from increasing the number of strands, which increases T(M), or by increasing the core NP diameter, which decreases T(M). Both results are consistent with experimental findings. Moreover, we show that the behavior of T(M) can be quantitatively described by the model introduced previously [F. Vargas Lara and F. W. Starr, Soft Matter, 7, 2085 (2011)].     

Hydration behavior of heart muscle studies by nuclear magnetic relaxation: Deuterium exchange of water protons in the myocardium

Proton transverse relaxation, deuterium and oxygen-17 NMR measurements on functional animal heart muscle were employed to study the distribution and exchange of water protons in the heart. Our nonlinear regression analysis of such data showed the presence of three proton transverse relaxation components that are likely to correspond, respectively, to two major types of water compartments in the heart muscle and the heart muscle matrix. A deuterium exchange study was undertaken to obtain additional information concerning the chemical exchange of water protons/deuterium within these two water compartments, and the effects of proton intermolecular dipolar interactions on the transverse relaxation of water protons. Our results are likely to influence the analysis and interpretation of MRI data for myocardium since it provides details of the microscopic water distribution in the myocardium which is important to the heart function.     

Oligonucleotide loaded polypeptide‐peptide nanoparticles towards mitochondrial‐targeted delivery

Nanoparticles (NPs) consisting of biodegradable and biocompatible polymers may have the ability to deliver a cargo to specific tissue, cell type, and organelle. Various diseases, which are linked to mitochondrial genome (mtDNA) mutations and have no effective treatments, may be approached by gene therapy strategies. In this study, we adapted the recently developed mitochondria delivering polypeptide‐peptide nanoparticles (PoP‐NPs) system to carry an oligonucleotide cargo to the proximity of the mitochondria. PoP‐NPs are formulated by self‐assembly of the negatively charged polypeptide, poly gamma glutamic acid (γ‐PGA), with an amphiphilic and cationic β‐sheet peptide (PFK). Here, we show that PFK interacts favorably with oligonucleotides and thereby enables the formation of DNA‐loaded PoP‐NPs (DNA‐PoP‐NPs). DNA‐PoP‐NPs could be assembled with different peptide to oligonucleotide (N/P) ratios, and their targeting to the proximity of mitochondria in cell culture could be facilitated through NPs coating with PFK peptide.     

Proton Transverse Relaxation as a Sensitive Probe for Structure Determination in Solid Proteins

Solid‐state nuclear magnetic resonance (NMR) spectroscopy has been successfully applied to elucidate the atomic‐resolution structures of insoluble proteins. The major bottleneck is the difficulty to obtain valuable long‐distance structural information. Here, we propose the use of distance restraints as long as 32 Å, obtained from the quantification of transverse proton relaxation induced by a methanethiosulfonate spin label (MTSL). Combined with dipolar proton–proton distance restraints, this method allows us to obtain protein structures with excellent precision from single spin‐labeled 1 mg protein samples using fast magic angle spinning.     

Direct Sensing of 5‐Methylcytosine by Polymerase Chain Reaction

The epigenetic control of genes by the methylation of cytosine resulting in 5‐methylcytosine (5mC) has fundamental implications for human development and disease. Analysis of alterations in DNA methylation patterns is an emerging tool for cancer diagnostics and prognostics. Here we report that two thermostable DNA polymerases, namely the DNA polymerase KlenTaq derived from Thermus aquaticus and the KOD DNA polymerase from Thermococcus kodakaraensis, are able to extend 3′‐mismatched primer strands more efficiently from 5 mC than from unmethylated C. This feature was advanced by generating a DNA polymerase mutant with further improved 5mC/C discrimination properties and its successful application in a novel methylation‐specific PCR approach directly from untreated human genomic DNA.     

