CCA paper: a new two-dimensional cyanuric chloride-activated matrix for universal application in molecular biology

A novel two-dimensional cyanuric chloride-activated (CCA) paper has been developed. It is composed of a cellulosic base, covalently bound cyanuric chloride, and microprecipitated complex cyanuric chloride-sodium chloride crystals on its surface. CCA paper covalently binds nucleic acids and proteins. Its binding capacity for nucleic acids is about 400 micrograms/cm2. Sealed into nitrogen-filled bags and stored at -20 degrees C, it retains its binding activity for at least a year and is always ready for use. CCA paper has been successfully used for capillary and electroblotting of DNA, RNA, and proteins (Southern, Northern, and Western blotting) as well as for dot tests. Furthermore, it was applied to colony and plaque hybridization. A unique property of it is that it permits the staining of proteins after blotting and subsequent performance of radioimmunological detection of specific protein components. This has proven advantageous in two-dimensional Western blotting experiments. Of further importance is its ability to bind DNA fragments from one up to several hundred bp from polyacrylamide sequencing gels.     

One-hour downward alkaline capillary transfer for blotting of DNA and RNA.

The downward alkaline capillary transfer of DNA and RNA from agarose gel to a hybridization membrane was performed using a transfer solution containing 3 M NaCl and 8 mM NaOH. Under mild alkaline conditions, DNA and RNA were completely eluted from the agarose gel and bound to a hybridization membrane within 1 h. On the basis of this new method of transfer a blotting protocol, downward alkaline blotting, was elaborated. It provides a fast and efficient alternative to commonly used Southern and Northern blotting protocols. The downward alkaline blotting of DNA and RNA can be completed in 2.5 and 1.5 h, respectively, and can be used with both plastic and nitrocellulose membranes. In addition, the downward alkaline blotting protocol allows for a hybridization efficiency of DNA and RNA higher than that of the standard blotting protocols performed at neutral pH.     

A reliable method for the use of oligonucleotides as probes in blot-hybridization experiments

We have developed a ligation and specificprimer radiolabeling method that allows the use of oligonucleotides as probes in blot-hybridization experiments. The major advantage of the protocol is that standard hybridization and washing conditions may be used and yield high signals and low background. The observed increase in the stability and intensity of the hybridization signals appears to result from both increased length and specific radioactivity of the hybridization probe.     

Optimization of DNA blot hybridization conditions for various types of membranes]

A set of experiments has been conducted to choose the optimal conditions for DNA transfer and fixation on two types of the nitrocellulose, three types of nylon membranes and on capron filters. The buffer capillary transfer systems, electroblotting and gel hybridization are analyzed. Two techniques for DNA binding have been tested under different transfer conditions for all the membrane types: a vacuum fixation at 80 degrees C and a UV-exposure. The results indicate the critical dependence of the efficiency of blot-hybridization on the conditions of UV-treatment. The UV-exposure longer or shorter than the optimal one resulted in a loss of the hybridization efficiency. The optimal DNA-transfer and fixation conditions are recommended for all the membranes tested. The dependence of the optimal transfer and binding conditions on the specific characteristics of different membrane types was demonstrated for maximal sensitivity of the blot-hybridization.     

Protein instability during HIC: describing the effects of mobile phase conditions on instability and chromatographic retention

Hydrophobic interaction chromatography (HIC) is known to be potentially denaturing to proteins, but the effects of mobile phase conditions on chromatographic behavior are not well understood. In this study, we apply a model describing the effects of secondary protein unfolding equilibrium on chromatographic behavior, including the effects of salt concentration on both stability and adsorption. We use alpha-lactalbumin as a model protein that in the presence and absence of calcium, allows evaluation of adsorption parameters for folded and unfolded species independently. The HIC adsorption equilibrium under linear binding conditions and solution phase protein stability have been obtained from a combination of literature and new experiments. The effect of salt concentration on protein stability and the rate constant for unfolding on the chromatographic surface have been determined by fitting the model to isocratic chromatography data under marginally stable conditions. The model successfully describes the effects of added calcium and ammonium sulfate. The results demonstrate the importance of considering the effects on stability of mobile phase modifiers when applying HIC to marginally stable     

