Correlation of molecular orientation and packing density in a dsDNA self-assembled monolayer observable with surface-enhanced Raman spectroscopy

Observations of two spectrally distinct ring breathing modes of guanine and adenine in the surface-enhanced Raman spectrum (SERS) of a dsDNA self-assembled monolayer on an Au nanoshell SERS substrate provide information concerning the orientation of its constituent molecules. The two modes vary with DNA concentration in a highly systematic manner, consistent with studies suggesting DNA molecules tend toward a more horizontal orientation at low-surface concentrations and a more vertical conformation at high concentrations. The introduction of small molecular spacers coadsorbed onto the Au nanoshell surface to "raise" the DNA molecules yields a SERS spectrum consistent with a more upright molecular orientation.     

Monitoring the hydration of DNA self-assembled monolayers using an extensional nanomechanical resonator

We have fabricated an ultrasensitive nanomechanical resonator based on the extensional vibration mode to weigh the adsorbed water on self-assembled monolayers of DNA as a function of the relative humidity. The water adsorption isotherms provide the number of adsorbed water molecules per nucleotide for monolayers of single stranded (ss) DNA and after hybridization with the complementary DNA strand. Our results differ from previous data obtained with bulk samples, showing the genuine behavior of these self-assembled monolayers. The hybridization cannot be inferred from the water adsorption isotherms due to the low hybridization efficiency of these highly packed monolayers. Strikingly, we efficiently detect the hybridization by measuring the thermal desorption of water at constant relativity humidity. This finding adds a new nanomechanical tool for developing a label-free nucleic acid sensor based on the interaction between water and self-assembled monolayers of nucleic acids.     

Hybridization with nanostructures of single-stranded DNA

Nanostructures of single-stranded DNA (ssDNA) were produced within alkanethiol self-assembled monolayers using nanografting, an atomic force microscopy (AFM) based lithography technique. Next, variations of the fabrication parameters, such as the concentration of ssDNA or lines per frame, allowed for the regulation of the density of ssDNA molecules within the nanostructures. The label-free hybridization of nanostructures, monitored using high-resolution AFM imaging, has proven to be highly selective and sensitive; as few as 50 molecules can be detected. The efficiency of the hybridization reaction at the nanometer scale highly depends on the ssDNA packing density within the nanostructures. This investigation provides a fundamental step toward sensitive DNA detection and construction of complex DNA architectures on surfaces.     

DNA在氨基功能化偶氮苯自组装膜表面的固定

采用简单快速的方法制备出将DNA固定在其表面的单分子层敏感膜.首先采用表面自组装技术将硅氧烷基偶氮苯衍生物H2NAzoCONHC3Si(OCH3)3(APDA-N-TMSPBA)组装在硅表面,在详细考察单分子层薄膜的化学结构、表面浸润性和分子表面形貌之后,又通过紫外吸收光谱(UV)在位考察了硅氧烷基偶氮苯衍生物的光学异构特性.在DNA在自组装薄膜固定后,X光电子能谱仪(XPS)结果显示出现了明显的磷元素信号,表明DNA分子可以成功固定在自组装膜表面.     

Inclusion of DNA into organic gelator fibers made of amphipathic molecules and its controlled release

When methyl 4,6-O-(p-nitrobenzylidene)-alpha-D-glucopyranoside (p-NO(2)Glu) was dissolved in water, p-NO(2)Glu molecules self-assembled to form a fiber (elemental fiber), and as a result, the solution became a partially transparent gel. When an equal (or more) amount of DNA was added to the gel, a white and crystalline gel was obtained. Energy-dispersive X-ray spectroscopy coupled with TEM and confocal microscopy suggested that DNA was included in the gel fibers made of p-NO(2)Glu molecules. The results imply that p-NO(2)Glu molecules are self-assembled to form an elemental fiber and these elemental fibers and DNA are twisted together to form higher hierarchic fibers. When the complexed gel made of plasmid DNA (pDNA) and p-NO(2)Glu was added to E. coli T7 S30 extract solution, the pDNA had less expression ability compared with naked one. When we added methyl-beta-cyclodextrin (MbetaCyD), the expression rate was recovered with increasing added amount of MbetaCyD. The present paper shows inclusion and controlled release of DNA from a novel supporting material of DNA and that technology could play an important role in the development of localized approaches to gene therapy.     