Electron attachment to solvated dGpdG: effects of stacking on base-centered and phosphate-centered valence-bound radical anions

To explore the nature of electron attachment to guanine-centered DNA single strands in the presence of a polarizable medium, a theoretical investigation of the DNA oligomer dinucleoside phosphate deoxyguanylyl-3',5'-deoxyguanosine (dGpdG) was performed by using density functional theory. Four different electron-distribution patterns for the radical anions of dGpdG in aqueous solution have been located as local minima on the potential energy surface. The excess electron is found to reside on the proton of the phosphate group (dGp(H-)dG), or on the phosphate group (dGp(.-)dG), or on the nucleobase at the 5' position (dG(.-)pdG), or on the nucleobase at the 3' position (dGpdG(.-)), respectively. These four radical anions are all expected to be electronically viable species under the influence of the polarizable medium. The predicted energetics of the radical anions follows the order dGp(.-)dG>dG(.-)pdG>dGpdG(.-)>dGp(H-)dG. The base-base stacking pattern in DNA single strands seems unaffected by electron attachment. On the contrary, intrastrand H-bonding is greatly influenced by electron attachment, especially in the formation of base-centered radical anions. The intrastrand H-bonding patterns revealed in this study also suggest that intrastrand proton transfer might be possible between successive guanines due to electron attachment to DNA single strands.     

Base-dependent electron photodetachment from negatively charged DNA strands upon 260-nm laser irradiation

DNA multiply charged anions stored in a quadrupole ion trap undergo one-photon electron ejection (oxidation) when subjected to laser irradiation at 260 nm (4.77 eV). Electron photodetachment is likely a fast process, given that photodetachment is able to compete with internal conversion or radiative relaxation to the ground state. The DNA [6-mer]3- ions studied here show a marked sequence dependence of electron photodetachment yield. Remarkably, the photodetachment yield (dG6 > dA6 > dC6 > dT6) is inversely correlated with the base ionization potentials (G < A < C < T). Sequences with guanine runs show increased photodetachment yield as the number of guanine increases, in line with the fact that positive holes are the most stable in guanine runs. This correlation between photodetachment yield and the stability of the base radical may be explained by tunneling of the electron through the repulsive Coulomb barrier. Theoretical calculations on dinucleotide monophosphates show that the HOMO and HOMO-1 orbitals are localized on the bases. The wavelength dependence of electron detachment yield was studied for dG63-. Maximum electron photodetachment is observed in the wavelength range corresponding to base absorption (260-270 nm). This demonstrates the feasibility of gas-phase UV spectroscopy on large DNA anions. The calculations and the wavelength dependence suggest that the electron photodetachment is initiated at the bases and not at the phosphates. This also indicates that, although direct photodetachment could also occur, autodetachment from excited states, presumably corresponding to base excitation, is the dominant process at 260 nm. Excited-state dynamics of large DNA strands still remains largely unexplored, and photo-oxidation studies on trapped DNA multiply charged anions can help in bridging the gap between gas-phase studies on isolated bases or base pairs and solution-phase studies on full DNA strands.     

Biotin-Conjugated Poly(Acrylic Acid)-Grafted Ultrasmall Gadolinium Oxide Nanoparticles for Enhanced Tumor Imaging

Herein, biotin (Bio)-conjugated poly(acrylic acid) (PAA)-grafted ultrasmall gadolinium oxide nanoparticles (Bio-PAA-Gd₂O₃ NPs) were synthesized for enhanced tumor imaging using Bio as a tumor-targeting ligand. The average particle diameter of Gd₂O₃ NPs was 2.1 nm. The Bio-PAA-Gd₂O₃ NPs exhibited excellent colloidal stability (i. e., no precipitation) and a high longitudinal water proton spin relaxivity (r₁) of 23.8 s⁻¹ mM⁻¹ (r₂/r₁=1.6 and r₂=transverse water proton spin relaxivity), which was ∼6 times higher than those of commercial Gd-chelated magnetic resonance imaging (MRI) contrast agents. Cytotoxicity tests using two cell lines showed that the Bio-PAA-Gd₂O₃ NPs were almost non-toxic up to the measured concentration of 500 μM Gd. The enhanced tumor imaging of the Bio-PAA-Gd₂O₃ NPs was demonstrated through their higher positive contrasts and longer contrast retention at the tumor after intravenous injection in T₁ MR images, compared with those of the control PAA-Gd₂O₃ NPs.     

