Antibodies specific to two deoxyribotrinucleotide sequences.

Antibodies to the deoxyribotrinucleotides dpApTpA and dpApApT were prepared by injecting the bovine serum albumin conjugates of the respective haptens in rabbits. The specificities of the antibodies were determined by estimating the inhibition of the binding of the tritiated haptens to the immunoglobulins by various nonradioactive mono- and oligonucleotides, using nitrocellulose membrane binding assay. Anti-dpApTpA and anti-dpApApT antisera were found to contain antibodies which were highly specific to the respective hapten sequence.     

Sequence specific antibodies to a deoxyribodinucleotide

Antibodies were elicited in rabbits to the dinucleotide, dpTpA, conjugated to a carrier protein. Among a few deoxyribomono- and oligonucleotides tested for binding to the antibodies by nitrocellulose tilter binding assay, only dpTpA and dpTpA containing oligonucleotides showed binding. The inhibition of the binding of 3H-dpTpA to the antibodies by various nonradioactive mono- and oligonucleotides showed that the antibodies were sequence specific and recognized the whole molecule of dpTpA. dpTpA specific antibodies were purified by a two step affinity chromatography. By competition studies, it was found that the purified antibodies bound denatured DNA at dpTpA sequences. The antibodies did not bind RNA.     

Specific and shared idiotypes found on hybridoma anti-DNA autoantibodies derived from rheumatoid arthritis and systemic lupus erythematosus patients

The idiotype determinants found on hybridoma anti-DNA autoantibodies produced from the fusion of peripheral blood lymphocytes from 13 systemic lupus erythematosus (SLE) and five rheumatoid arthritis (RA) patients with the GM 4672 human lymphoblastoid line were analyzed. A total of 47 SLE and 21 RA hybridomas were studied, of which 26 SLE and 10 RA produced anti-DNA autoantibodies. Rabbit antisera, raised to six of the SLE hybridoma anti-DNA IgM antibodies, were rendered idiotype specific by multiple absorptions on human IgM and IgG immunoabsorbent columns. In direct binding radioimmunoassays, all six anti-idiotype antisera reacted specifically with the anti-DNA antibody used as immunogen. In competition studies, five anti-idiotype antisera were able to inhibit the binding of their homologous idiotype to DNA-coated tubes. In addition, DNA and polynucleotides inhibited the binding of the five idiotypes to anti-idiotype-coated tubes, suggesting that these anti-idiotypes react with idiotype determinants located within the antigen-combining sites of the anti-DNA antibody molecules. Shared idiotypes were detected among the 68 hybridoma antibodies by direct binding studies on anti-idiotype-coated tubes. Our results revealed that 58% (21/36) of the anti-DNA antibodies and 16% (5/32) of the non-DNA-binding antibodies reacted with at least one anti-idiotype serum. Five anti-idiotype antisera reacted only with hybridoma anti-DNA antibodies from SLE patients. The other anti-idiotype antiserum reacted with both SLE- and RA-derived hybridoma anti-DNA and non-DNA-binding antibodies. These studies indicate that some anti-idiotype antisera may detect specific idiotypes found only on SLE-derived anti-DNA auto-antibodies, whereas other antisera detect shared idiotypes found on both RA and SLE DNA-binding and non-DNA-binding antibodies.     

The role of phosphoric acid residues in the formation of antigenic determinants of the structural components of DNA

The inhibitory activity of thymidine, thymidine triphosphate and thymidyl oligonucleotides was studied in thymidine-antithymidine antibodies reaction. Thymidine was shown to have the greatest inhibitory effect, with thymidine triphosphate and thymidyl oligonucleotide inhibitory activity less expressed and reducing with the increase in oligonucleotide length. The effect of thymidine, thymidine triphosphate and thymidyl oligonucleotides on the interaction of antisera and SLE patients' sera with denatured DNA was studied. It was shown that thymidine triphosphate and particularly thymidyl oligonucleotides are characterized by greater inhibitory capacity, as compared to thymidine. It was found that only thymine dimers bound by phosphate groups can inhibit the interaction of UV-irradiated DNA with antiserum specific for UV-modified DNA. The data obtained suggest that the charge determined by phosphoric acid residues plays an essential role in the interaction of antibodies induced to charged structural DNA components.     

Cellular origins of different forms of gastrin. The specific immunocytochemical localization of related peptides.

We have localized the antigenic determinants for the main forms of gastrin (big gastrin, G34, and little gastrin, G17) in hog antral mucosa using sequence specific antibodies and an indirect immunofluorescence technique. Populations of monospecific antibodies were obtained after affinity immunoadsorption to remove populations of unwanted specificity. The specificity of the purified antisera was established by direct binding of 125I labeled peptides to antisera at the same dilutions as those used in immunocytochemistry. The results indicate that in hog antral mucosa there is a single population of cells with the antigenic determinants of the C-terminal region of G17 and G34, the N-terminal region of G17, the N-terminal region of G34, and the intact G17 molecule. In duodenum there are cells with only C-terminal reactivity; since gastrin and CCK share a common C-terminal sequence it is concluded that this cell type contains CCK-like peptides rather than gastrin.     