Quantitative molecular hybridization on nylon membranes

A study of DNA hybridization to DNA covalently bound to nylon membranes was made in order to develop a quantitative method for molecular hybridization using a nylon-based matrix. Chloroplast DNA was covalently attached to nylon membranes by irradiation at 254 nm. Under hybridization conditions the initial rate of DNA loss from the nylon membranes was 5-10% per 24 h, while under comparable conditions DNA bound to nitrocellulose membranes was lost at a rate of 38 to 61% per 24 h. Several sets of hybridization conditions were examined to select one giving reasonable hybridization rates and minimal loss of bound DNA. Under the conditions selected [Denhardt's solution (D. Denhardt, 1966, Biochem. Biophys. Res. Commun. 23, 641-646), 0.5 M NaCl, 0.1% sodium dodecyl sulfate, and 31.4% formamide at 50 degrees C for 92 h], hybridization was observed to be 29% more efficient on nylon membranes than on nitrocellulose. Several attempts to remove previously hybridized DNA from nylon membranes proved only partially successful. Reuse of the membranes, therefore, was of limited value. Quantitative hybridization of total radiolabeled tobacco cellular DNA to cloned tobacco chloroplast DNA attached to nylon yielded results similar to those previously reported using nitrocellulose membranes. However, use of nylon membranes greatly facilitated the manipulations required in the procedure.     

A multiphasic hollow fiber reactor for the whole-cell bioconversion of 2-methyl-1,3-propanediol to (r)-beta-hydroxyisobutyric acid

This paper describes the bioconversion of 2-methyl-1,3-propanediol to (R)-beta-hydoxyisobutyric acid (HIBA) by Acetobacter ALEI in a hollow fiber membrane bioreaction system arrangement that allows the integration of three liquid phases: the aqueous bioconversion phase, the organic phase consisting of a solution of trioctyl phosphine oxide (TOPO) in isooctane, and the third phase consisting of a basic stripping solution that allows reextraction of HIBA from the organic phase. A comparison of HIBA mass transfer experiments was carried out in the membrane reactor with two and three phases for different pH and TOPO concentrations. The use of the three-phase arrangement allows the extraction of high quantities of HIBA from the aqueous medium (higher than 85%) independently of the pH, whereas in the two-phase system the percentage of HIBA extracted from the aqueous medium was lower, 42% in the best case, and strongly influenced by the pH. The percentage of the extractive agent TOPO in the organic phase influenced on the mass transfer rate in both bi- and triphasic arrangements. By simply integrating the re-extraction phase in the system it was possible to increase the extraction yield by 2-fold, reduce the amount of TOPO by 4-fold, and operate at the more favorable pH 4. A bioconversion experiment was done in these conditions (pH = 4, TOPO = 5%) to confirm the advantages of including the third stripping solution. Fed-batch operation of the triphasic membrane reactor was maintained for more than 20 h, reaching an HIBA concentration in the stripping solution of 29 g L(-)(1).     

A new sensitive non-isotopic method using sulfonated probes to detect picogram quantities of specific DNA sequences on blot hybridization

The use of non-radioactive systems to detect target DNA or RNA displays many advantages such as safe manipulation, potential use in non-specialized scientific area and prolonged lifetime of the probes (one year or more). We here describe a method we have improved and optimized using sulfonated DNA probes for hybridization on dot and Southern blots. Sulfonation is an easy chemical modification procedure which does not require enzymatic coctail as does nick-translation. Sensitivity of this method has been particularly improved by using a new blocking solution, containing heparin, which allows easy and fast detection of picogram quantities of DNA. This method allows the use of nitrocellulose as well as nylon membranes with very low background. Equal resolution is obtained in comparative experiments involving both sulfonated and 32P-radiolabelled probes. Single copy gene sequences are readily detected in nuclear DNA. These results allow the use of this procedure for restriction fragment length polymorphism (RFLP) studies.     

Application of a subtraction hybridization technique involving photoactivatable biotin and organic extraction to solution hybridization analysis of genomic DNA

We have adapted a subtraction hybridization technique involving photoactivatable biotin, streptavidin binding, and organic extraction for solution hybridization analysis of mammalian genomic DNA. By combining maximal hybridization conditions of high salt, dextran sulfate, and formamide with successive hybridization steps and sequence enrichment by agarose gel electrophoresis, up to 97% of tracer DNA can be reproducibly driven to hybridize with photobiotinylated driver DNA. We demonstrate that the fractionation of hybridized from unhybridized sequences by this technique differs from hydroxyapatite chromatography with respect to the handling of nondenatured tracer, foldback sequences, and tracer-tracer hybrids. Strategies are presented to control the contribution of these species to the final subtracted product thereby making this technology a useful adjunct to solution hybridization approaches such as deletion cloning.     

