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Efficient methods for the preparation of combinatorial libraries of receptors have been reported recently and, in most cases, these have led to the identification of host-like molecules that bind a particular substrate selectively. Dynamic libraries of macrocycles have also been synthesised that could open the way to a new selection approach to receptors and catalysts.
(1) Bulk mRNA from germinated wheat embryos was denatured with methylmercury and subjected to electrophoresis in agarose gel to obtain a fraction of mRNA that was modestly enriched with respect to its complement of translatable germin mRNA. This fraction of mRNA was used as a source of primary templates for preparing a cDNA library. (2) Escherichia coli JM101 was transfected with recombinant pUC8 plasmids containing cDNA inserts. Colonies of transformed bacteria (ca. 4 x 10(3)) were differentially screened by hybridizing them with cDNA probes that were prepared from RNA populations containing different proportions of translatable germin mRNA. (3) A 160 base pair (bp) cDNA, which hybridized more strongly to the probe made from the RNA population containing the greater proportion of translatable germin mRNA in colony hybridizations, also hybridized more strongly to the RNA population containing the greater proportion of translatable germin mRNA when it was used as a probe for Northern analysis. (4) As judged by peptide mapping of a protein made by cell-free translation, the 160-bp cDNA selected virtually pure germin mRNA from the bulk mRNA of germinated wheat embryos when it was used in "hybrid release" experiments. The same 160-bp cDNA was used to select a "full length" germin cDNA from a library prepared by the Gubler-Hoffman method.
Formalin fixed paraffin embedded (FFPE) tissues have long been used for immunohistological analyses. FFPE tissues can be stored at room temperature for several years enabling analyses to be performed later. Ease of storage and transport makes these tissues an attractive source of biological material. However, formalin fixation results in chemical modifications of proteins and nucleic acids that poses a major challenge to any type of analysis. Recovery of nucleic acids for quantitative assays is rendered difficult due to degradation resulting from fixation and long-term storage, producing low usable yields. Extensive efforts in the last 20 years have led to significant improvements in use of FFPE tissues for DNA and RNA analyses and resulted in development of sensitive assays for a wide range of applications, including next-generation sequencing. In this chapter, we describe the optimization of methods for sequential extraction of DNA and RNA from FFPE tissue and subsequent preparation of DNA-seq and RNA-seq libraries for use with the Illumina platform using commercially available reagents/kits.
The estradiol-dominated baboon oviduct synthesizes and secretes a glycoprotein (mol wt, 120,000) that binds to oocyte zona pellucida in vivo. This glycoprotein separates into two major isoelectric variants (pl 8.0 and 4.5) on two-dimensional electrophoretic gels. This study was undertaken to further characterize the steroid-controlled gene expression of this glycoprotein. A recombinant cDNA library was prepared to poly(A)+ RNA isolated from oviducts obtained from estradiol-treated baboons. The library was screened with a polyclonal antibody prepared against the acidic component (pl 4.5) of the glycoprotein. A single positive plaque was purified. Digestion of the recombinant plasmid with EcoRI revealed fragments of 230 and 1000 basepairs. The antibody used to screen the library was epitope selected against the fusion protein produced by the purified recombinant phage. The epitope-selected antibody, when incubated with Western blots of oviductal explant culture medium obtained from estradiol-treated baboons, recognized both the acidic and the basic variants of the glycoprotein. Northern blot hybridization with a 32P-labeled insert indicated that a single message of 2.8 kilobases was present in oviducts obtained from estradiol-treated baboons; no hybridization was detectable to RNA from oviducts obtained from progesterone-treated baboons. A mRNA of comparable size was also found in human, hamster, rabbit, and mouse oviduct tissue. In vitro translation of oviductal poly(A)+ RNA from an estradiol-treated baboon followed by immunoprecipitation with the polyclonal antibody against the acidic component indicated that the protein component of the oviductal glycoprotein had a mol wt of 66,000.(ABSTRACT TRUNCATED AT 250 WORDS)
The preparation of solid supported glycine phosphonate and its utilization for the total synthesis of two natural products is presented. The proposed protocol combines diversity with accessibility and speed, which makes this scaffold suitable for automated parallel synthesis and combinatorial chemistry. The preparation of a small library of dehydro-2,5-diketopiperazines, combining several natural amino acids with diverse heterocycles (including thiazoles, pyridines, indoles and imidazoles), is also demonstrated.
