Optical spectroscopy of inorganic-organic host-guest nanocrystals organized as oriented monolayers

Oriented and densely packed zeolite L monolayers were prepared on a glass support. The one-dimensional channels of zeolite L, being all oriented perpendicular to the glass and parallel to each other, were sequentially filled by ion exchange with two strongly fluorescent dye molecules. First N-methylacridine (MeAcr⁺) was inserted followed by 3,3′-diethylthiacarbocyanine (DTC⁺). The shorter MeAcr⁺ is oriented perpendicular to the channel axis while the longer DTC⁺ is parallel, due to the constraints imposed by the geometry of the zeolite L channels, as deduced from fluorescence anisotropy of single MeAcr⁺-zeolite L and DTC⁺-zeolite L crystals. The dye molecules can enter the channels only from the top side of the monolayer, since the entrances on the bottom are blocked by the glass support. The resulting ordering has been observed by fluorescence microscopy of single DTC⁺, MeAcr⁺-zeolite L crystals. Conditions were found to suppress the pronounced Rayleigh scattering of zeolite monolayers. Thus high quality absorption spectra of DTC⁺, MeAcr⁺-zeolite L monolayers on glass could be measured at different angles between the incident light and the layer. The results deliver a direct proof that microscopic ordering of the dyes in the channels of zeolite L as well as macroscopic organization of the dye-zeolite L monolayer on the glass support was achieved. Thus a high level of organization was obtained by controlled assembly of the zeolite L crystals into oriented structures followed by subsequent insertion of strongly luminescent dyes.     

Microwave absorption spectroscopy of DNA

By utilizing a novel approach to microwave spectrometry, we have measured the absolute absorption spectrum of plasmid DNA (pUC8.c2), in buffered aqueous solution, from 5 to 20 GHz. Our technique does not suffer from the same experimental difficulties that plague other methods. We observe no absorption resonances in this frequency range, but we do see broadband differences, between DNA and pure buffer, that are attributable to changes in the ionic conductivity of the solutions. These results constitute the first verification, by a totally different technique, of the absence of resonances in the microwave absorption spectrum of DNA, and the first data obtained by any technique in the 10–20-GHz band. © 1993 John Wiley & Sons, Inc.     

Simian virus 40 DNA replication in nuclear monolayers.

Simian virus 40 DNA replication has been studied in nuclear monolayers prepared by treatment of monolayers of BSC-1 monkey kidney cells with Nonidet P-40. These nuclear monolayers incorporated [3H]TTP into two types of viral replicative intermediates that sediment as 25-26S and 22-23S species, respectively, in neutral sucrose gradients. The 22-23S species behaves, in dye buoyant density equilibrium gradients, as a late replicative intermediate. Examination of both species in alkaline sucrose gradients revealed the presence of two types of newly synthesized strands: (i) 4-7S strands and (ii) full-length, or nearly full-length, 10-16S strands. At low TTP concentrations (less than 0.5 muM), the two size classes were found in approximately equal amounts. However, at 10 to 50 muM TTP, the proportion of the longer strands increased, with a corresponding decrease in the relative amount of the 4-7S species. Thus, the joining of small, Okazaki-like fragments to the growing chain appears to require a much higher concentration of TTP than the synthesis of the fragments themselves. Replicating simian virus 40 DNA synthesized in the nuclear monolayers is is associated with "M bands", as previously demonstrated for replicating simian virus 40 DNA in cultured whole cells.     

Characterization of complex gramicidin monolayers by light reflection and Fourier transform infrared spectroscopy

The reflectivities of monomolecular films of water-insoluble fatty alcohols and fatty acid methyl esters are measured at the air/water interface. A correlation between chain length and reflectivity of the monofilm is established which agrees with calculated values derived from a theoretical model. The correlation is used to estimate thickness of a monolecular film of gramicidin A. Fourier transform infrared (FTIR) spectroscopy is applied to transferred mixed layers of ion-channel-forming gramicidin A and dioctadecyldimethylammonium bromide in order to evaluate the structure of gramicidin. Transfer conditions for these monofilms are elaborated. Results of the reflection method and FTIR spectroscopy demonstrate that gramicidin exists as double-stranded beta-helix inside the monolayer at a lateral pressure similar to that found in biomembranes.     