A Fluorescence Assay Based on GoldMag-CS Nanoparticles for Hepatitis B Virus DNA

A sensitive fluorescence assay for hepatitis B virus (HBV) DNA was developed based on the dissociation of bio-bar-code DNA probes from GoldMag-CS nanoparticles (NPs) and magnetic separation. In this method, the target sequence (HBV DNA) was recognized through sandwich hybridization by the catching probes and the detection probes. Catching probes were modified with biotins, and were specifically bound on streptavidin-coated 96-well microplates; detection probes were all attached on the GoldMag-CS nanoparticles, which also bound bio-bar-code strands with fluorescent tags. Bio-bar-codes were dissociated from the NPs by dithiothreitol (DTT) after DNA target recognition and magnetic separation, and then quantified. Streptavidin-coated 96-well microplates diminished the nonspecific binding of DNA-conjugated GoldMag-CS nanoparticles, thus lowering the background; and GoldMag-CS nanoparticles provided easy separation and significant signal amplification. Together, these two effects brought about the detection limit as low as 7.52 fM.     

Electrical detection of single methylcytosines in a DNA oligomer

We report label-free electrical detections of chemically modified nucleobases in a DNA using a nucleotide-sized electrode gap. We found that methyl substitution contributes to increase the tunneling conductance of deoxycytidines, which was attributed to a shift of the highest occupied molecular orbital level closer to the electrode Fermi level by methylation. We also demonstrate statistical identifications of methylcytosines in an oligonucleotide by tunneling current. This result suggests a possible use of the transverse electron-transport method for a methylation level analysis.     

pH-Responsive Reversible DNA Self-assembly Mediated by Zwitterion

pH-Responsive DNA assembles have drawn growing attentions owing to their great potential in diverse areas.However,pH-responsive motifs are limited to specific DNA sequences and annealing is usually needed for DNA assemblies;therefore,sequence-independent pH-responsive DNA assembly at room temperature is highly desired as a more general way.Here,we propose a reversible pH-responsive DNA assembly strategy at room-temperature using zwitterion,glycine betaine(GB),as charge-regulation molecules.The reversible assembly and disassembly of DNA nanostructures could be achieved by alternatively regulating the acidic and basic environments in the presence of GB,respectively.In an acidic environment,carboxylate group in GB was protonated and GB was positively charged,which facilitated to shield the inherent electrostatic repulsion of DNA strands.Molecular simulation showed that the newly formed carboxyl group in protonated GB could form hydrogen bonds with bases in DNA to promote the assembly of DNA strands.In a basic solution,carboxylate group in GB was deprotonated and GB was neutral,thus inducing the dissociation of DNA assembly.     

多孔岩心的渗透性

The relaxation properties of water saturated in porous core are discussed and the distribution of proton transverse relaxation time and bi-exponential model of longitudiual relaxation time are obtained, which provide an illustration for two-model of fluids saturated in porous media. The cutoff value of T_1 based on relaxation specific property of fluids in porous core is adopted to improve the correlation between permeability and ?4T1b2.     

Magnetic relaxation dispersion of lithium ion in solutions of DNA

The magnetic field dependence of the nuclear spin-lattice relaxation rate constant defines the magnetic relaxation dispersion (MRD) and provides a direct characterization of the molecular dynamics that cause fluctuations in the magnetic couplings in the system and may also indicate the dimensional constraints on the motion. The counterion cloud surrounding a linear polyelectrolyte ion, such as DNA in solution, provides an interesting opportunity for ion confinement that helps in understanding the thermodynamics and the dynamics of the interactions between the polyion and other solutes. The MRD profiles of lithium ion and tetramethylammonium ion were recorded in dilute aqueous solutions of native calf thymus DNA, which provides a long, charged rod that reorients slowly. The 7Li ion relaxes through the nuclear electric quadrupole coupling and the proton-lithium dipole-dipole coupling; the protons of the tetramethylammonium ion relax by dipole-dipole coupling. MRD profiles of the 7Li+ ion are dominated by transient interactions with the DNA that yield a linear dependence of the spin-lattice relaxation rate constant on the logarithm of the Larmor frequency. This magnetic field dependence is consistent with diffusive ion motions that modulate two spatial coordinates that characterize the relaxation couplings in the vicinity of the polyion. Motions around the rod and fluctuations in the ion distance from the rod are consistent with these constraints for lithium. The magnetic field dependence of the tetramethylammonium ion proton relaxation rate constant is weak, but also approximately a linear function of the logarithm of the Larmor frequency, which implies that the field dependence is caused in part by local order in the DNA solution.     

