Hybridization of DNA at the surface of phospholipid monolayers. Effect of orientation of oligonucleotide chains

We studied the properties of lipid monolayers formed at the air-water interface composed of dioleoylphosphatidylcholine (DOPC) with incorporated short (19-mer) oligonucleotides. These oligonucleotides were modified by oleylamine at both (3' and 5') terminals or only at one (3') terminal. Interaction of single-stranded (19-mer) oligonucleotides without oleylamine with DOPC monolayers resulted only in slight increase of surface pressure and the area per phospholipid molecule, while more substantial and significant increase of these values were observed following incorporation of oligonucelotides modified by oleylamine. This influence is similar for both types of oligonucleotide modifications. However, considerable differences in changes of monolayer properties took place after hybridization with complementary oligonucleotides. The hybridization of oligonucleotides with the DNA modified by oleic acid at both 3' and 5' terminals at the surface of lipid monolayer resulted in further increase of surface pressure and in the increase of the area per phospholipid molecule, while decrease of both the surface pressure and the area per phospholipid molecules were observed for hybridization with DNA modified by oleic acid at 3' terminal. It is possible that in latter case, the hybridization caused the loss of hybridized molecules from monolayers. Interaction of noncomplementary chains with DOPC monolayers with incorporated oleyl acid-modified DNA also influenced the properties of monolayers, but the effect was weaker in comparison with that observed for complementary chains.     

Structural properties and Raman spectroscopy of lipid Langmuir monolayers at the air-water interface

Spectra of octadecylamine (ODA) Langmuir monolayers and egg phosphatidylcholine (PC)/ODA-mixed monolayers at the air-water interface have been acquired. The organization of the monolayers has been characterized by surface pressure-area isotherms. Application of polarized optical microscopy provides further insight in the domain structures and interactions of the film components. Surface-enhanced Raman scattering (SERS) data indicate that enhancement in Raman spectra can be obtained by strong interaction between headgroups of the surfactants and silver particles in subphase. By mixing ODA with phospholipid molecules and spreading the mixture at the air-water interface, we acquired vibrational information of phospholipid molecules with surfactant-aided SERS effect.     

气/液界面Langmuir单分子膜的原位拉曼光谱

提出了一种原位测量气/液界面Langmuir单分子膜拉曼光谱的新方法, 即利用SERS技术, 通过降低亚相的方法来获得气/液界面Langmuir单分子膜的原位拉曼光谱. 利用这种方法, 用原位拉曼光谱测量系统得到了信噪比较好的十八胺及二棕榈酰磷脂酰胆碱单分子膜的拉曼光谱, 在分子水平上获取了单分子膜中的结构信息.     

气液界面磷脂单分子膜的表面增强拉曼光谱

采用纳米银胶作为成膜亚相, 原位获得了十八胺单分子膜、十八胺/卵磷脂复合膜的表面增强拉曼信号.研究表明,增强主要来源于亚相中的银粒子与成膜分子之间较强的作用.通过在磷脂膜内添加十八胺分子辅助增强而获取了卵磷脂的分子振动信息.     

Langmuir monolayers of an inclusion complex formed by a new calixarene derivative and fullerene

The design of new molecules with directed interactions to functional molecules as complementary building blocks is one of the main goals of supramolecular chemistry. A new p-tert-butylcalix[6]arene monosubstituted derivative bearing only one alkyl chain with an acid group (C6A3C) has been synthesized. The C6A3C has been successfully used for building Langmuir monolayers at the air-water interface. The C6A3C molecule adopts a flatlike orientation with respect to the air-water interface. The molecular structure gives the molecule amphiphilic character, while allowing the control of both the dissociation degree and the molecular conformation at the air-water interface. The C63AC has been combined with pristine fullerene (C60) to form the supramolecular complex C6A3C:C60 in 2:1 molar ratio (CFC). The CFC complex retains the ability of C6A3C to form Langmuir monolayers at the air/water interface. The interfacial molecular arrangement of the CFC complex has been convincingly described by in situ UV-vis reflection spectroscopy and synchrotron X-ray reflectivity measurements. Computer simulations complement the experimental data, confirming a perpendicular orientation of the calixarene units of CFC with respect to the air-water interface. This orientation is stabilized by the formation of intermolecular H-bonds. The interfacial monolayer of the CFC supramolecular complex is proposed as a useful model for the well-defined self-assembly of recognition and functional building blocks.     

