Methods of stretching DNA molecules using flow fields

Using fluorescence microscopy, we compare the degree of adsorption and stretching of DNA onto surfaces achieved by published stretching methods that use fluid flow: molecular combing, spin-stretching, and air-blowing. Molecular combing uses a receding meniscus to stretch out and deposit the DNA onto a hydrophobic surface. In spin-stretching, we find that the effect of radial hydrodynamic flow created by the centrifugal force of the rotating disk is minimal and that the DNA is stretched out on a hydrophobic substrate by the moving meniscus. In air-blowing, a jet of gas pushes liquid across a substrate, depositing stretched DNA molecules along the way. In our study, DNA molecules either combed or spin-stretched onto hydrophobic surfaces stretch to a greater degree than those that are air-blown; fewer are deposited at pH 8.0 than at lower pH, apparently because at pH 8.0 DNA adhesion occurs primarily only at the DNA extremities and so avoids trapped regions of incompletely stretched DNA, with the side effect that more molecules avoid adhesion altogether. We find by high-speed video microscopy that there is complex droplet deformation and motion during air-blowing, which complicates the deposition and stretching process, leading to radial alignment. Our results are a first step toward understanding and optimizing the various proposed methods of DNA stretching and anchoring onto surfaces, which is important in studying their interactions with proteins.     

Properties of monolayers of crown ethers bearing an azo and azoxy group in the macrocycle

Two methods are described for preparing monomolecular layers of crown ethers with an azo or azoxy group in the macrocycle. When the molecules used to build the monolayer are soluble in aqueous solutions, adsorptive preconcentration on mercury electrodes was used to prepare the monolayer coating. The monolayer was electroactive due to the presence of the azo or azoxy unit in the molecules. Monolayers of crown ethers bearing an azo group in the macrocycle were shown to recognize alkali metal cations present in the solution. Changes of the parameters of the voltammetric reduction peaks - peak potential and peak width, served as an indication of specific interactions of the monolayer of 13-membered and 16-membered azocrown ethers with Na⁺ and K⁺ cations, respectively.The monolayers capable of recognizing cations have also been prepared on the aqueous solution-air interface, using the Langmuir technique. In this approach, amphiphilic derivatives of the azocrowns were synthesized and the monolayer has been assembled on the subphase containing metal cations. Binding of the cation by the macrocycle has a stabilizing effect on the monolayer and higher collapse pressures are achieved than on the pure water subphase. The monolayer was transferred from the air-water interface on the solid substrate using the Langmuir-Blodgett technique. Thin mercury film electrodes on the Ag substrate, or An films evaporated on glass slides were employed as the electrode substrates. The former gave monolayer modified electrodes of higher stability.Presented at the Sixth International Seminar on Inclusion Compounds, Istanbul, Turkey, 27–31 August, 1995.     

TPPS和Gemini表面活性剂的复合膜及其手性的研究

研究了一种新的gemini表面活性剂(C12H24-α,ω-(C12H25N＋(CH3)2Br－)2, （简写为C12-C12-C12）和TPPS在气液界面上形成的复合膜及其手性.实验发现,单独C12-C12-C12不能在纯水表面形成稳定的单分子膜，但当亚相中存在TPPS时，可形成稳定的单分子膜.通过水平提拉法将复合膜转移到固体基板上，发现在适当的pH值条件下，TPPS可在复合膜中形成J-聚集体，并且发现，尽管Gemini表面活性剂和TPPS 都 是非手性的，TPPS的J-聚集体表现出强烈的Cotton效应.另外，gemini表面活性剂的两个正电荷中心对TPPS的J-聚集体的手性并不能表现出协同效应.     

Orientation of DNA and the agarose gel matrix in pulsed electric fields

Transient electric birefringence has been used as an analytical tool to study the orientation of DNA in agarose gels, and to study the orientation of the matrix alone. The sign of the birefringence of DNA oriented in an agarose gel is negative, as observed in free solution, indicating that the DNA molecules orient parallel to the direction of the electric field. If the median pore diameter of the gel is larger than the contour length of the DNA molecule, the DNA effectively does not see the matrix and the birefringence relaxation time is the same as observed in free solution. However, if the median pore diameter of the gel is smaller than the contour length of the DNA, the DNA molecule becomes stretched as well as oriented. For DNA molecules of moderate size (less than or equal to 4 kb), stretching in the gel causes the birefringence relaxation times to increase to the values expected for fully stretched molecules. Complete stretching is not observed for larger DNA molecules. The orientation and stretching of DNA molecules in the gel matrix indicates that end-on migration, or reptation, is a likely mechanism for DNA electrophoresis in agarose gels. When the electric field is rapidly reversed in polarity, very little change in the orientation of the DNA is observed if the DNA molecules were completely stretched and had reached their equilibrium orientation before the field was reversed in direction. Hence completely stretched, oriented DNA molecules are able to reverse their direction of migration in the electric field with little or no loss of orientation. However, if the DNA molecules were not completely stretched or if the equilibrium orientation had not been reached, substantial disorientation of the DNA molecules is observed at field reversal. The forced rate of disorientation in the reversing field is faster than the field-free rate of disorientation. Complicated patterns of reorientation can be observed after field reversal, depending on the degree of orientation in the original field direction. The effect of pulsed electric fields on the orientation of the agarose gel matrix itself was also investigated.(ABSTRACT TRUNCATED AT 400 WORDS)     