Artificially Induced Water and Sulfate Transport through Sunflower Roots

A new experimental method is used to determine simultaneously the quantity and composition of the sap exuded by a detopped root system at the same time that a pressure deficit of desired magnitude can be applied to the stem stump. The technique was used in a study of the transport of radioactive sulfate through the roots of young sunflower plants placed on complete nutrient solutions labelled with ³⁵S. The complications by the time factor on the composition and rate of the sap stream in experiments of this type were observed and discussed. The time of detopping the roots was very critical as the conditions of sulfate transport were greatly changed some time after the excision. A rectilinear connection existed between the rate of sulfate transport in the sap and the water flow at sap flow velocities comparable with transpiration rates. When the transport of water was very slow, the rate of sulfate transport became constant and independent of the water stream. It was suggested that diffusion or water flow could act as motive force for the ion transport in some non-metabolic phase of transfer in the roots. The addition of 2,4-DNP to the test solution severely interfered with the water and sulfate transport conditions in the roots.     

Mismatch formation in solution and on DNA microarrays: how modified nucleosides can overcome shortcomings of imperfect hybridization caused by oligonucleotide composition and base pairing

The DNA microarray technology is a well-established and widely used technology although it has several drawbacks. The accurate molecular recognition of the canonical nucleobases of probe and target is the basis for reliable results obtained from microarray hybridization experiments. However, the great flexibility of base pairs within the DNA molecule allows the formation of various secondary structures incorporating Watson-Crick base pairs as well as non-canonical base pair motifs, thus becoming a source of inaccuracy and inconsistence. The first part of this report provides an overview of unusual base pair motifs formed during molecular DNA interaction in solution highlighting selected secondary structures employing non-Watson-Crick base pairs. The same mispairing phenomena obtained in solution are expected to occur for immobilized probe molecules as well as for target oligonucleotides employed in microarray hybridization experiments the effect of base pairing and oligonucleotide composition on hybridization is considered. The incorporation of nucleoside derivatives as close shape mimics of the four canonical nucleosides into the probe and target oligonucleotides is discussed as a chemical tool to resolve unwanted mispairing. The second part focuses non-Watson-Crick base pairing during hybridization performed on microarrays. This is exemplified for the unusual stable dG.dA base pair.     

Tertiary structure of animal tRNATrp in solution and interaction of tRNATrp with tryptophanyl-tRNA synthetase

Alkylation in beef tRNATrp of phosphodiester bonds by ethylnitrosourea and of N-7 in guanosines and N-3 in cytidines by dimethyl sulfate and carbethoxylation of N-7 in adenosines by diethyl pyrocarbonate were investigated under various conditions. This enabled us to probe the accessibility of tRNA functional groups and to investigate the structure of tRNATrp in solution as well as its interactions with tryptophanyl-tRNA synthetase. The phosphate reactivity towards ethylnitrosourea of unfolded tRNA was compared to that of native tRNA. The pattern of phosphate alkylation of tRNATrp is very similar to that found with other tRNAs studied before using the same approach with protected phosphates mainly located in the D and T psi arms. Base modification experiments showed a striking similarity in the reactivity of conserved bases known to be involved in secondary and tertiary interactions. Differences are found with yeast tRNAPhe since beef tRNATrp showed a more stable D stem and a less stable T psi stem. When alkylation by ethylnitrosourea was studied with the tRNATrp X tryptophanyl-tRNA synthetase complex we found that phosphates located at the 5' side of the anticodon stem and in the anticodon loop were strongly protected against the reagent. The alkylation at the N-3 position of the two cytidines in the CCA anticodon was clearly diminished in the synthetase X tRNA complex as compared with the modification in free tRNATrp; in contrast the two cytidines of the terminal CCA in the acceptor stem are not protected by the synthetase. The involvement of the anticodon region of tRNATrp in the recognition process with tryptophanyl-tRNA synthetase was confirmed in nuclease S1 mapping experiments.     

Choice of labeled precursors in synthesis of DNA for molecular hybridization

Tritiated deoxyguanosine triphosphate, labeled in the 8 position of the purine ring, is frequently used as a precursor in the preparation of complementary DNA to be used in molecular hybridization reactions. This compound has been reported to exchange the labeled tritium with water in solution at high temperature. We have investigated the loss of label from DNA prepared with this compound, under conditions commonly used for molecular hybridization reactions. The loss of label follows first order kinetics, with a half time of 17 hrs. under the conditions used. This loss of label influences the reliability of the results of the hybridization reactions, and in some cases may confuse their interpretation. It is recommended that use of complementary DNA labeled with [8-³H]-dGTP be avoided in molecular hybridization experiments.     

