nucleotide mapping


Summary: Two-dimensional separation and analysis of nucleotides.

Top Publications

  1. Fling M, Kopf J, Richards C. Nucleotide sequence of the dihydrofolate reductase gene of Saccharomyces cerevisiae. Gene. 1988;63:165-74 pubmed
    ..As isolated from the Saccharomyces library, the DFR gene was not expressed in E. coli. When the gene was present on a 1.8-kb BamHI-SalI fragment subcloned into the E. coli vector, pUC18, weak expression in E. coli was observed. ..
  2. Thompson D, Melchers L, Idler K, Schilperoort R, Hooykaas P. Analysis of the complete nucleotide sequence of the Agrobacterium tumefaciens virB operon. Nucleic Acids Res. 1988;16:4621-36 pubmed
    ..In view of the conjugative T-DNA transfer model, the VirB proteins are suggested to act at the bacterial surface and there play an important role in directing T-DNA transfer to plant cells...
  3. White R, Phillips D. Bidirectional transcription footprinting of DNA binding ligands. Biochemistry. 1989;28:6259-69 pubmed
    ..Because of the nature of the transcription assay, all occupied ligand sites were detected by this method, in contrast to DNase I footprinting where many sequences are not probed, and where ligand sites are often not accurately defined. ..
  4. Edwards A, Voss H, Rice P, Civitello A, Stegemann J, Schwager C, et al. Automated DNA sequencing of the human HPRT locus. Genomics. 1990;6:593-608 pubmed
    ..005) and those sequences in the latter half of the locus oriented randomly (5'----3' = 67%, P less than 0.5). The development and performance of the sequencing strategy and the features of the human HPRT gene are presented. ..
  5. Loh S, Cram D, Skurray R. Nucleotide sequence and transcriptional analysis of a third function (Flm) involved in F-plasmid maintenance. Gene. 1988;66:259-68 pubmed
    ..This phenomenon provides a third mechanism, additional to ParFIA and Ccd functions, to ensure maintenance of the F plasmid in a growing bacterial population...
  6. Melancon P, Lemieux C, Brakier Gingras L. A mutation in the 530 loop of Escherichia coli 16S ribosomal RNA causes resistance to streptomycin. Nucleic Acids Res. 1988;16:9631-9 pubmed
    ..Since this effect primarily results from a perturbation of the translational proofreading control, our results also provide evidence that the 530 loop of the 16S rRNA is involved in this accuracy control. ..
  7. Bai Y, Pontoglio M, Hiesberger T, Sinclair A, Igarashi P. Regulation of kidney-specific Ksp-cadherin gene promoter by hepatocyte nuclear factor-1beta. Am J Physiol Renal Physiol. 2002;283:F839-51 pubmed
    ..Mutations of HNF-1beta, as occur in humans with inherited renal cysts and diabetes, may cause dysregulated Ksp-cadherin promoter activity. ..
  8. Nimer S, Morita E, Martis M, Wachsman W, Gasson J. Characterization of the human granulocyte-macrophage colony-stimulating factor promoter region by genetic analysis: correlation with DNase I footprinting. Mol Cell Biol. 1988;8:1979-84 pubmed
  9. Roy B, Reisman D. Positive and negative regulatory elements in the murine p53 promoter. Oncogene. 1996;13:2359-66 pubmed
    ..This was demonstrated by the observation that promoter mutations that abolished binding to this site, showed an increased level of activity as compared to the wild type promoter. ..