Translational motion inside self-assembled encapsulation complexes

The motion of guests inside a cylindrical self-assembled host is studied through NMR techniques. Small molecules encapsulated alone, such as the gas molecules cyclopropane and butane, are found to exchange locations slowly but measurably on the NMR time scale using 2D techniques. These molecules can move past one another while still inside the capsule. When gases are coencapsulated with longer flexible molecules such as alkanes, less motion is apparent yet these can still slip by one another and folding of the alkanes also can be detected. Activation barriers for these processes are in the range of 15-17 kcal/mol.     

DNA imaged on a HOPG electrode surface by AFM with controlled potential

Single-molecule AFM imaging of single-stranded and double-stranded DNA molecules self-assembled from solution onto a HOPG electrode surface is reported. The interaction of DNA with the hydrophobic surface induced DNA aggregation, overlapping, intra- and intermolecular interactions. Controlling the electrode potential and using the phase images as a control method, to confirm the correct topographical characterization, offers the possibility to enlarge the capability of AFM imaging of DNA immobilized onto conducting substrates, such as HOPG. The application of a potential of +300 mV (versus AgQRE) to the HOPG enhanced the robustness and stability of the adsorbed DNA molecules, increasing the electrostatic interaction between the positively charged electrode surface and the negatively charged DNA sugar-phosphate backbone.     

Detection of DNA immobilized on bare gold electrodes and gold nanoparticle-modified electrodes via electrogenerated chemiluminescence using a ruthenium complex as a tag

Electrogenerated chemiluminescence (ECL) for DNA hybridization detection is demonstrated based on DNA that was self-assembled onto a bare gold electrode and onto a gold nanoparticles modified gold electrode. A ruthenium complex served as an ECL tag. Gold nanoparticles were self-assembled on a gold electrode associated with a 1,6-hexanedithiol monolayer. The surface density of single stranded DNA (ssDNA) on the gold nanoparticle modified gold electrode was 4.8?×?10¹⁴ molecules per square centimeter which was 12-fold higher than that on the bare gold electrode. Hybridization was induced by exposure of the target ssDNA gold electrode to the solution of ECL probe consisting of complementary ssDNA tagged with ruthenium complex. The detection limit of target ssDNA on a gold nanoparticle modified gold electrode (6.7?×?10^?12 mol L^?1) is much lower than that on a bare gold electrode (1.2?×?10^?10 mol L^?1). The method has been applied to the detection of the DNA sequence related to cystic fibrosis. This work demonstrates that employment of gold nanoparticles self-assembled on a gold electrode is a promising strategy for the enhancement of the sensitivity of ECL detection of DNA.     

Solvent molecules in an epitaxially grown scaffold of star-shaped nanographenes

A scanning tunneling microscopy (STM) study of a star-shaped hexa-peri-hexabenzocoronene (HBC-star) derivative at solid-solution interfaces is presented. The star-shape of the molecules provides voids at their periphery which can be filled by smaller molecules. The use of solvents with different affinities to fill the voids allows for the fine-tuning of the structure of self-assembled architectures of HBC-stars. This concept is demonstrated by the use of solvents of different polarity and size, which leads to the formation of complex, epitaxial architectures at the interface. For small polar solvent molecules, a surprising decrease of the tunneling barrier is observed. The self-assembled architecture may serve as a useful model system for studying the dependence of electron tunneling on order, mobility, and polarity of adsorbates.     

DNA molecule manipulation by motor proteins for analysis at the single-molecule level

Massively parallel and individual DNA manipulation for analysis has been demonstrated by designing a fully self-assembled molecular system using motor proteins. DNA molecules were immobilized by trapping in a polyacrylamide gel replica, and were digested by a restriction enzyme, XhoI, for DNA analysis. One end of the λDNA was modified with biotin and the other end was modified with digoxin molecules by fragment labeling and ligation methods. The digoxin-functionalized end was immobilized on a glass surface coated with anti-digoxigenin antibody. The biotinylated end was freely suspended and experienced Brownian motion in a buffer solution. The free end was attached to a biotinylated microtubule via avidin–biotin biding and the DNA was stretched by a kinesin-based gliding assay. A stretched DNA molecule was fixed between the gel and coverslip to observe the cleavage of the DNA by the enzyme, which was supplied through the gel network structure. This simple process flow from DNA manipulation to analysis offers a new method of performing molecular surgery at the single-molecule scale. Figure DNA molecule manipulation by motor proteins for analysis at the single-molecule level     

Self-assembled monolayers: influence of complementarity between chemisorbed and crystallizing molecules in polymorph selection

The role of self-assembled monolayers in dictating the arrangement of molecules at the interface in a developing solid is explored. A self-assembled monolayer incorporating a complementary backbone structure between chemisorbed and crystallizing molecules of 4-hydroxybiphenyl favors its crystallization in a new monoclinic crystal packing arrangement.     

