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Southern molecular hybridization experiments with parallel complementary DNA probes.

We have detected the specific binding in Southern blot hybridization experiments of both complementary antiparallel and parallel 40 bp synthetic DNA probes, corresponding to a cloned Drosophila DNA fragment. The highly cooperative annealing and melting were observed in solution with these probes, which are complementary in the same direction and possess 17 GC pairs. The binding of ethidium bromide is indicative of formation of a perfect parallel DNA duplex. The specific binding was also detected in both genomic and in plaque hybridization experiments.

Animals↗

Conformational change of a nucleotide by a base-pair mimic nucleoside in the complementary DNA strand.

On the basis of the non-covalent bond interactions in nucleic acids, we have synthesized a novel adenosine derivative tethering a phenyl group. Structure and thermal stability of the DNA duplexes bearing the adenosine derivative in the middle of a strand were investigated by CD spectra and the UV melting curves. We found that the conformation and the interactions of the duplexes were similar regardless of the nucleotide facing with the adenosine derivative in a duplex. This observation suggests the base pair-mimic geometry of the adenosine derivative accompanied with a conformational change of the nucleotide in the complementary strand.

Adenosine↗

Synthesis of double-stranded DNA complementary to lysozyme, ovomucoid, and ovalbumin mRNAs. Optimization for full length second strand synthesis by Escherichia coli DNA polymerase I.

Sequential reverse transcriptase, DNA polymerase, and S1 nuclease reactions can be employed to synthesize double-stranded DNA representing messenger RNA. Using reverse transcriptase products made from partially purified lysozyme, ovomucoid, and ovalbumin messengers from hen oviduct, we have characterized the Escherichia coli DNA polymerase I reaction. We have optimized for a high yield of full length second strands under conditions which require only a small amount of mRNA. The effects of several parameters (time, enzyme levels, salt concentration, monovalent cation, and temperature) on the length of products synthesized by DNA polymerase I have been investigated. Each has a significant influence on the proportion of products which are full length. Under our conditions the three reactions are efficient in synthesizing full length duplex DNA from partially purified mRNA fractions or from total poly(A)-containing RNA.

Animals↗

Beta-tubulin complementary DNA sequence variations observed between cyathostomins from benzimidazole-susceptible and -resistant populations.

The molecular mechanism of benzimidazole (BZ) resistance in cyathostomins of horses is still unclear. Previous studies revealed that the TTC or TAC polymorphism in codon 200 of the beta-tubulin isotype 1 gene is not as strictly correlated with BZ resistance as in trichostrongyles in sheep. To identify further sites of polymorphism within the beta-tubulin gene related to BZ resistance, complete complementary DNAs (cDNAs) encoding beta-tubulin of adult worms of Cylicocyclus nassatus, Cyathostomum pateratum, Cyathostomum coronatum, Cyathostomum catinatum, Cylicostephanus longibursatus, and Cylicostephanus goldi of a BZ-resistant cyathostomin population were characterized using specific primers. The cDNA sequence of each species spans 1,429 bp, encoding a protein of 448 amino acids. The interspecific identities are 95.2-99.6% at the nucleotide and 98.7-100.0% at the peptide level. The comparison of the amino acid sequences of individuals isolated from the BZ-resistant cyathostomin population with those from individuals of Cc. nassatus, Cy. coronatum, Cy. pateratum, and Cy. catinatum of a BZ-susceptible one showed differing amino acids in 11 positions. The commonness of a phenylalanine to tyrosine mutation at position 167 in all the 6 cyathostomin species isolated from a BZ-resistant population suggests its involvement in the molecular mechanism in BZ resistance.

Amino Acid Sequence↗

Identification of partial complementary DNA clones encoding a 59-kd protein with characteristics of a unique oncofetal antigen.