In our work we performed a combinatorial solid-phase synthesis in aqueous medium to prepare peptide libraries from which to select an amino acid sequence with binding properties towards aflatoxins. We used polystyrene beads, functionalised with carboxylic groups as solid support and eight amino acids as monomers. During the first step 64 different sequences of two amino acids were prepared by exploiting the principles of combinatorial chemistry; then the binding properties of all sequences towards aflatoxin B(1 )were checked. We determined binding constants towards aflatoxin B(1) and towards aflatoxins B(2), G(1) and G(2). Results were promising, so we prepared a new library by using the selected dipeptide as the starting solid phase. After selecting the best tetrapeptide sequences, we determined binding constants towards the quoted aflatoxins. We obtained binding constants ( K>10(4) M(-1)) similar to those shown by human serum albumin for similar compounds. Preliminary studies on an extraction column were promising for the development of an SPE system and for its application in food matrices.
A cDNA library was prepared from poly(A)-containing C57BL/6J mouse hair-root-enriched mRNA. The library was screened using a radiolabeled nucleic acid probe prepared from a sheep wool, Type I keratin cDNA clone (SWK2). Clone MHKA-1 was shown to contain a mouse hair, Type I keratin cDNA insert by positive hybridization-selection translation assay, and by the corresponding deduced amino acid sequence. The size of the cDNA insert is 1585 bp (excluding homopolymer tails) and on the basis of Northern blot analysis it corresponds to a mRNA of approximately 1.6 Kb. The cloned cDNA sequence includes the entire coding region for a protein of 416 amino acids (including the initiation methionine). Comparison of the deduced amino acid sequence with that of sheep wool, Type I keratin (8c1) reveals an overall corresponding sequence identity of 87%. In contrast, the MHKA-1 protein is significantly less similar to non-hair Type I keratins. An additional 3 amino acids (adjacent proline residues) not present in the wool protein have been identified near the middle of the carboxy-terminal end of the mouse protein. MHKA-1 is the first of a series of mouse hair follicle cDNA clones to be identified and characterized that will enable us to study follicular regulatory mechanisms and the interrelationships among the proteins in the mammalian hair follicle.
The pathogenicity of fungal pathogens is presumably dependent on genes that are expressed during infection. In order to isolate such genes from the tomato pathogen Cladosporium fulvum, and to test the hypothesis that starvation-induced genes are also plant induced, a cDNA library was prepared from mycelia grown in a defined medium and then transferred to a starvation medium. The library was then screened with cDNA prepared from starved and replete fungal mycelium. Five unique, differentially expressed cDNAs were isolated from 1,000 clones screened. Northern (RNA) hybridization confirmed that all five were starvation induced. Interestingly, all five were also found to be plant induced. The identity of two of the clones was indicated by partial DNA sequencing as alcohol and aldehyde dehydrogenase. The observed correlation between starvation induction and plant induction in discussed.
To facilitate the preparation of beta-peptide libraries in parallel, we have adapted reaction conditions for the solid-phase synthesis of 14-helical beta-peptides for use in a multimode microwave reactor. The low temperature/pressure requirements of microwave-assisted beta-peptide synthesis were found to be compatible with multiwell filter plates composed of polypropylene. Microwave heating of the 96-well plate was sufficiently homogeneous to allow the rapid preparation of a beta-peptide library in acceptable purity.
The chemoenzymatic preparation of a nine-member Ugi condensation library is described. The carboxylic acid and amine precursors are based on 3-hydroxybutyrate and 4-amino-1-butanol, respectively, and have been acylated selectively using a variety of acyl donors catalyzed by porcine pancreatic lipase. The enzyme is selective for the hydroxyl functionalities on both precursors, thereby yielding 3-acyl-butyric acid and 4-amino-1-acyl compounds. These enzymatically generated derivatives were then subjected to a four-component Ugi condensation reaction in the presence of acetaldehyde and methyl isocyanoacetate. Isolated yields of the alpha-(acylamino)amide Ugi products ranged from 72-95%. The inherent chemoselectivity of enzymatic catalysis may play an increasingly important role in expanding the structural diversity that can be achieved by chemical multicomponent condensation reactions.