Preparation and partial characterization of polyclonal antibodies raised against a preselected sequence of calcium dependent lectins

The synthetic-peptide strategy was used to generate antibodies raised against calcium-dependent lectins of vertebrates. We demonstrate that a synthetic peptide predicted from the amino acid sequence of the carbohydrate recognition domain can induce blocking antibodies which would react with, or in close vicinity of, the binding site of the parent molecule. As the preselected sequence was chosen in a consensus sequence region, we also present preliminary investigations of the use of specific antisera as a common biological probe against calcium dependent lectins. The availability of monospecific polyclonal sera opens new possibilities in biochemical and structural studies as well as immunodection of calcium dependent lectins.     

Conformations of oligonucleotides in solution as determined by sequence-specific antibodies

The conformations of some related oligoribonucleotides in solution were investigated immunochemically with antisera specific for two synthetic oligonucleotide sequences, A-A-U and A-A-U-U. Radioimmunoassay showed differences of as much as three or more orders of magnitude in binding among oligonucleotides with commonly shared sequences. These large differences, which reflect the loss of many points of contact with antibody because of changes in overall conformation, allow the following conclusions: (1) A-A-U and A-A-U-U have conformations distinct from any present in the Un family of oligomers. (2) Conformations of A-A-U and A-A-U-U differ markedly from those of oligomers of A. The dinucleotide A-A, in particular, bears little resemblance in conformation to the A-A sequence in A-A-U and A-A-U-U. (3) The recognizable conformational unit appears to be the triplet A-A-U, which binds as well as A-A-U-U and far better than its component dimers. Interactions between non-adjacent bases may be a factor here, as well as in codon recognition. The immunological data support the conclusion that, in oligonucleotides, as in polypeptides, primary sequence can determine conformation in solution.     

Determination of recognition-sequences for DNA-binding proteins by a polymerase chain reaction assisted binding site selection method (BSS) using nitrocellulose immobilized DNA binding protein.

We have developed a simple procedure for rapid determination of a DNA sequence recognized by a DNA binding protein based on immobilization of the protein on nitrocellulose filters. The procedure consists of the following steps: A recombinant protein with a functional DNA binding domain is expressed in E. coli. The protein is purified to homogeneity, immobilized on nitrocellulose paper, and exposed to a pool of double stranded oligonucleotides carrying in the central part a 20 bp random sequence, which is flanked by conserved sequences with restriction endonuclease recognition sites for analytical and subcloning purposes and sequences complementary to polymerase chain reaction primers. Oligonucleotides retained by the DNA-binding protein are liberated by increasing the ionic strength and used in a new binding process after amplification by the polymerase chain reaction technique. Finally the amplified product is cloned for determination of the DNA sequence selected by the DNA-binding protein. Murine Zn-finger and basic helix-loop-helix DNA binding proteins were used to demonstrate the efficiency of the method. We show that the yield of oligonucleotides binding to the protein was increased by several consecutive rounds of filter binding and amplification, and that the protein extracted a specific sequence from the pool of random oligonucleotides.     

A local antigenic determinant distribution in a continuous antigenic region at residues 38-54 of hen egg white lysozyme

The precise location of the antigenic determinants in a continuous antigenic region at residues 38–54 of hen egg white lysozyme (lysozyme) was investigated using the inhibition test of binding of N^α-[¹⁴C]acetyl fragment 38–54 with goat (three individuals) and sheep (four individuals) anti-lysozyme antisera by various synthetic and proteolytic fragments of lysozyme. From these inhibition studies, we found that in this region there were three independent antigenic determinants, consisting of residues 38–45, 40–48, and 44–54, respectively. The existence and the specificity of the antibodies directed to these determinants were further examined with isolating the specific antibodies by affinity chromatography on columns to which the fragment 38–45, 44–48, and 46–54 were bound. The results indicated that these determinants partially overlapped one another in amino acid sequence, but the antibodies directed to them could recognize only each corresponding determinant. These antibodies were also shown to be reactive with native lysozyme as well as a reduced and S-carboxymethylated derivative of lysozyme, and to be found in goat and sheep anti-lysozyme antibodies. The amounts of these antibodies calculated from the binding capacities were in the range from 0 to 48 μg/ml of antisera. These values corresponded to a small fraction of the total precipitable anti-lysozyme antibodies and were as high as 0.8% of the total. The ratios of the amounts of these antibodies differ in individuals or in different species of animals. The binding affinities of N^α-[¹⁴C]acetyl fragment 38–54 with these antibodies were in the range from 1.3 × 10⁷ to 2.6 × 10⁸m^?1. The double-reciprocal plots of the antigen binding with these antibodies drew almost a straight line compared with those of a mixture of several antibody populations, that is, whole antisera.     