Polyelectrolyte-templated synthesis of bimetallic nanoparticles

Bimetallic nanoparticles (NPs) are known to exhibit enhanced optical and catalytic properties that can be optimized by tailoring NP composition, size, and morphology. Galvanic deposition of a second metal onto a primary metal NP template is a versatile method for fabricating bimetallic NPs using a scalable, solution-based synthesis. We demonstrate that the galvanic displacement reaction pathway can be controlled through appropriate surface modification of the NP template. To synthesize bimetallic Au-Ag NPs, we used colloidal Ag NPs modified by layer-by-layer (LBL) assembled polyelectrolyte layers to template the reduction of HAuCl(4). NPs terminated with positively and negatively charged polyelectrolytes yield highly contrasting morphologies and Au surface concentrations. We propose that these charged surface layers control galvanic charge transfer by controlling nucleation and diffusion at the deposition front. This surface-directed synthetic strategy can be advantageously used to tailor both overall NP morphology and Au surface concentrations.     

Electrochemical strategy for sensing DNA methylation and DNA methyltransferase activity

The present work demonstrates a novel signal-off electrochemical method for the determination of DNA methylation and the assay of methyltransferase activity using the electroactive complex [Ru(NH₃)₆]³⁺ (RuHex) as a signal transducer. The assay exploits the electrostatic interactions between RuHex and DNA strands. Thiolated single strand DNA1 was firstly self-assembled on a gold electrode via Au–S bonding, followed by hybridization with single strand DNA2 to form double strand DNA containing specific recognition sequence of DNA adenine methylation MTase and methylation-responsive restriction endonuclease Dpn I. The double strand DNA may adsorb lots of electrochemical species ([Ru(NH₃)₆]³⁺) via the electrostatic interaction, thus resulting in a high electrochemical signal. In the presence of DNA adenine methylation methyltransferase and S-adenosyl-l-methionine, the formed double strand DNA was methylated by DNA adenine methylation methyltransferase, then the double strand DNA can be cleaved by methylation-responsive restriction endonuclease Dpn I, leading to the dissociation of a large amount of signaling probes from the electrode. As a result, the adsorption amount of RuHex reduced, resulting in a decrease in electrochemical signal. Thus, a sensitive electrochemical method for detection of DNA methylation is proposed. The proposed method yielded a linear response to concentration of Dam MTase ranging from 0.25 to 10 U mL⁻¹ with a detection limit of 0.18 U mL⁻¹ (S/N = 3), which might promise this method as a good candidate for monitoring DNA methylation in the future.     

Polyaniline nanowires on Si surfaces fabricated with DNA templates

It is essential to put individual, free-standing nanowires onto insulating substrates and integrate them to useful devices. Here we report a strategy for fabrication of conducting polymer nanowires on thermally oxidized Si surfaces by use of DNA as templates. The direct use of stretched and immobilized DNA strands as templates avoids the agglomeration of DNA caused by shielding of charges on DNA when polyaniline/DNA complexes formed in solution. Most importantly, the oriented DNA strands immobilized on the Si surface predetermine the position and the orientation of the nanowires. The approach described here is the first step toward uniting the programmable-assembly ability of DNA with the unique electronic properties of conducting polymers for high-density functional nanodevices. The conductivity of the nanowires is very sensitive to the proton doping-undoping process, suggesting that the nanowires hold great promise for sensitive chemical sensor applications.