More Information


  1. Tiwary B, Bisen P, Sinha U. Demonstration of an altered phenylalanyl-tRNA synthetase in an analogue-resistant mutant of Aspergillus nidulans. Mol Gen Genet. 1987;209:164-9 pubmed
    ..It is suggested that mutation in the fpaU gene brings about a structural alteration in Phe-tRNA synthetase. ..
  2. Gonzalez J, McCormick J, Kiley M. Genetic variation among Lassa and Lassa-related arenaviruses analysed by T1-oligonucleotide mapping. Ann Inst Pasteur Virol. 1988;139:405-20 pubmed
    ..Total RNA and small RNA species of several African arenavirus strains have been studied by T1-oligonucleotide mapping. Genetic heterogeneity is observed and discussed on the basis of evolutionary biology of the Lassa complex. ..
  3. Kuhn R, Schafer U, Schafer M. Cis-acting regions sufficient for spermatocyte-specific transcriptional and spermatid-specific translational control of the Drosophila melanogaster gene mst(3)gl-9. EMBO J. 1988;7:447-54 pubmed
  4. Miyamura K, Takeda N, Tanimura M, Ogino T, Yamazaki S, Chen C, et al. Evolutionary study on the Coxsackievirus A 24 variant causing acute hemorrhagic conjunctivitis by oligonucleotide mapping analysis of RNA genome. Arch Virol. 1990;114:37-51 pubmed
    ..The phylogenetic tree constructed indicates that CA 24 v appeared from one focal place in July 1968 +/- 25 months, very close to the time of the first world epidemic of, then newly recognized, acute hemorrhagic conjunctivitis...
  5. Stros M, Nishikawa S, Dixon G. cDNA sequence and structure of a gene encoding trout testis high-mobility-group-1 protein. Eur J Biochem. 1994;225:581-91 pubmed
    ..amp; Yoshida, M. (1992). J. Biol. Chem. 267, 6641-6645] suggesting the evolution of HMG-1 and HMG-2 genes from a common ancestor. ..
  6. Gilmour D, Dietz T, Elgin S. UV cross-linking identifies four polypeptides that require the TATA box to bind to the Drosophila hsp70 promoter. Mol Cell Biol. 1990;10:4233-8 pubmed
    ..Both the extended footprint and the polypeptides identified by UV cross-linking indicate that the Drosophila TATA factor is a multicomponent complex. ..
  7. Lechner J, Sumper M. The primary structure of a procaryotic glycoprotein. Cloning and sequencing of the cell surface glycoprotein gene of halobacteria. J Biol Chem. 1987;262:9724-9 pubmed
    ..14 threonine residues are clustered adjacent to this membrane anchor and linked to these threonines are all the disaccharides of the cell surface glycoprotein. 12 N-glycosylation sites are distributed over the polypeptide chain...
  8. Veidt I, Lot H, Leiser M, Scheidecker D, Guilley H, Richards K, et al. Nucleotide sequence of beet western yellows virus RNA. Nucleic Acids Res. 1988;16:9917-32 pubmed
    ..Similar mechanisms have been proposed for expression of the corresponding ORFs of BYDV(PAV) (1). ..
  9. Dailey L, Caddle M, Heintz N, Heintz N. Purification of RIP60 and RIP100, mammalian proteins with origin-specific DNA-binding and ATP-dependent DNA helicase activities. Mol Cell Biol. 1990;10:6225-35 pubmed
    ..The cofractionation of an ATP-dependent DNA helicase with an origin-specific DNA-binding activity suggests that RIP60 and RIP100 may be involved in initiation of chromosomal DNA synthesis in mammalian cells. ..
  10. Xun L, Orser C. Purification of a Flavobacterium pentachlorophenol-induced periplasmic protein (PcpA) and nucleotide sequence of the corresponding gene (pcpA). J Bacteriol. 1991;173:2920-6 pubmed
    ..pcpA was found to be part of a 1.35-kb transcript with a transcriptional start site 67 bp upstream of the translational start site. Data base search comparisons yielded no sequences of high similarity to pcpA or its protein product...
  11. Martino M, Fasolato L, Montemurro F, Rosteghin M, Manfrin A, Patarnello T, et al. Determination of microbial diversity of Aeromonas strains on the basis of multilocus sequence typing, phenotype, and presence of putative virulence genes. Appl Environ Microbiol. 2011;77:4986-5000 pubmed publisher
    ..A Web-based MLST sequence database ( specific for the Aeromonas genus was developed and implemented with all the results. ..