BACKGROUND: Oncofetal antigens (OFAs) are conserved tumor-associated autoantigens or transplantation antigens present on the surface of all major classes of rodent and human tumors and on midgestational fetal cells but not on normal neonatal or adult human and rodent tissues. A syngeneically derived monoclonal antibody, MAb-115, recognizes murine OFAs of 44 and 200 kd in molecular mass. PURPOSE: Our goal was to clone and characterize the complementary DNAs (cDNAs) that encode these murine OFAs. METHODS: Rabbit antiserum raised against purified 44-kd OFA glycoprotein was used to screen a mouse embryo cDNA-lambda phage expression library. Recombinant phage clones positive for the expression of OFAs were detected by immunohistochemical staining, then isolated and plaque purified. The presence of an OFA-encoding sequence in the recombinant phage was confirmed by specific reaction of the expressed protein with MAb-115. Recombinant fusion protein was purified from the extracts of corresponding lysogens. Rabbit antiserum against purified recombinant fusion protein was raised, and the capacity of this antiserum to detect the expression of OFA on rodent tumor and fetal cells was determined by flow cytometry. In addition, immunoreactivity of tumor bearer and hyperimmune murine sera to bacterially expressed recombinant OFA protein was evaluated by enzyme-linked immunosorbent assay. The OFA-expressing insert DNA from plaque-purified lambda clones was subcloned into phagemid vectors for sequencing analysis. RESULTS: Antiserum derived against the isolated recombinant mouse embryo polypeptide mimicked MAb-115 in its specific binding to all OFA-positive rodent tumor and fetal cell lines tested and likewise did not show reactivity to normal adult tissues. This antiserum specifically recognized the native 44- and 200-kd OFAs in extracts of murine lymphocytic lymphoma. Furthermore, sera of tumor-bearing mice or mice immunized with purified OFA or intact, irradiated OFA-positive lymphocytic lymphoma cells also reacted with the recombinant fusion protein. The characterization of the isolated clone included nucleotide sequence information followed by analysis of the deduced primary structure of the protein. CONCLUSIONS: These data suggest that the isolated cDNA clones encode a distinct gene product which is widely expressed on the surface of tumor and fetal cells and represents the first characterized sequence of a true OFA. IMPLICATIONS: The availability of this cDNA, encoding a protein expressed only on tumor and fetal cells, provides a direct means to assess biological characteristics of malignant tissue which can be assayed by biochemical, histochemical, and molecular methods.

Amino Acid Sequence↗

Resolution of pluripotential intermediates in murine hematopoietic differentiation by global complementary DNA amplification from single cells: confirmation of assignments by expression profiling of cytokine receptor transcripts.

Although hematopoiesis is known to proceed from stem cells through a graded series of multipotent, oligopotent, and unipotent precursor cells, it has been difficult to resolve these cells physically one from another. There is, therefore, corresponding uncertainty about the exact distribution and timing of the expression of genes known to be important in hematopoietic differentiation. In earlier work, the generation of a set of amplified complementary DNAs (cDNAs) from single precursor cells was described, whose biologic potential was determined by the outcome of cultured sibling cells. In this study, the new acquisition of cDNA from multipotent myeloid precursor cells is described, as is the mapping of RNA-level expression of 17 distinct cytokine receptors (c-kit, Flk-1, Flk-2/Flt-3, c-fms, gp130, erythropoietin receptor, GM-CSFRalpha, G-CSFR, TNFR1, IL-1RI, IL-1RII, IL-2Rbeta, IL-3-specific beta receptor, IL-4R, IL-6Ralpha, IL-7Ralpha, and IL-11Ralpha) to the enlarged sample set, spanning stages from pentapotent precursors through oligopotent intermediates to committed and maturing cells in the myeloid and lymphoid lineages. Although the enhanced scope and resolving power of the analysis yielded previously unreported observations, there was overall agreement with known biologic responsiveness at individual stages, and major contradictions did not arise. Moreover, each precursor category displayed a unique overall pattern of hybridization to the matrix of 17 receptor probes, supporting the notion that each sample pool indeed reflected a unique precursor stage. Collectively, the results provide supportive evidence for the validity of the cDNA assignments to particular stages, the depth of the information captured, and the unique capacity of the sample matrix to resolve individual stages in the hematopoietic hierarchy.

Animals↗

Molecular cloning of the complementary DNA for an additional member of the family of aortic aneurysm antigenic proteins.