Fabrication of phytic acid sensor based on mixed phytase-lipid Langmuir-Blodgett films

This paper reports the surface activity of phytase at the air-water interface, its interaction with lipid monolayers, and the construction of a new phytic acid biosensor on the basis of the Langmuir-Blodgett (LB) technique. Phytase was inserted in the subphase solution of dipalmitoylphosphatidylglycerol (DPPG) Langmuir monolayers, and its incorporation to the air-water interface was monitored with surface pressure measurements. Phytase was able to incorporate into DPPG monolayers even at high surface pressures, ca. 30 mN/m, under controlled ionic strength, pH, and temperature. Mixed Langmuir monolayers of phytase and DPPG were characterized by surface pressure-area and surface potential-area isotherms, and the presence of the enzyme provided an expansion in the monolayers (when compared to the pure lipid at the interface). The enzyme incorporation also led to significant changes in the equilibrium surface compressibility (in-plane elasticity), especially in liquid-expanded and liquid-condensed regions. The dynamic surface elasticity for phytase-containing interfaces was investigated using harmonic oscillation and axisymmetric drop shape analysis. The insertion of the enzyme at DPPG monolayers caused an increase in the dynamic surface elasticity at 30 mN m(-)(1), indicating a strong interaction between the enzyme and lipid molecules at a high-surface packing. Langmuir-Blodgett (LB) films containing 35 layers of mixed phytase-DPPG were characterized by ultraviolet-visible and fluorescence spectroscopy and crystal quartz microbalance nanogravimetry. The ability in detecting phytic acid was studied with voltammetric measurements.     

Sequence-specific control of azobenzene assemblies by molecular recognition of DNA

We investigated the molecular recognition between the amphiphile AzoAde, which is composed of azobenzene in the hydrophobic and adenine in the hydrophilic portion of the molecule, and oligonucleotides having a homogeneous base (dA30, dT30, dG30, and dC30) at the air-water interface. On the basis of the complementary base-pairing of DNA in the duplex, orderly arrangement of AzoAde on templated dT30 was examined using pi-A isotherm, UV-vis RAS, FT-IR RAS, and XPS measurements. Although there was little interaction between AzoAde and mismatched oligonucleotides (dA30, dG30, and dC30), AzoAde prepared on a dT30 subphase stoichiometrically assembled and interacted with dT30, subsequently forming a J-form assembly at the air-water interface. AFM observation of the LB films revealed the nanostructure of the J-formed AzoAde monolayer on the dT30 subphase as well as the domain structures of the H-formed monolayers on the other oligonucleotide subphases. Therefore, dT30 has a potential application as a template for assembling AzoAde at the air-water interface.     

Amino-substituted amphiphilic calixarenes: self-assembly and interactions with DNA

The amphiphilic 5,11,17,23-tetramino-25,26,27,28-tetradodecyloxycalix[4]arene is shown to self-assemble as stable and well-defined Langmuir monolayers at the air-water interface. The effect of the presence of DNA in the subphase reveals interactions taking place at the interface between the positively charged surface and the negatively charged DNA, causing an expansion of the monolayers and a phase transition from a liquid-condensed to a liquid-expanded phase; a slight decrease in the stability of the monolayers is also observed. The title compound is shown to self-assemble, with the absence of a cosurfactant, as stable colloidal suspensions. Photon correlation spectroscopy, zeta-potential measurements, and atomic force microscopy reveal that these colloidal suspensions present a monodisperse size distribution and are composed of positively charged solid lipid nanoparticles (SLNs), with an average hydrodynamic diameter of 190 nm and a surface potential of +13.2 mV. The interaction of these SLNs with double-stranded DNA is demonstrated.     