Single DNA molecule stretching in sudden mixed shear and elongational microflows

High-throughput stretching and monitoring of single DNA molecules in continuous elongational flow offers compelling advantages for biotechnology applications such as DNA mapping. However, the polymer dynamics in common microfluidic implementations are typically complicated by shear interactions. These effects were investigated by observation of fluorescently labeled 185 kb bacterial artificial chromosomes in sudden mixed shear and elongational microflows generated in funneled microfluidic channels. The extension of individual free DNA molecules was studied as a function of accumulated fluid strain and strain rate. Under constant or gradually changing strain rate conditions, stretching by the sudden elongational component proceeded as previously described for an ideal elongational flow (T. T. Perkins, D. E. Smith and S. Chu, Science, 1997, 276, 2016): first, increased accumulated fluid strain and increased strain rate produced higher stretching efficiencies, despite the complications of shear interactions; and second, the results were consistent with unstretched molecules predominantly in hairpin conformations. More abrupt strain rate profiles did not deliver a uniform population of highly extended molecules, highlighting the importance of balance between shear and elongational components in the microfluidic environment for DNA stretching applications. DNA sizing with up to 10% resolution was demonstrated. Overall, the device delivered 1000 stretched DNA molecules per minute in a method compatible with diffraction-limited optical sequence motif mapping and without requiring laborious chemical modifications of the DNA or the chip surface. Thus, the method is especially well suited for genetic characterization of DNA mixtures such as in pathogen fingerprinting amidst high levels of background DNA.     

Sequence-specific DNA affinity chromatography: Application of a group-specific adsorbent for the isolation of restriction endonucleases

The use of sequence-specific DNA affinity adsorbents for the isolation of restriction endonucleases EcoRI and SphI to near homogeneity has been reported. However, the high cost of these adsorbents is a limiting factor for their wider application. This paper reports the application of sequence-specific DNA affinity ligands containing recognition sequences for 34 restriction endonucleasesas group-specific ligands in the isolation of restriction endonucleases. Crude samples of six restriction endonucleases, namely BshFI, BamHI, SmaI, SacII, PvuII and SalI, were shown to bind to these adsorbents and could be eluted at different KCl concentrations. High purification factors and recoveries were obtained. Restriction endonuclease BshFI, an isoschizomer of HaeIII, from the microorganism Bacillus sphaericus was purified to near homogeneity employing a two-step procedure which involves DNA-cellulose chromatography and oligonucleotide- ligand affinity chromatography. The enzyme exists as a monomer with an apparent relative molecular mass of 34 000 as determined by both sodium dodecyl sulphate-polyacrylamide gel electrophoresis and size-exclusion chromatography.     

Elimination of aggregates of ferredoxin from its self-assembled monolayer on silicon substrate

The self-assembled ferredoxin monolayer onto the (100) surface of the silicon substrate was prepared and the nonspecifically adsorbed aggregates of ferredoxin on the substrate were successfully eliminated by using a zwitterionic surfactant, 3-[(3-cholamidopropyl) dimethylammonio]-1-propanesulfonate (CHAPS). The AFM image of the self-assembled ferredoxin monolayer on the silicon substrate treated with CHAPS clearly shows that the size of ferredoxin clusters is about 20–30 nm, which is on the order of an aggregate of about five ferredoxin molecules, whereas the size of ferredoxin aggregates on the substrate without CHAPS treatment was measured to be about 100–200 nm. Those results offer a useful method for the elimination of the nonspecific adsorption of proteins onto inorganic substrates, which has been a long-term problem in the fabrication of biomolecular electronic devices by the self-assembly technique.     