Flower senescence in daylily (Hemerocallis)

This paper reviews recent developments in the use of molecular probes for analyzing the genetic makeup of somatic hybrids. Successful application of somatic hybridization to the interspecific transfer of traits encoded in the nucleus is still having limited success. A major difficulty is hybrid infertility, particularly in hybrids between sexually incompatible species. The formation of asymmetric hybrids is being explored as an approach for improving hybrid fertility. Evaluation of the degree of chromosome elimination and chromosome stability and instability in asymmetric hybrids is difficult when the traditional approaches of chromosome counting and isozyme analysis are used. Two new approaches are resolving this difficulty. The use of species-specific repetitive DNA probes in dot blotting and in situ hybridization to chromosomes is providing quantitative data on chromosome elimination and allows detection of translocations. Use of restriction fragment length polymorphism (RFLP) probes for analysis of hybrids between genetically mapped species makes it possible to account for the presence or absence of individual chromosomes and chromosomes arms. Wider use of such molecular probes should greatly improve our understanding of the genetics of both symmetric and asymmetric somatic hybrids and may lead to new strategies for the effective interspecific transfer of nucleus-encoded traits by protoplast fusion.     

Vibrational dynamics of bio- and nano-filaments in viscous solution subjected to ultrasound: implications for microtubules

In this paper, using a new analytical method, we solved the beam equation for a uniform bio- and nano-filament in a viscous solution. The filament is assumed to be attached at its two ends and driven by ultrasound plane waves. To obtain analytical solutions, we converted the beam equation to an equation that allows us the use of the method of separation of variables. We then reconstructed the solution of the original beam equation from the solution of the converted equation. Subsequently, we have used the parametric equations derived in this paper to investigate the resonance condition for a microtubule (MT) in an aqueous solution. We show that by using ultrasound plane waves, one cannot satisfy a resonance condition for MTs treated as rigid rods. In order to achieve resonance, a single mode of the MT vibration must be excited with a harmonic number larger than a threshold value found here. Single mode excitation not only helps to transfer a minimum amount of energy to the surrounding medium compared with multi-mode excitation, but it also allows for a simultaneous high amplitude and high mode quality that is impossible using plane waves. In order to overcome this difficulty, we propose to use an ultrasound generation device as a potential technical solution characterized by both frequency control and optimized energy transfer to the MT. Finally, the minimum required intensity of the ultrasound at the location of the MT in order to break it is shown to be on the order of 10⁵ W/m², which corresponds to 170 dB.     

Reliable hybridization of oligonucleotides as short as six nucleotides

Although there are many new applications for hybridizing short, synthetic oligonucleotide probes to DNA, such applications have not included determining unknown sequences of DNA. The lack of clear discrimination in hybridization of oligo probes shorter than 11 nucleotides and the lack of a theoretical understanding of factors influencing hybridization of short oligos have hampered the development of their use. We have found conditions for reliable hybridization of oligonucleotides as short as seven nucleotides to cloned DNA or to oligonucleotides attached to filters. Low-temperature hybridization and washing conditions, in contrast to the high stringency conditions currently used in hybridization experiments, have the potential for allowing the simple use of all oligos of six nucleotides or longer in meaningful hybridizations. We also present the hybridization discrimination theory that provides the conceptual framework for understanding these results.     

Innovative integrated system for real-time measurement of hybridization and melting on standard format microarrays

Despite the great popularity and potential of microarrays, their use for research and clinical applications is still hampered by lengthy and costly design and optimization processes, mainly because the technology relies on the end point measurement of hybridization. Thus, the ability to monitor many hybridization events on a standard microarray slide in real time would greatly expand the use and benefit of this technology, as it would give access to better prediction of probe performance and improved optimization of hybridization parameters. Although real-time hybridization and thermal denaturation measurements have been reported, a complete walk-away system compatible with the standard format of microarrays is still unavailable. To address this issue, we have designed a biochip tool that combines a hybridization station with active mixing capability and temperature control together with a fluorescence reader in a single compact benchtop instrument. This integrated live hybridization machine (LHM) allows measuring in real time the hybridization of target DNA to thousands of probes simultaneously and provides excellent levels of detection and superior sequence discrimination. Here we show on an environmental single nucleotide polymorphism (SNP) model system that the LHM enables a variety of experiments unachievable with conventional biochip tools.