金属卟啉对杂环及DNA分子识别研究进展

介绍了近几年国内外关于组装金属卟啉对杂环分子、DNA碱基以及RNA的分子识别的研究进展, 并简述了本课题组对金属卟啉与杂环及药物分子复合物的理论研究工作. 金属卟啉广泛存在于自然界和生物体中, 此识别过程对研究和模拟生命体中各种细胞之间的相互作用具有重要意义. 组装后的金属卟啉可通过轴向配位、氢键及π-π堆积作用等识别杂环分子. 金属卟啉对DNA的识别主要有四种作用方式, 而金属卟啉对DNA以及RNA分子的识别主要靠疏水作用力、静电力以及自堆叠作用. 卟啉阳离子与DNA的结合位点受主体侧链取代基的空间结构影响. 金属卟啉对药物分子的识别靠配位键和氢键进行, 以配位键结合的复合物通常具有更高的结合能.     

A tetrafluorophenyl activated ester self-assembled monolayer for the immobilization of amine-modified oligonucleotides

A tetrafluorophenyl (TFP) ester-terminated self-assembled monolayer (SAM) for the fabrication of DNA arrays on gold surfaces is described. Activated ester SAMs are desirable for biomolecule array fabrication because they readily react with amine-containing molecules to form a stable amide linkage. N-Hydroxysuccinimide (NHS) ester SAMs are commonly used for this purpose but are subject to a competing hydrolysis side reaction, limiting their effectiveness under basic conditions. TFP was evaluated here as an alternative activated ester leaving group with a potentially greater stability under basic conditions. It is shown that TFP SAMs are much more stable to basic pH than their NHS analogs and are also more hydrophobic, which is an advantage in the fabrication of high-density spotted arrays. DNA arrays prepared on TFP SAMs at pH 10 have a 5-fold greater surface density of DNA molecules, reduced fluorescence background, and smaller spot radii than those prepared on NHS SAM analogs.     

Thiolated dendrimers as multi-point binding headgroups for DNA immobilization on gold

The synthesis of multithiolated DNA molecules that can be used to produce self-assembled monolayers of single-stranded DNA oligonucleotides on gold substrates is described. Generation 3 polyamidoamine (PAMAM) dendrimers were conjugated to DNA oligomers and functionalized with ~30 protected thiol groups. The protected thiol groups-thioacetate groups-allowed the dendrimer-DNA constructs to be stored in a buffer solution for at least 2 months before deprotection without any observable decrease in their ability to assemble into functional layers. The monolayers formed using these multithiolated DNA probe strands demonstrate target capture efficiencies comparable to those of analogous monolayers assembled with DNA functionalized with single thiol groups. A functional advantage of using dendrimer headgroups is the resistance to probe strand loss in prolonged exposure to buffer solutions at a high temperature (95 °C).     

Two-potential electrochemical probe for study of DNA immobilization

A two-potential electrochemical method is applied to study DNA immobilization, by the simultaneous characterization of capture probe DNA self-assembled monolayers and hybridized target DNA molecules on a given gold electrode surface. Capture probe and target DNA strands are labeled with ferrocenes composed of differing chemical environments, to permit their simultaneous, yet independent signaling at different formal potentials, so that their respective signals may be de-convoluted and assessed for relative surface concentration. Some special attributes of the nondestructive two-potential electrochemical probe described herein include surface sensitivity, chemical and orientation specificity, and the ability to provide a real-time, in situ probe that does not need any wash steps for stringency. This electrochemical probe is applied to study the kinetics, surface architecture, coverage, and orientation of DNA during its immobilization on gold. On the basis of our results primarily from this electrochemical probe, and validated by N(1s) core-level X-ray photoelectron spectra, we judge significant DNA deposition within 5 min of incubation in the deposition solutions, with the capture probe DNA anchored predominantly via the thiol end, even at low coverages. Surface coverage for DNA immobilization plateaus within 30 min of incubation time to approximately 2 x 10(13) molecules/cm(2) and the immobilization kinetics as determined from this electrochemical method are consistent with surface re-organization as the rate-determining step.     