Formation of complex Langmuir and Langmuir-Blodgett films of water soluble rosebengal

This communication reports the formation of complex Langmuir monolayer at the air-water interface by charge transfer types of interaction with the water soluble N-cetyl N,N,N-trimethyl ammonium bromide (CTAB) molecules doped with rosebengal (RB), with the stearic acid (SA) molecules of a preformed SA Langmuir monolayer. The reaction kinetics of the formation of RB-CTAB-SA complex monolayer was monitored by observing the increase in surface pressure with time while the barrier was kept fixed. Completion of interaction kinetics was confirmed by FTIR study. This complex Langmuir films at the air-water interface was transferred onto solid substrates at a desired surface pressure to form multilayered Langmuir-Blodgett films. Spectroscopic characterizations reveal some molecular level interactions as well as formation of microcrystalline aggregates depending upon the molar ratios of CTAB and RB within the complex LB films. Presence of two types of species in the complex LB films was confirmed by fluorescence spectroscopy.     

Biochemical assays of immobilized oligonucleotides with mass spectrometry

This paper reports the use of mass spectrometry to characterize oligonucleotides immobilized to the surfaces of biochips. Biotinylated oligonucleotides were immobilized to self-assembled monolayers that present a streptavidin layer and then treated with a complementary strand to present short duplexes. Treatment of the surface with 5-methoxysalicylic acid and ammonium citrate matrix allows the individual oligonucleotides to be observed by matrix-assisted laser desorption/iozation and time-of-flight mass spectrometry (MALDI-TOF MS). Examples are shown wherein this method is applied to assays of hybridization, of cleavage by a deoxyribozyme, of a dephosphorylation reaction, and of the adducts formed on treatment of DNA with cis-platin. This work provides an early example of the application of mass spectrometry to DNA biochips and may substantially expand the applications of the now common oligonucleotide arrays.     

Interaction of DNA oligomers with cationic lipidic monolayers: complexation and splitting

Interactions of native DNA with octadecylamine (ODA) and hexadecymdimethylammonium bromide (HTAB) monolayers at the air/water interface were studied by pi-A isotherms, ellipsometry, and X-ray reflectivity. We show that the microscopic structure of ODA-DNA complexes is definitely consistent with a single-stranded form for DNA. On the contrary, with HTAB, DNA complexes in its native form. The crucial difference in the behavior of these two fairly similar lipids is due to the presence of the amine group in ODA. These results should be relevant to applications such as DNA chips and sensors.     

DNA分子在气液界面的组装相变特性及其LB膜结构研究

对十八胺与DNA在气液界面上组装及其相变过程进行了研究，利用AFM观察了不 同压力下转移的DNA复合LB膜结构。发现在低表面压时，DNA复合单分子膜表现为技 术发散的分形结构；随着压力的升高，DNA复合膜逐渐由紧密的网状排布结构变为 团聚的块状和团簇结构。表明通过调节膜压，可使膜内DNA分子的构象发生大的变 化，从而生成具有特定形态的二维纳米图案。这种具有特殊形态和结构的DNA LB膜 可望为合成新型生物纳米结构有序功能体系提供模板。     

Voltammetric determination of DNA hybridization using methylene blue and self-assembled alkanethiol monolayer on gold electrodes

An electrochemical DNA biosensor based on the recognition of single stranded DNA (ssDNA) by hybridization detection with immobilized complementary DNA oligonucleotides is presented. DNA and oligonucleotides were covalently attached through free amines on the DNA bases using N-hydroxysulfosuccinimide (NHS) and N-(3-dimethylamino)propyl-N′-ethylcarbodiimide hydrochloride (EDC) onto a carboxylate terminated alkanethiol self-assembled monolayers (SAM) preformed on a gold electrode (AuE). Differential pulse voltammetry (DPV) was used to investigate the surface coverage and molecular orientation of the immobilized DNA molecules. The covalently immobilized probe could selectively hybridize with the target DNA to form a hybrid on the surface despite the bases being attached to the SAM. The changes in the peak currents of methylene blue (MB), an electroactive label, were observed upon hybridization of probe with the target. Peak currents were found to increase in the following order: hybrid-modified AuE, mismatched hybrid-modified AuE, and the probe-modified AuE which indicates the MB signal is determined by the extent of exposed bases. Control experiments were performed using a non-complementary DNA sequence. The effect of the DNA target concentration on the hybridization signal was also studied. The interaction of MB with inosine substituted probes was investigated. Performance characteristics of the sensor are described.     