PURPOSE: We have purified and partially sequenced a protein from the adventitia of the human aorta (aortic aneurysm antigenic protein 40 kDa; AAAP-40) that has homologies to bovine aortic microfibril-associated glycoprotein (MAGP-36). It is immunoreactive with immunoglobulin G (IgGs) purified from the serum and aortic wall of patients with abdominal aortic aneurysms. AAAP-40 and MAGP-36 have fibrinogen-like and vitronectin-like motifs. Screening an expression library constructed from human aortic adventitial messenger RNA has resulted in the cloning of three complementary DNAs whose gene products are immunoreactive with immunoglobulin G from patients with abdominal aortic aneurysms. Two strongly resemble each other and have been described separately. The purpose of this article is to report the third clone. METHODS: Messenger RNA from a specimen of human aortic aneurysmal adventitia was reverse-transcribed for insertion into the phagemid Uni Zap XR (Stratagene). A strain of Escherichia coli, engineered for expression (XL 1-Blue MFR', Stratagene), was transfected, and rabbit antihuman vitronectin antibody as used to identify positive clones. Sequencing of the positive clones was performed by the Core Laboratories at Columbia University. RESULTS: The hypothetical protein of rAAAP-CL4 (clone 4) shares sequence motifs with known microfibril-associated glycoproteins (MAGPs). The recombinant protein (rAAAP-CL4) is immunoreactive with serum from patients (three of four abdominal aortic aneurysm sera). In addition, similarities have been detected with immunoglobulins of the kappa family and with a protein from cytomegalovirus that is a potential molecular mimic. CONCLUSIONS: There may several members of a novel family of human aortic autoantigenic proteins implicated in abdominal aortic aneurysm disease.

Amino Acid Sequence↗

[Cloning and determination of the primary structure of DNA complementary to the mRNA of human ribosomal protein L11].

A polymerase chain reaction strategy was employed to isolate cDNA encoding L11 human ribosomal protein. Based on the known nucleotide sequence of 5'-region of the ribosomal protein L11 mRNA, we have designed primers and used them in amplification of corresponding sequence of human cDNA from total placenta cDNA. The fragment of RPS26 cDNA was cloned in plasmid vector and sequenced. Sequence analysis showed that there is high homology (88%) between coding regions of RPS26 mRNAs in rat liver and human placenta. The amino acid exchanges were observed at positions: 91 (Asp-->Glu), 217 (Thr-->Ala), 352 (Lys-->Glu).

Amino Acid Sequence↗

[Primary structure of DNA, complementary for mRNA for the Baikal omul growth hormone].

The pregrowth hormone DNA was synthesized by polymerase chain reaction from a pituitary gland cDNA library of Baikal omul (Coregonus autumnalis Pallas). A cDNA was sequenced and found to encode a precursor protein of 210 amino acid residues, which included a putative signal peptide of 22 amino acid residues. Sequence comparison reveals close similarity of the omul growth hormone to those of other Salmoniformes species.

Amino Acid Sequence↗

Corticotropin and beta-endorphin: construction and analysis of recombinant DNA complementary to mRNA for the common precursor.

A cDNA fragment synthesized from mouse mRNA (ACTH/LPH mRNA) that codes for the precursor polypeptide containing corticotropin (ACTH), beta-lipotropin (LPH), and several other peptides has been cloned in bacteria. The mRNA was enriched for ACTH/LPH mRNA translational activity (to about 75%) prior to cDNA synthesis. It appears to contain about 1200 bases, of which approximately 450 bases are not translated. The cloned DNA fragment is complementary to the region of the mRNA coding for the protein fragment beta-LPH-(44--90); this contains all of the amino acids of [Met]-enkephalin (residues 61--65 of beta-LPH), most of the amino acids of beta-melanocyte-stimulating hormone, and all but the carboxy-terminal amino acid of beta-endorphin. Based on assignment of the amino acid sequence of mouse beta-LPH from the nucelic acid sequence, it appears that there is extensive homology of mouse beta-LPH with human and porcine beta-LPH. The data also establish the linkage between beta-melanocyte-stimulating hormone and beta-endorphin as a Lys-Arg sequence. It is hoped that this cloned DNA can be used as a probe to study the expression and structure of the ACTH/LPH gene.

Adrenocorticotropic Hormone↗

Orientation isomers of the mitomycin C interstrand cross-link in non-self-complementary DNA. Differential effect of the two isomers on restriction endonuclease cleavage at a nearby site.