平行四面体纳米孔道中DNA超结构的组装和离子输运特性

<正>受生物膜离子通道结构和功能的启发,人工制备固体纳米孔道门控开关器件一直备受关注[1,2].基于仿生纳米孔道的非对称离子传输性质制备的离子二极管和场效应管装置对于构建离子电路和能量转换的纳米器件至关重要[3,4].然而,仿生制备的固体纳米孔道在离子传输过程中有漏电流的存在,严重影响了固体纳米孔道应用的灵敏度和信噪比[5].针对这一问题,研究者利用DNA分子的特殊识别和自组装的功能特性,相继构筑了基于DNA和纳米孔道的智能响应体系[6,7].但在之前的研究工作中,分[8]     

New electronic and magnetic properties emerging from adsorption of organized organic layers

New electronic and magnetic properties are induced by the adsorption of closed packed monolayers on solid substrates. For many thiolated molecules self-assembled on gold, a surprisingly large paramagnetism is observed. In the case where the layers are made from chiral molecules, in addition an unexpectedly large electronic dichroism is observed, which manifests itself as spin specific electron transmission. This dichroism was observed for monolayers made from polyalanine and from DNA. Self-assembled monolayers of double-stranded DNA oligomers on gold interact with polarized electrons similarly to a strong and oriented magnetic field. The direction of the field for right-handed DNA is away from the substrate. Moreover, the layer shows very high paramagnetic susceptibility. Interestingly, thiolated single-stranded DNA oligomers on gold do not show this effect. All the observations can be rationalized by assuming organization induced charge transfer between the substrate and the organic layer. The charge transfer results in spin alignment of the transferred electrons/holes. While for achiral molecules the spin alignment varies among the domains, in the case of monolayer made from chiral molecules the alignment is the same across the entire sample. When magnetic field is applied, large magnetic moment is observed that results from orbital magnetism.     

Two-dimensional LNA/DNA arrays: estimating the helicity of LNA/DNA hybrid duplex

We measured the helical repeats of a non-natural nucleic acid, locked nucleic acid (LNA), by incorporating LNA strands into the outer arms of a DNA double crossover (DX) molecule; atomic force microscopy (AFM) imaging of the two-dimensional (2D) arrays self-assembled from these DX molecules allows us to derive the helical repeat of the LNA/DNA hetero-duplex to be 13.2 +/- 0.9 base pairs per turn.     

Effect of pH and applied potential on the adsorption of DNA on highly oriented pyrolytic graphite electrodes. Atomic force microscopy surface characterisation

Single-stranded and double-stranded DNA electrochemical biosensors prepared by adsorption during 3 min on HOPG, with or without an applied potential, at pH 5.3 and 7.0, were characterised by MAC mode AFM. During adsorption DNA condenses on the substrate forming complex network films with pores exposing the HOPG surface. The thin films formed in pH 5.3 acetate buffer always presented a better coverage of the HOPG surface with DNA molecules than films formed in pH 7.0 phosphate buffer. The application of a positive potential of 300 mV during adsorption enhanced the robustness and stability of the DNA films with the formation of bigger network holes and a more condensed and compact self-assembled DNA lattice. The knowledge of the morphology of adsorbed DNA on electrode surfaces explains non-specific adsorption on the electrode surface and can be used to improve and develop DNA-electrochemical biosensors.     

Solvent effect on self-assembled structures of 3,8-bis-hexadecyloxy-benzo[c]cinnoline on highly oriented pyrolytic graphite

3,8-Bis-hexadecyloxy-benzo[c]cinnoline (BBC16) self-assembled into two structures at highly oriented pyrolytic graphite (HOPG) surface: one was formed by molecules with a V-like configuration (C2v symmetry) and the other by molecules with a Z-like configuration (C(s) symmetry). The self-assembled structures could be tweaked by the solvents used. In the self-assembled monolayers (SAMs) on HOPG, the BBC16 molecule adopted the V-like configuration in polar solvents and the Z-like configuration in nonpolar solvents. Moreover, the solvent viscosity, solvent dissolvability of BBC16, and substrate temperature also played some roles in tuning the two-dimensional self-assembled structures.