Sequence-selective extraction of single-stranded DNA using DNA-functionalized reverse micelles

We report here sequence-specific liquid/liquid extraction of single-stranded DNA using reverse micelles (water-in-oil microemulsions), in which hybridization between a DNA-surfactant and a target DNA having a complementary sequence allows selective transport of the target DNA to an organic phase from a mixture of DNA oligonucleotides.     

Kinetic mechanisms in morpholino-DNA surface hybridization

Morpholinos (MOs) are DNA analogues whose uncharged nature can bring fundamental advantages to surface hybridization technologies such as DNA microarrays, by using MOs as the immobilized, or "probe", species. Advancement of MO-based diagnostics, however, is challenged by limited understanding of the surface organization of MO molecules and of how this organization impacts hybridization kinetics and thermodynamics. The present study focuses on hybridization kinetics between monolayers of MO probes and DNA targets as a function of the instantaneous extent of hybridization (i.e., duplex coverage), total probe coverage, and ionic strength. Intriguingly, these experiments reveal distinct kinetic stages, none of which are consistent with Langmuir kinetics. The initial stage, in which duplex coverage remains relatively sparse, indicates confluence of two effects: blockage of target access to unhybridized probes by previously formed duplexes and deactivation of the solid support due to consumption of probe molecules. This interpretation is consistent with a surface organization in which unhybridized MO probes localize near the solid support, underneath a layer of MO-DNA duplexes. As duplex coverage builds, provided saturation is not reached first, the initial stage can transition to an unusual regime characterized by near independence of hybridization rate on duplex coverage, followed by a prolonged approach to equilibrium. The possible origins of these more complex latter behaviors are discussed. Comparison with published data for DNA and peptide nucleic acid (PNA) probes is carried out to look for universal trends in kinetics. This comparison reveals qualitative similarities when comparable surface organization of probes is expected. In addition, MO monolayers are found capable of a broad range of reactivities that span reported values for PNA and DNA probes.     

Stepwise "click" chemistry for the template independent construction of a broad variety of cross-linked oligonucleotides: influence of linker length, position, and linking number on DNA duplex stability

Cross-linked DNA was constructed by a "stepwise click" reaction using a bis-azide. The reaction is performed in the absence of a template, and a monofunctionalized oligonucleotide bearing an azido-function is formed as intermediate. For this, an excess of the bis-azide has to be used compared to the alkynylated oligonucleotide. The cross-linking can be carried out with any alkynylated DNA having a terminal triple bond at any position of the oligonucleotide, independent of chain length or sequence with identical or nonidentical chains. Short and long linkers with terminal triple bonds were introduced in the 7-position of 8-aza-7-deaza-2'-deoxyguanosine (1 or 2), and the outcome of the "stepwise" click and the "bis-click" reaction was compared. The cross-linked DNAs form cross-linked duplexes when hybridized with single-stranded complementary oligonucleotides. The stability of these cross-linked duplexes is as high as respective individual duplexes when they were ligated at terminal positions with linkers of sufficient length. The stability decreases when the linkers are incorporated at central positions. The highest duplex stability was reached when two complementary cross-linked oligonucleotides were hybridized.     

Fluorescence images of DNA-bound YOYO between coupled silver particles

Oligonucleotide-bound silver particles were coupled through hybridization with target complementary oligonucleotides. YOYO molecules were intercalated into DNA duplexes bound between the coupled metal particles. Fluorescence images of YOYO molecules were monitored by scanning confocal microscopy. Relative to the free single YOYO, the emission brightness of the image was enhanced 80-fold after intercalating the fluorophores into the DNA duplexes between the coupled silver particles. Some images of the labeled metal particle dimers were observed to be dumbbell-shaped, suggesting that the stretching of intercalated YOYO molecules was restricted because of the orientation effect of fluorophores. The shortened lifetime of YOYO molecules between the coupled metal particles indicated that the fluorescence was enhanced via a near-field interaction mechanism between the fluorophore and the metal nanoparticle.     