Despite the acknowledge importance of Bacteroides gingivalis as a periodontal pathogen, relatively little is known about the molecular basis for its pathogenicity. Recombinant DNA technology has created the opportunity to identify and characterize the virulence determinants. A Bact. gingivalis library was prepared in Escherichia coli JM83 with the vector pUC18. The library was screened for surface antigens by colony immunoblot and 337 putative surface antigen recombinants were identified. Two of these clones were found to have haemagglutinating activity. Antiserum raised against one of these clones reacted with a 43 kDa Bact. gingivalis protein that has haemagglutinating activity.
The properties of naiveté and large diversity are considered to be essential starting features for combinatorial antibody libraries that eschew immunization by evolution in vitro. We have prepared large libraries with such properties by using random oligonucleotide synthesis, which has the potential to create approximately 10(20) complementarity-determining regions for antibody heavy chains. When combined with light chains and expressed on phage surfaces, high-affinity antibodies could be selected from 5.0 x 10(7) Escherichia coli transformants. Remarkably, antibodies selected only for binding displayed both general structural features known to be important in nature's own antibodies and specific consensus sequences thought to be critical for interaction with the hapten against which the library was selected. Semisynthetic and ultimately totally synthetic combinatorial libraries when coupled with mutation and selection procedures should replace immunization for generation of reagent, therapeutic, and catalytic antibodies.
Microgel polymers containing a series of functional groups have been prepared. These microgels were composed of cross-linked poly(styrene) and were prepared by radical polymerization in solution. The microgel polymers exhibit good solubility in an array of different organic solvents, and in addition, they can be efficiently precipitated by the addition of methanol and isolated by filtration. A nine-member phthalide library was synthesized using an aminomethyl-functionalized microgel 5. To further demonstrate the versatility of these microgel polymers, tris(2-aminoethyl)amino microgel 11 was examined as a scavenger reagent to remove unreacted isocyanate after a urea synthesis. Finally, a microgel-supported ammonium borohydride reagent 14 was successfully prepared and used as a reducing agent. Notable features of these microgels are that in all applications the progress of the reaction could be monitored by standard NMR techniques and their preparation is performed using common glassware and techniques found in all organic laboratories.
Using mRNA isolated from Neurospora crassa mycelium, grown for 14 h at normal growth temperature of 28 degrees C, and heat shocked for 1 h at 48 degrees C, a cDNA library was prepared in the expression vector lambda gt11. Following immunoscreening of this library with a polyclonal antiserum raised against a 80-kilodalton heat-shock protein (HSP80), cDNA clones containing 1.1- and 1.4-kilobase inserts were selected. Analysis of the partial nucleotide sequence and the deduced amino acid sequence of the cDNA clones revealed a remarkable extent of homology with other eukaryotic stress-90 family proteins; 85% identity of the amino acid sequence with that of yeast HSP90(82) was seen. The C-terminal end of the sequence contained the MEEVD motif, characteristic of eukaryotic stress proteins with a predominantly cytosolic localization. The gene for N. crassa HSP80 was mapped to the right arm of linkage group V, using restriction fragment length polymorphism mapping. Its expression during heat shock and recovery was monitored by probing Northern blots of RNA isolated from mycelium grown under various stress conditions.
In the present era, acquired immunodeficiency syndrome (AIDS) is the most fatal disorder for which no completely successful chemotherapy has been developed so far. The pandemic spread of this disease has prompted an unprecedented scientific and clinical effort to understand and combat it. A number of targets has been identified to stop the replication of the virus at different stages of its life cycle: Reverse Transcriptase (RT), protease (PR) and CCR5 are the most promising targets. Although highly active antiretroviral therapy (HAART) has been effective in reducing the mortality and morbidity in recent years, adverse side effects of the chemotherapy, patient non-compliance and the development of viral resistance remain major problems. With the aim to find better drug candidates with minor adverse side effects in recent years, several groups have investigated combinatorial approaches for the generation of libraries of HIV PR inhibitors while only few contributions to the preparation of libraries of HIV Reverse Transcriptase (RT) and CCR5 inhibitors are available. This review summarizes the recent developments of combinatorial chemistry in this area.