Reductively activated mitomycin C (MC) forms DNA interstrand cross-links between two guanines at CG.CG sequences. It is predictable that such cross-links should occur in two isomeric strand orientations in duplex DNA (except when located in the center of a self-complementary duplex). This was verified by the isolation and characterization of a pair of two isomeric oligonucleotides in each case of five non-self-complementary duplexes of 8-bp length, cross-linked by MC. Isomer separation was accomplished by reverse-phase HPLC. The isomers in a pair were formed in approximately 1:1 proportion. Their structures were rigorously characterized by a two-step cross-linking procedure: first, 1''-monoalkylation of each strand, followed by conversion to a cross-linked duplex by annealing the monoalkylated strand to its complement in the presence of a reducing agent. The resulting individual authentic orientation isomers were used as standards for identification of the two isomers formed in the original (one-step) cross-linking reactions. A 16-bp duplex oligonucleotide was synthesized featuring the AluI cognate sequence, separated from a MC cross-link site by only 1 bp. Its two MC cross-linked isomers were prepared separately, and their rate of cleavage by AluI was determined using HPLC. Cleavage of both the unmodified and cross-linked duplexes was nonsymmetrical. The isomer in which the 2''-NH3+ of MC is oriented toward the AluI site was cleaved essentially at the same rate as the control duplex, while cleavage of the isomer with the MC indoloquinone group oriented toward the AluI site was inhibited 2-fold at the faster-cleaved strand.(ABSTRACT TRUNCATED AT 250 WORDS)

Base Sequence↗

Self-complementary DNA sequences within the BRc gene of Chironomus thummi.

The Balbiani ring c (BRc) DNA of Chironomus thummi consists of tandemly arranged 249-base pair (bp) repeats, which represent the major part of the gene (Bäumlein et al. 1982a) and are transcribed and translated in a periodic polypeptide of unusual size. To obtain further information on the DNA sequence organization of that gene a recombinant phage (lambda CthBRc-1) with a relatively long insert (containing predominantly 249-bp repeats) was studied by electron microscopy (EM). lambda CthBRc-1 was found to undergo specific sequence elimination of BRc DNA resulting in heterogeneous size distribution of insert length within the limits of the cloning capacity of the phage with a maximum around 15 kilobase pairs (kb). The EM analysis of R loops formed between recombinant molecules and poly(A)+RNA (containing the transcripts of BRc and BRb) revealed the existence of self-complementary inverted and direct repeats as further sequence elements of BRc DNA scattered throughout a long portion of the BRc transcription unit. Different intrastrand structures (stems, hairpins, complex loops) originate from the renaturation of several sets of self-complementary repeats. Most double-stranded regions fell into one main-size class with an average length of 0.1 kb. The overall data suggest that self-complementary repeats belong to the same DNA sequence family and are able to cooperate in the formation of loops of different size and complexity. The results are discussed in relation to the functional significance of self-complementary inverted repeats (palindromes) for BRc expression.

Animals↗

Hybridization of pigeon globin messenger RNA with complementary DNA synthesized in vitro by reverse transcription: influence of the homopolymeric regions.

The kinetics of hybridization of pigeon globin messenger RNA with complementary cDNA synthesized by means of AMV reverse transcriptase is complex. Addition of poly A or poly U in excess to the reaction mixture normalized the kinetics. It is concluded that association of the complementary homopolymeric regions of mRNA and cDNA accelerates the complex formation between heteropolymeric sequences in a fraction of the molecules.

Adenine Nucleotides↗

Cloning of duck PRL cDNA and genomic DNA.

Complementary DNA (cDNA) and genomic DNA, including flanking regions of the prolactin (PRL) gene of domesticated duck, were cloned and sequenced. Duck PRL was found to have 92.0, 91.7, and 91.4% sequence identity at the cDNA level to PRL of chicken, turkey, and quail, respectively. The predicted amino acid sequence had an overall similarity with a comparable region of chicken (93.4%), turkey (91.3%), and quail (91.3%) PRL. Mature duck PRL contains the consensus sequence for N-linked glycoslylation at position 6 which is not present in either chickens or turkeys. Thus, duck PRL is likely to be post-translationally modified differently from other avian species. Based on the cDNA sequence, the genomic structure of the gene was characterized. The duck PRL gene consists of 5 exons and 4 introns. Moreover, sequence analysis of the proximal region of duck PRL promoter revealed a high degree of similarity to that of chicken and turkey PRL promoter. These results suggest that the mechanisms, which regulate expression of the PRL gene, may be widely conserved in avian species.

Amino Acid Sequence↗