Use of UV-vis reflection spectroscopy for determining the organization of viologen and viologen tetracyanoquinodimethanide monolayers

UV-vis reflection spectroscopy has been used for proving in situ the organization of pure viologen and hybrid viologen tetracyanoquinodimethanide monolayers at the air-water interface. Other more classical measurements concerning Langmuir monolayers, including surface pressure-area and surface potential-area isotherms, are also provided. The organization of the viologen in the Langmuir monolayer was investigated upon the different states of compression, and the tilt angle of the viologen moieties with respect to the water surface was determined. A gradual transition of the viologen molecules from a flat orientation in the gas phase to a more tilted position with respect to the water surface in the condensed phases occurs. The addition of a tetracyanoquinodimethane (TCNQ) salt in the subphase leads to the penetration of TCNQ anions into the positively charged viologen monolayer forming a hybrid viologen tetracyanoquinodimethanide film where a charge-transfer interaction between the two moieties is observed. From a quantitative analysis of the reflection spectra, an organization model of these hybrid monolayers at the air-water interface is proposed, suggesting a parallel arrangement of viologen and TCNQ units with a 1:2 stoichiometry.     

Synthesis and RNA-selective hybridization of α-l-ribo- and β-d-lyxo-configured oligonucleotides

Three α-l-ribofuranosyl analogues of RNA nucleotides (α-l-RNA analogues) have been synthesized and incorporated into oligonucleotides using the phosphoramide approach on an automated DNA synthesizer. The 4′-C-hydroxymethyl-α-l-ribofuranosyl thymine monomer was furthermore synthesized. Relative to the unmodified duplexes, incorporation of a single α-l-RNA monomer into a DNA strand leads to reduced thermal stability of duplexes with DNA complements but unchanged thermal stability of duplexes with RNA complements, whereas incorporation of more than one α-l-RNA monomer lead to moderately decreased thermal stability also of duplexes with RNA complements. Efficient hybridization with an RNA complement and no melting transition with a DNA complement were observed with stereoregular chimeric oligonucleotides composed of a mixture of α-l-RNA and affinity enhancing α-l-LNA monomers (α-l-ribo-configured locked nucleic acid). Furthermore, duplexes formed between oligodeoxynucleotides containing an α-l-RNA monomer and complementary RNA were good substrates for Escherichia coli RNase H. RNA-selective hybridization was also achieved by the incorporation of 1-(4-C-hydroxymethyl-β-d-lyxofuranosyl)thymine monomers into a DNA strand, whereas stable duplexes were formed with both complementary DNA and RNA when these monomers were incorporated into an RNA strand.     

Synthesis and supramolecular self-assembly study of a novel porphyrin molecule in Langmuir and Langmuir-Blodgett films

The self-assembly and supramolecular engineering of porphyrins into ordered arrays have recently attracted much interest because of their promising application potential in molecular and electronic devices, spintronics, energy harvesting and storage, catalysis, and sensor development. We herein report the synthesis and supramolecular self-assembly study of a novel porphyrin molecule, 2Por-TAZ, in Langmuir and Langmuir-Blodgett films. The 2Por-TAZ molecule contains two porphyrin macrocycles attached to a triaminotriazine headgroup. Triaminotriazines are known to form a highly ordered linear supramolecular self-assembly through complementary hydrogen bonding with barbituric acid molecules at the air-water interface. Surface pressure-area isotherm measurements and polarized UV-vis absorption spectroscopic studies indicate that the 2Por-TAZ molecules adopted an edge-on orientation at the air-water interface. Polarized UV-vis absorption study also revealed that the 2Por-TAZ molecules formed linear supramolecular networks on pure water and barbituric acid subphase with porphyrin flat planes facing toward the compression direction. The binding of barbituric acid with 2Por-TAZ molecules was observed from the expansion of the Langmuir monolayer film. Compared to the transferred LB film from pure water subphase, both the UV-vis absorbance and fluorescence emission intensity of the LB film transferred from barbituric acid subphase increased significantly.