A cDNA library was prepared from Artemisia annua, and a 129-bp fragment was amplified from this library using primers corresponding to sequences conserved in known dicot sesquiterpene synthases. A 1641-bp open reading frame that encoded a predicted protein 35-38% identical to dicot sesquiterpene synthases was cloned using this fragment as a hybridization probe. The gene product expressed in Escherichia coli cyclized farnesyl diphosphate to a 96:4 mixture of (-)8-epicedrol and cedrol. Neither cedrol epimer was detected by GC-MS in an A. annua extract prepared from the same specimen as the cDNA.
Reported here is the preparation of tetraphenylporphyrin libraries via efficient combinatorial solution-phase syntheses, their purification, and preliminary results from a bioorganic study on their uptake in liposome membranes. Libraries with up to 666 components were prepared with substituents including Br, CF3, Cl, CN, CO2Me, Et, F, OAc, and Ph. Further, a first example for the synthesis of more diverse libraries via a "latent libraries" approach is presented. This involves masking polar groups with lipophilic protecting groups. After purification of the latent library, the masking protecting groups are removed in a quantitative reaction that produces the library compounds as the only non-volatile components. Libraries were characterized by laser desorption time-of-flight mass spectrometry, NMR, and UV-vis spectroscopy. In vitro uptake into membranes of small sonicated liposomes was measured, both in terms of total porphyrin incorporation and in terms of structure-incorporation relationships. The latter were determined from isotopically-resolved laser-desorption mass spectra under conditions that yield quantitative results. Smaller libraries showed increased uptake of porphyrins bearing OH and CF3 substituents and lower uptake of ester-, alkyl-, and halide-bearing porphyrins. This structure-dependent selectivity disappears for larger libraries, however, where uniformly high uptake is observed, i.e., at a constant lipid:porphyrin ratio the total porphyrin incorporation is higher for libraries than for single compounds of similar polarity. We propose that the decreased concentration of individual compounds in large libraries is responsible for this effect. Membrane incorporation has previously been shown to correlate with photodynamic activity in vitro and in vivo.16 Therefore, these results may help to explain why photodynamic therapy of tumors, a modern anti-cancer treatment modality, is successfully performed with a complex mixture of porphyrins.
Rodents are susceptible to the effects of chemical carcinogens and have been widely used in the study of mammary-gland carcinogenesis. However, little information is available regarding specific phenotypic changes that occur during mammary-gland carcinogenesis. In this study, subtraction hybridization was used to identify specific genes whose expression in N-methyl-N-nitrosourea (MNU)-induced rat mammary tumors had been altered. mRNA isolated from normal rat mammary tissue and tumors induced by treatment of 50-d-old female rats with MNU (50 mg/kg) was used to produce normal and tumor cDNA libraries. Total inserts prepared from each cDNA library were used to produce a subtracted tumor-normal probe. Differential screening of the tumor library with the subtracted probe and normal cDNA yielded 20 clones that appeared to be differentially expressed. Northern analysis of mRNA isolated from normal mammary tissue and tumor tissue confirmed that four of these clones were differentially expressed. The expression of clones 4 and 15 was greatly increased (13-fold and tenfold, respectively) in most MNU-induced mammary tumors, whereas the expression of clones 10 and 27 was decreased (13-fold and fourfold, respectively). Sequence analysis revealed that clones 15 and 27 were highly homologous to calcyclin and a cDNA isolated from HL-60 cells, respectively. The differential expression of clones 4 and 10 was due to the presence within these clones of retroviral sequences and a fragment of transferrin, respectively. These clones may represent markers useful for studying the development of MNU-induced mammary-gland neoplasias.