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     

Langmuir-Blodgett单分子膜功能体系的研究(Ⅲ).有序单分子膜内的J-聚体

本文讨论了单分子膜内J-聚体的性质、稳定性以及影响J-聚体形成的因素。实验中发现,制备有序单分子膜时,机械振动是影响J-聚体形成的重要因素;利用分子的电性质,靠外加电场的作用,可以增加J-聚体的成份。载于玻璃载片上单分子膜中的J-聚体在室温下就可以破坏,在低温下能够得以保存。根据J-聚体的能级性质及其在能量转移中的作用,作者认为,J-聚体可以形成激子态,J-聚体内的能量转移是激子转移。     

基于自组装纳米金单层膜的全内反射SERS研究

采用静电自组装技术分别在玻璃基片和30 nm厚的金膜表面固定一层金纳米粒子（GNP）制得两种表面增强拉曼散射（SERS）基底,然后通过棱镜全内反射（TIR）激励和背向收集模式分别测试了两种基底上吸附的染料单分子层SERS光谱. 实验结果表明两种SERS基底的拉曼增强效果均高度依赖于入射激光的偏振状态,对于玻璃/纳米金SERS基底,s 光全内反射导致的拉曼增强因子是线偏振光（p）光的2-5 倍,说明该基底上的“热点”位于纳米金单层膜内相邻粒子之间;对于玻璃/金膜/纳米金SERS基底,只有采用p光在特定的全内反射角下才能激发SERS信号,而且测得的SERS信号比玻璃/纳米金基底增强了近30 倍. 究其原因是p 光在金膜表面共振激发的传播表面等离子体与纳米金局域表面等离子体耦合,进而导致显著场增强. 实验结果指出在背向收集模式下,由p 光激发的SERS信号是非偏振光,包含强度几乎相等的s 和p 成分. 利用玻璃/金膜/纳米金基底还实现了拉曼光定向发射和收集,测得的SERS信号是p光.     

Energieelastizität von Polystyrol bei der Warmverstreckung

Zusammenfassung Es wurde das Verhalten der Inneren Energie von amorphem, chemisch unvernetztem Polystyrol beim uniaxialen Dehnen oberhalb der Glastemperatur untersucht. Isotrope Proben dieser Substanz, deren Moleküle ein physikalisches Netzwerk bilden, wurden unter de finierten Bedingungen (konstante Verstrecktemperatur und Verstreckzeit) auf Dehnungsgrade zwischen 0,2 und 4,0 verstreckt. Die während des Verstreckvorganges aufgewendete Arbeit sowie die Doppelbrechung der verstreckten Proben wurden gemessen. Bei Raumtemperatur wurde sodann in einem Lösungskalorimeter die Lösungswärme der verstreckten Proben in Toluol bestimmt. Die Differenz zwischen der Lösungswärme einer verstreckten Probe und der einer unverstreckten Vergleichsprobe ist im vorliegenden Fall gleich der Differenz der Inneren Energie beider Proben.

---

Summary The change of the inner energy of amorphous and chemically non crosslinked polystyrene after uniaxial stretching above glass temperature was investigated.For this reason isotropic samples of polystyrene, the molecules of which form a physical network, were stretched under well defined conditions (constant temperature and constant time for stretching inclusive quenching below glass temperature) for different degrees of elongation between 0.2 and 4.0. The work expended in stretching and the birefringence of the stretched samples were measured too. Then at room temperature the heat of solution in toluene for the diverse samples was determined. The difference of the heats of solution for stretched and non stretched samples is identical with the difference of the inner energies.

---

---

Mit 14 Abbildungen und 4 Tabellen

---

Auszug aus der Dissertation vonJ. Stölting (Marburg, Juli 1968).     

Induced Collapse in the Formation of Alternating Langmuir–Blodgett Films

Two compounds whose molecules have large dipole moments, strereoregular perfluorinated alkylmethacrylate-co-methacrylic acid (A) and p-octadecylaminoazobenzene-p"-sulfamide (B), were used to assemble Langmuir–Blodgett polar films by the alternating method to achieve high polarization. According to estimates, the dipole moment of the dimeric unit of copolymer A is equal to about 4 D, the dipole moment of compound B, to 12 D. Unusually high (several units) transfer ratio was observed for the monolayer B when preparing the structures of (AB) _n type. The monolayers were stable during their formation process. Upon the pause of a substrate when passing through the monolayer B, the monolayer area remained strictly constant. According to the model proposed, the monolayer looses its stability and locally collapses in the meniscus zone at the contact line of the monolayer B and substrate due to an increase in the electrostatic repulsion between the dipoles of molecules B. The validity of this model is confirmed by the data of small-angle X-ray diffraction and atomic force microscopy for various alternating Langmuir–Blodgett films.     