Sensing minute changes in biological cell monolayers with THz differential time-domain spectroscopy

We used terahertz differential time-domain spectroscopy (THz-DTDS) to measure minute changes of bovine lung microvessel endothelial cells (BLMVEC) in response to vascular endothelial growth factor (VEGF). These changes were reflected by alterations in THz wave attenuations and THz dielectric properties of the treated cells. The VEGF-induced THz attenuations of cell monolayers correlated well with changes in transendothelial resistance, as measured using electric cell-substrate impedance sensing (ECIS). However, the morphological differences that gave rise to these changes were not observed with standard optical phase contrast microscopy. We conclude that THz-DTDS is a highly sensitive, non-invasive, powerful new tool to measure minute changes in the morphology of live, cultured cell monolayers. This method enables spectroscopic investigations of cells in the THz band, providing information unavailable through other conventional methods such as optical phase contrast microscopy and ECIS.     

Responses of bacterial monolayers to gaseous nutrients observed by surface plasmon resonance spectroscopy

Monolayers of live bacterial cells adsorbed on Ag/Al₂O₃ film caused surface plasmon resonance angle shifts upon provision of specific gaseous nutrients, probably because of the changes in the cell volume attending the metabolic response.     

A DNA assembly model of sentence generation

Recent results of corpus-based linguistics demonstrate that context-appropriate sentences can be generated by a stochastic constraint satisfaction process. Exploiting the similarity of constraint satisfaction and DNA self-assembly, we explore a DNA assembly model of sentence generation. The words and phrases in a language corpus are encoded as DNA molecules to build a language model of the corpus. Given a seed word, the new sentences are constructed by a parallel DNA assembly process based on the probability distribution of the word and phrase molecules. Here, we present our DNA code word design and report on successful demonstration of their feasibility in wet DNA experiments of a small scale.     

Polarization-modulated FTIR spectroscopy of lipid/gramicidin monolayers at the air/water interface

Monolayers of gramicidin A, pure and in mixtures with dimyristoylphosphatidylcholine (DMPC), were studied in situ at the air/H2O and air/D2O interfaces by polarization-modulated infrared reflection absorption spectroscopy (PM-IRRAS). Simulations of the entire set of amide I absorption modes were also performed, using complete parameter sets for different conformations based on published normal mode calculations. The structure of gramicidin A in the DMPC monolayer could clearly be assigned to a beta6.3 helix. Quantitative analysis of the amide I bands revealed that film pressures of up to 25-30 mN/m the helix tilt angle from the vertical in the pure gramicidin A layer exceeded 60 degrees. A marked dependence of the peptide orientation on the applied surface pressure was observed for the mixed lipid-peptide monolayers. At low pressure the helix lay flat on the surface, whereas at high pressures the helix was oriented almost parallel to the surface normal.     

Interaction of proteins with lipid monolayers at the air-solution interface studied by reflection spectroscopy

The interaction of a fluorescein-labelled insulin and of cytochrome C with the air-solution interface and with lipid monolayers at the air-solution interface has been studied by measuring the change in surface pressure at constant area and by reflection spectroscopy. Chromophores at the interface only give rise to enhanced light reflection without contribution to the signal from chromophores in the bulk. The accumulation of labelled insulin at the solution surface is very weak as concluded from the shape of the spectrum and reflection intensity. No interaction with a monolayer of dipalmitoyl-phosphatidylcholine at initial surface pressure of 5mN/m was detected. In contrast, the interaction with monolayers of dioctadecyl-dimethyl-ammonium bromide at initial surface pressures between 5 and 40 mN/m is much stronger, leading to a remarkable increase of surface pressure at constant area and strong reflection signal. The technique was also used to detect cytochrome C at the air-solution interface.     

Multi-nanopore force spectroscopy for DNA analysis

The need for low-cost DNA sequence detection in clinical applications is driving development of new technologies. We demonstrate a method for detection of mutations in a DNA sequence purely by electronic means, and without need for fluorescent labeling. Our method uses an array of nanopores to perform synchronized single-molecule force spectroscopy measurements over many molecules in parallel, yielding detailed information on the kinetics of hundreds of molecule dissociations in a single measurement.     

Thermal fluctuation spectroscopy of DNA thermal denaturation

We have developed the technique of thermal fluctuation spectroscopy to measure the thermal fluctuations in a system. This technique is particularly useful to study the denaturation dynamics of biomolecules like DNA. Here we present a study of the thermal fluctuations during the thermal denaturation (or melting) of double-stranded DNA. We find that the thermal denaturation of heteropolymeric DNA is accompanied by large, non-Gaussian thermal fluctuations. The thermal fluctuations show a two-peak structure as a function of temperature. Calculations of enthalpy exchanged show that the first peak comes from the denaturation of AT rich regions and the second peak from denaturation of GC rich regions. The large fluctuations are almost absent in homopolymeric DNA. We suggest that bubble formation and cooperative opening and closing dynamics of basepairs causes the additional fluctuation at the first peak and a large cooperative transition from a partially molten DNA to a completely denatured state causes the additional fluctuation at the second peak.     