Efficient strategies for the conjugation of oligonucleotides to antibodies enabling highly sensitive protein detection

Three methods for the conjugation of oligonucleotides to antibodies and the subsequent application of these conjugates to protein detection at attomole levels in immunoassays are described. The methods are based on chemical modification of both antibody and oligonucleotide. Aldehydes were introduced onto antibodies by modification of primary amines or oxidation of carbohydrate residues. Aldehyde- or hydrazine-modified oligonucleotides were prepared either during phosphoramidite synthesis or by post-synthesis derivatization. Conjugation between the modified oligonucleotide and antibody resulted in the formation of a hydrazone bond that proved to be stable over long periods of time under physiological conditions. The binding activity of each antibody-oligonucleotide conjugate was determined to be comparable to the corresponding unmodified antibody using a standard sandwich ELISA. Each oligonucleotide contained a unique DNA sequence flanked by universal primers at both ends and was assigned to a specific antibody. Highly sensitive immunoassays were performed by immobilizing analyte for each conjugate onto a solid support with cognate capture antibodies. Binding of the antibody-oligonucleotide conjugate to the immobilized analyte allowed for amplification of the attached DNA. Products of amplification were visualized using gel electrophoresis, thus denoting the presence of bound analyte. The preferred conjugation method was used to generate a set of antibody-oligonucleotide conjugates suitable for high-sensitivity protein detection.     

Idiotypic analysis of anti-GL phi antibodies. I. Identification and strain distribution of GL-1 idiotypes

We utilized both the inhibition of antigen binding and direct idiotype binding methods to identify a new set of common idiotype determinants on anti-GL antibodies of various mouse strains. Three anti-idiotypic antisera, each prepared against individually purified B10.WB anti-GL phi antibodies, were able to detect antibody-combining site-associated common idiotypic determinants, designated GL-1 idiotype(s), in antisera with GLT-binding activity obtained from all mouse strains except strains bearing Igh-1e allotype. Anti-GL phi antisera obtained from rabbits, guinea pigs, and rats did not express detectable levels of GL-1 idiotypes. Nonresponder mice to GL phi, upon immunization with GL-F gamma G or GL phi-F gamma G produced anti-GL antibodies expressing GL-1 idiotypes. Although the magnitude of the immune response to various GL-containing polymers is controlled by distinct Ir genes, the common GL-related antigenic determinants on these polymers are able to induce anti-GL antibodies with GL-1 idiotypic specificities.     

噬菌体短肽库的构建及其随机短肽的多样性

噬菌体短肽库是将随机合成的寡核苷酸序列通过与单链噬菌体外壳蛋白基因融合,从而将随机短肽表达于噬菌体的表面。将体外随机化学合成的寡聚核苷酸序列重组到单价噬菌体表达载体,构建了噬菌体短肽库,证明其库容为２×１０￣７集落形成单位（ｃｆｕ）,重组率为９３％。同时将１１个随机克隆进行序列测定,证实其寡聚核苷酸序列和氨基酸的分布几乎是完全随机的,其多样性可以满足特异性短肽筛选的要求。     

发育阶段M-CAT结合因子的组织分布及表达动力学

采用胶阻滞和DNA-蛋白质印迹技术分析了鸡胚和雏鸡发育不同阶段骨骼肌、心肌、胗、肝和脑组织核抽提物中M-CAT结合因子(MCBF)与含CATTCCT、CATTGCT核心序列的寡核苷酸的相互作用.胶阻滞实验结果表明,被检的五种组织均有MCBF结合活性存在,但结合模样不完全相同;两寡核苷酸探针与同一骨骼肌核抽提物结合模样也不相同.采用两寡核苷酸为探针对五种组织核抽提物进行DNA-蛋白质印迹分析均检出一分子质量约30 ku 核因子,提示30 ku核因子是存在于五种组织中的普遍因子,该因子可直接或以同二/多聚体结合CATTCCT、CATTGCT序列,属MCBF结合活性的基本组成成分.除普遍因子外,胶阻滞分析结果不排除各组织存在的特异因子通过蛋白质-蛋白质相互作用、与30 ku因子形成杂聚体结合DNA的可能性.骨骼肌组织30 ku因子在胚胎发育18天前表达,出生后消失.     

Structural characterization of a cross-reactive idiotype shared by monoclonal antibodies specific for the human CD4 molecule.