基于自组装纳米金单层膜的全内反射SERS研究

采用静电自组装技术分别在玻璃基片和30 nm厚的金膜表面固定一层金纳米粒子(GNP)制得两种表面增强拉曼散射(SERS)基底,然后通过棱镜全内反射(TIR)激励和背向收集模式分别测试了两种基底上吸附的染料单分子层SERS光谱.实验结果表明两种SERS基底的拉曼增强效果均高度依赖于入射激光的偏振状态,对于玻璃/纳米金SERS基底,s光全内反射导致的拉曼增强因子是线偏振光(p)光的2-5倍,说明该基底上的"热点"位于纳米金单层膜内相邻粒子之间;对于玻璃/金膜/纳米金SERS基底,只有采用p光在特定的全内反射角下才能激发SERS信号,而且测得的SERS信号比玻璃/纳米金基底增强了近30倍.究其原因是p光在金膜表面共振激发的传播表面等离子体与纳米金局域表面等离子体耦合,进而导致显著场增强.实验结果指出在背向收集模式下,由p光激发的SERS信号是非偏振光,包含强度几乎相等的s和p成分.利用玻璃/金膜/纳米金基底还实现了拉曼光定向发射和收集,测得的SERS信号是p光.     

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.     

Substrate‐induced formation of a recognition structure in a four‐polypeptide–lipid monolayer system

Poly(γ‐methyl L ‐glutamate)s with Ser, His, Asp, and Glu residues at the amino terminal as the serine protease catalytic site were prepared. The number‐average degree of polymerization of the polypeptides was 51. A dipalmitoylphosphatidylcholine monolayer containing the polypeptides was formed at the air–water interface and was transferred onto gold‐deposited glass plates. The binding of N‐acetyltyrosine ethyl ester, a typical substrate of the serine protease, to the monolayer was characterized by surface plasmon resonance measurements. The four‐polypeptide–lipid monolayer system conditioned on an aqueous solution containing the substrate N‐acetyltyrosine ethyl ester exhibited Langmuir‐type binding of the substrate. Its binding constant of 6.1 × 10⁴ M⁻¹ was about 20 times larger than that observed for a monolayer prepared on pure water. The behavior may have arisen from a substrate‐induced rearrangement of the four kinds of polypeptides in the monolayer, forming a substrate‐binding structure similar to that found in serine protease. © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 38: 2186–2191, 2000     

On the formation and structure of self-assembling monolayers. I. A comparative atr-wettability study of Langmuir—Blodgett and adsorbed films on flat substrates and glass microbeads

Organized oleophobic monolayers of several long chain compounds and steroid derivatives produced on flat solid substrates by spontaneous adsorption from organic solutions are compared with Langmuir—Blodgett (LB) monolayers transferred on identical substrates from the water-air interface. Quantitative infrared ATR and polarized ATR spectroscopy, and wettability measurements are used to correlate the various films and to determine their molecular density and orientation, mode of film-to-surface binding, and other structural characteristics. Formation of oleophobic adsorbed monolayers on a model powder substrate—smooth glass microbeads—is also investigated. It is concluded that, irrespective of the mode of film-to-surface binding (ionic, covalent, or hydrogen bonding), and the nature of the substrate (Ge, Si, ZnSe, glass slides, glass microbeads), saturation of the adsorption leads in all studied systems to the formation of tightly packed and highly oriented monolayers, structurally equivalent to LB monolayers of same or similar compounds deposited on the bare surfaces of the respective substrates. These findings are interpreted in terms of a cooperative surface process leading to aggregation of molecules into a characteristic “monolayer phase.” Significant structural differences may develop in LB built-up films thicker than one monolayer. A mechanism for the formation of covalently bonded silane monolayers is proposed.     

Subcellular topological effect of particle monolayers on cell shapes and functions