Two-dimensional crystallization of DNA gyrase B subunit on specifically designed lipid monolayers

The B subunit of DNA gyrase formed two-dimensional crystals when bound to a specifically recognized phospholipid spread into a monolayer at the air/water interface. The especially designed lipids consisted of novobiocin coupled through the 3' or 2" hydroxyl group and a hydrophilous linker of a given length to dioleoylphosphatidic acid. Two-dimensional crystals of the gyrase B subunit are formed under physiological conditions of pH and ionic strength, with no precipitant added to the solution. Crystal diffraction extended to a 2.7 nm resolution in negative stain, with unit cell parameters a = 6.1 nm, b = 7.6 nm and gamma = 64 degrees.     

A new generation of scanners for DNA chips

Today, most of the DNA chips are used with fluorescent markers. Associated with fluorescence confocal scanners, this technology achieves remarkable performances in terms of sensitivity and accuracy. The main technical issues related to these scanners have already been reviewed. However, these scanners are costly, especially when high density chips are used. In this case, a mechanical precision of 1 microm or less is required to achieve the measurement precision required. This cost level prevents the spread of this technology in the diagnostic market. We will present a new concept for scanners with equivalent or superior performances, with a cost cut of 5-10. This concept is inspired from the field of optical disk and reader. Basically, an optical format is added to the chip, before DNA deposition. This format contains tracks which are superimposed to the DNA features. These tracks define the path that an optical head of a CD player must follow in order to scan the surface of the DNA chip. Such a head is a very cheap component, and has a precision of less than 100 nm thanks to real-time focus and tracking. These functions are fulfilled by electromagnetic actuators mounted on the support of the frontal lens. We show here that it is possible to use such a head to build a fluorescence confocal scanner with equivalent or even better performances than conventional scanners.     

Characterization of DNA structures by laser Raman spectroscopy

Oriented fibers drawn from aqueous gels of calf-thymus DNA were maintained at constant relative humidites of 75 and 92% to yield canonical A-DNA and B-DNA structures, respectively. Raman spectra of the two forms of DNA were recorded over the spectral range 300–4000 cm^?1. The authenticated DNA fibers were deuterated in hygrostatic cells containing D₂O at appropriate relative humidities, and the corresponding spectra of deuterated DNAs were also obtained. The spectra reveal all of the Raman scattering frequencies and intensities characteristic of A- and B-DNA structures in both nondeuterated and deuterated froms, as well as the frequencies and intensities of adsorbed solvent molecules from which the hydration content of DNA fibers can be calculated. Numerous conformation-sensitive vibrational modes of DNA bases and phosphate groups have been identified throughout the 300–1700-cm^?1 interval. Evidence has also been obtained for conformation sensitivity of deoxyribosyl CH stretching modes in the 2800–3000-cm^?1 region. Raman lines of both the backbone and the bases are proposed as convenient indicators of A- and B-DNA structures. The results are extended to Z-DNA models investigated previously. Some implications of these findings for the determination of DNA or RNA structure from Raman spectra of nucleoproteins and viruses are considered.     

Investigation of DNA structural changes by infrared spectroscopy

DNA-oriented samples of various origins were studied under different conditions of humidiity and sodium chloride content by means of infrared spectroscopy. (1) Oriented DNA (M. Lysodeikticus, E. coli, calf thymus and salmon sperm) films at 3–4% sodium chloride yield polarized spectra which show drastic changes at relative humidities (r.h.) between 94% and 0% indicative of conformational changes: B form → a form → disordered form The measurements of the infrared dichroism at frequencies of about 1230 cm^?1 and at about 1090 cm^?1 allow one to determine the orientation of the phosphate group, whereas the measurements at 1710 cm^?1 characterize the base orientation. At humidities higher than 90% r.h. (B form) the bisector of OPO forms an angle of 70° relative to the helix axis, whereas at lower humidities, between 75% and 50% r.h. (A form) a rotation to about 45° is observed. Simultaneously, the 0—0 line of phosphate group changes its orientation from 55° to 65° to the helix when B → A transition takes place. The results are in general agreement with that of X-ray diffraction and allow one to determine the orientation of the phosphate group with greater precision. (2) The B–A conformational change is not observed for satellite DNA, isolated from Cancer pagurus, of which the guanine + cytosine content is below 5%. As a function of decreasing humidities, one observes the transition: B form → disordered form A diagram of conformational changes of DNA's as a function of base composition and of r.h., suggests that B–A transition will occur for DNA of relatively higher G + C content, whereas for high (A + T) content, base sequence may be of importance. The B–A transition is prevented in DNA at a relatively high or very low sodium chloride content.