A panel of mouse monoclonal anti-CD4 antibodies was characterized in terms of idiotypic expression by using specific anti-idiotypic antibody (anti-Id) reagents generated in rabbits immunized with anti-Leu3a, a monoclonal anti-CD4 which inhibits the human immunodeficiency virus (HIV) gp120 binding to CD4. Direct binding and competitive inhibition assays demonstrate that the majority of monoclonal anti-CD4 antibodies able to recognize CD4 epitopes overlapping the epitope recognized by anti-Leu3a expressed an antigen-combining site-related cross-reactive idiotype (IdX). Western blot analysis was used to demonstrate that this IdX is associated primarily with the light (L) chain of the monoclonal anti-CD4 antibodies. To further characterize the structural basis of the IdX, the nucleotide sequence of the variable region of the L kappa chain of anti-Leu3a was determined. Peptides corresponding to the first, second, and third complementarity determining regions (CDRs) of the L chain of anti-Leu3a were synthesized and used to immunize rabbits. All anti-peptide antisera recognized the immunizing peptide, the cognate anti-Leu3a molecule, and several other monoclonal anti-CD4 antibodies by direct binding assays. Western blot analysis utilizing the anti-CDR peptide reagents demonstrates that the reactivity to the monoclonal anti-CD4 antibodies was L chain-specific. The anti-Id generated by immunizing with the intact anti-Leu3a molecule failed to recognize the three L chain-derived CDR synthetic peptides, suggesting that the IdX requires the presence of the three-dimensional configuration of the L chain for its expression. The broad range of reactivity exhibited by the antipeptide antisera indicates that the majority of mouse monoclonal anti-CD4 antibodies characterized in this study utilize L chains encoded by a single germ line variable (V) region kappa (V kappa) chain gene or by V kappa genes that belong to the same gene family.     

Cycled DNA immunoprecipitation procedure to enrich the target sequences for DNA binding proteins with the fold purification monitored.

Using centromere DNA binding protein (CENP-B) expressed as a fusion to beta-galactosidase in Escherichia coli, we established a cycled DNA immunoprecipitation procedure for enriching CENP-B binding sequences and monitoring the enrichment process. Degenerated synthetic oligonucleotides for an authentic CENP-B binding sequence, inserted into a pUC-derived vector, were incubated with the crude CENP-B extract. DNA-protein complexes formed in vitro were immunologically precipitated utilizing the beta-galactosidase moiety as a tagged antigen. The effectiveness of repeating cycles of immunoprecipitation was demonstrated by the color selection method designed for pUC-derived plasmids, after introducing the precipitated plasmids into Escherichia coli. After three cycles of DNA immunoprecipitation, only a few kinds of sequences constituted the majority. By repeating two more cycles, the most predominant sequence was finally enriched until homogeneous, indicating the enrichment of the binding sequences in a hierarchical order. Further application to human genomic DNA showed that two EcoRI DNA fragments, 0.49 and 0.78 kb in size, were exclusively identified. This procedure can be applied to the systematic analysis of binding sequences for any other DNA binding proteins without production of any specific antibodies or further purification.     

Antibodies specific for branched ribonucleic acids.

A chemically synthesized branched tetranucleotide, G3'p5'A [2'p5'G]3'p5'C corresponding to the consensus sequence at the branch point in introns undergoing RNA splicing, was used as a hapten to elicit antibranch antibodies. Binding assays with 32P-labeled hapten and unlabeled structurally related haptens indicated that the antibodies are highly specific for the branch structure and have some specificity for the A2'p5'G sequence at the branch point, but have essentially none for a variety of other 2'p5' or 3'p5' dinucleotides or for the linear trinucleotide G3'p5'A3'p5'C. Purification of these antibodies by binding to A2'p5'G covalently linked to Sepharose followed by covalent attachment of the purified antibodies to protein A-Sepharose has provided an adsorbent that immunospecifically retains branched oligonucleotides as well as branched introns released from RNAs during in vitro splicing.     

Expression,purification, and characterization of minimized chicken riboflavin carrier protein from a synthetic gene in Escherichia coli

Minimized proteins have long been used to elicit immune response to particular regions of a protein antigen. Most efforts to derive minimized proteins have employed synthetic peptide fragments. Here we describe molecular cloning and production of a minimized chicken riboflavin carrier protein (mini-RCP) sequence that harbours all the four neutralizing epitopes but lacks the sequences that otherwise elicit undesirable antibodies. The gene encoding mini-RCP is engineered by contiguous alignment of nucleotide sequences coding for selected epitopes of chicken RCP separated by leucyl alanine residues. The gene has been constructed from eight oligonucleotides by employing overlapping PCR strategy and expressed in Escherichia coli, using the T7 promoter system. The recombinant protein could be purified to homogeneity by a single step Ni2+ affinity chromatography. Western blot experiments using epitope specific antisera confirm that the corresponding linear amino acid sequences are available for immunorecognition in the engineered protein. This methodology enables continuous production and purification in bulk amounts of the minimized RCP as a source of candidate immunocontraceptive vaccine in mammals.