We studied topological effects of subcellular roughness displayed by a closely packed particle monolayer on adhesion and growth of endothelial cells. Poly(styrene-co-acrylamide) (SA) particles were prepared by soap-free emulsion copolymerization. Particle monolayers were prepared by Langmuir–Blodgett deposition using particles, which were 527 (SA053) and 1270 nm (SA127) in diameter. After 24-h incubation, cells tightly adhered on a tissue culture polystyrene dish and randomly spread. On the other hand, cells attached on particle monolayers were stretched into a narrow stalk-like shape. Lamellipodia spread from the leading edge of cells attached on SA053 monolayer to the top of the particles and gradually gathered to form clusters. This shows that cell–cell adhesion became stronger than cell–substrate interaction. Cells attached to SA127 monolayer extended to the reverse side of a particle monolayer and engulfed particles. They remained immobile without migration 24 h after incubation. This shows that the inhibition of extensions on SA127 monolayer could inhibit cell migration and cell proliferation. Cell growth on the particle monolayers was suppressed compared with a flat TCPS dish. The number of cells on SA053 gradually increased, whereas that on SA127 decreased with time. When the cell seeding density was increased to 200,000 cells cm⁻², some adherent cells gradually became into contact with adjacent cells. F-actin condensations were formed at the frame of adherent cells and the thin filaments grew from the edges to connect each other with time. For the cell culture on SA053 monolayer, elongated cells showed a little alignment. Cells showed not arrangement of actin stress fibers but F-actin condensation at the contact regions with neighboring cells. Interestingly, the formed cell monolayer could be readily peeled from the particle monolayer. These results indicate that endothelial cells could recognize the surface roughness displayed by particle monolayers and the response was dependent on the pitch of particle monolayers.     

Hybridization of oligonucleotide by using DNA self-assembled monolayer

The interaction between DNA immobilized on surface and oligonucleotides at the interface is important in detection and diagnostic processes. However, it is difficult to immobilize DNA with maintaining its activity and to realize an efficient hybridization in previous methods. Here, to establish a novel DNA-functionalized surface, the DNA self-assembled monolayer (SAM) was constructed on a gold substrate using thiolated DNA composed of double-stranded (ds) and single-stranded (ss) portion. The DNA SAM was characterized by surface plasmon resonance (SPR), XPS. The hybridization of ss portion of DNA was attempted using the SAM, and in situ monitored by SPR. XPS measurement indicated that the thiolated DNA could form a stable monolayer on a gold substrate through sulfur–gold interaction. SPR measurement implied that the long axis of the DNA standing on the substrate. These results indicated formation of the DNA SAM on the substrate. Hybridization of target DNA containing a complementary sequence for the probe portion was observed by SPR. Moreover, one mismatch of oligonucleotide could be distinguished using the DNA SAM. The SPR result indicates that hybridization of target DNA and probe DNA on the DNA SAM occurs on the DNA SAM.     

DNALB膜的AFM形貌观察

DNA分子本身所具有的独特性质使其在生物学、医学和遗传学等领域占有极其重要的位置 ,近年来 ,人们意识到利用 DNA作为模板剂建造具有特殊结构和功能的纳米材料的可行性 [1] ,如 Braun等 [2 ]将寡聚核苷酸连接在两个金电极之间 ,用 DNA分子作为模板剂生长出 1 2 μm长、直径 1 0 0 nm的银纳米线 ;Mirkin等 [3]将 3 和 5 端连有巯基的寡聚核苷酸与金纳米粒子结合 ,通过互补的碱基形成介观尺寸的组装体 ;Alivisatos等 [4]利用 DNA的特点 ,使其与之相连的金纳米粒子按预计的形式排布形成人造分子 .我们尝试利用 LB技术将 DNA分子复合到…     

Preparation and characterization of redox cellulose Langmuir–Blodgett films containing a ferrocene derivative

The 3‐ferrocenoylpropanoyl group, one of the redox species, was introduced at C‐2 and/or C‐3 positions of 6‐O‐(4‐stearyloxytrityl)cellulose. The spreading behavior of the cellulose derivatives on the water surface and the properties of Langmuir–Blodgett (LB) films were investigated. The surface pressure–area isotherm of the cellulose monolayer was changed by the subphase temperature. Uniform monolayers of 6‐O‐(4‐stearyloxytrityl)cellulose 3‐ferrocene propionate (STCFc) could be deposited successively onto several substrates by the horizontal lifting method at 10 mN m^?1, and this produced X‐type LB films. The successive uniform depositions of STCFc were confirmed by ultraviolet–visible absorption spectra. X‐ray diffraction measurements indicated that the thickness of the STCFc molecules in the LB films was 1.99 nm. Fourier transform infrared spectroscopy measurements supported the idea that hydrocarbon chains in the LB films were highly ordered (trans‐zigzag) and oriented considerably perpendicular to the surface of the substrate. Moreover, the C?O group of the ferrocenoyl groups was perpendicular to the surface of the substrate, and the ferrocene group was occupied in the water phase. Cyclic voltammograms for the STCFc monolayer on a gold electrode exhibited surface waves. The interfacial electron‐transfer process between the redox site incorporated into the cellulose LB monolayer and the electrode surface was fast enough at a scanning rate lower than 100 mV s^?1. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 5023–5031, 2005