  12. Froussard P, Chastagner P, Somme G, Abadie A, Greene W, Theze J, et al. p55 IL-2 receptor mRNA precursors in murine T lymphocyte nuclei. J Immunol. 1988;141:1358-64 pubmed
    ..Similar data were obtained for the Th cell clone 52.3 and the cytotoxic T cell line CTLL. All these results indicate that the T cell nucleus contains significant amounts of immature p55 IL-2R mRNA. ..
  13. Komine Y, Adachi T, Inokuchi H, Ozeki H. Genomic organization and physical mapping of the transfer RNA genes in Escherichia coli K12. J Mol Biol. 1990;212:579-98 pubmed
  14. Bourbon H, Prudhomme M, Amalric F. Sequence and structure of the nucleolin promoter in rodents: characterization of a strikingly conserved CpG island. Gene. 1988;68:73-84 pubmed
    ..Our findings shed some light on the putative role of the CpG island. We show that CpG-rich sequence motifs are under strong selective pressure over the whole 5'-terminal region and are presumably involved in regulatory mechanisms. ..
  15. Daub E, Zawadzke L, Botstein D, Walsh C. Isolation, cloning, and sequencing of the Salmonella typhimurium ddlA gene with purification and characterization of its product, D-alanine:D-alanine ligase (ADP forming). Biochemistry. 1988;27:3701-8 pubmed
    ..C., Kenan, D. J., Sweeney, J., & Donachie, W. D. (1986) J. Bacteriol. 167, 809-817]. Because of differences between the S. typhimurium gene and the E. coli ddl gene, the S. typhimurium gene has been named ddlA. ..
  16. Robertson H. Escherichia coli ribonuclease III. Methods Enzymol. 1990;181:189-202 pubmed
  17. Allawi H, Dong F, Ip H, Neri B, Lyamichev V. Mapping of RNA accessible sites by extension of random oligonucleotide libraries with reverse transcriptase. RNA. 2001;7:314-27 pubmed
    ..Finally, we discuss the relationship between RNA extendible sites and RNA accessibility. ..
  18. Blomberg P, Wagner E, Nordstrom K. Control of replication of plasmid R1: the duplex between the antisense RNA, CopA, and its target, CopT, is processed specifically in vivo and in vitro by RNase III. EMBO J. 1990;9:2331-40 pubmed
    ..Hence, cleavage by RNase III seems to be a key event in the copy number control system of plasmid R1. ..
  19. Giallongo A, Oliva D, Cali L, Barba G, Barbieri G, Feo S. Structure of the human gene for alpha-enolase. Eur J Biochem. 1990;190:567-73 pubmed
    ..Furthermore, various sequences similar to known regulatory elements were detected. ..
  20. Lavia P, Macleod D, Bird A. Coincident start sites for divergent transcripts at a randomly selected CpG-rich island of mouse. EMBO J. 1987;6:2773-9 pubmed
    ..The results support the view that HTF islands often mark genes, and they suggest that bidirectional transcription may be a common feature of island promoters. ..
  21. Murakawa G, Nierlich D. Mapping the lacZ ribosome binding site by RNA footprinting. Biochemistry. 1989;28:8067-72 pubmed
    ..The enhanced reactivity of a site distal to the initiation site--flanked by the AUG codon and a site previously identified as conserved in a study of initiation sequences--may indicate a region where the mRNA is specifically exposed. ..
  22. Le Van Kim C, Colin Y, Mitjavila M, Clerget M, Dubart A, Nakazawa M, et al. Structure of the promoter region and tissue specificity of the human glycophorin C gene. J Biol Chem. 1989;264:20407-14 pubmed
  23. Ohyama S, Adachi K, Sugawara K, Hongo S, Nishimura H, Kitame F, et al. Antigenic and genetic analyses of eight influenza C strains isolated in various areas of Japan during 1985-9. Epidemiol Infect. 1992;108:353-65 pubmed
    ..This raises the possibility that C/Nara/1/85 may be a recombinant virus which receives its HE gene from the C/Mississippi/1/80-related parent. ..
  24. Scott G, Marden C, Xu F, Kirk L, Benz C. Transcriptional repression of ErbB2 by histone deacetylase inhibitors detected by a genomically integrated ErbB2 promoter-reporting cell screen. Mol Cancer Ther. 2002;1:385-92 pubmed
    ..These findings suggest that further studies are warranted to determine whether ErbB2-positive human cancers represent unusually sensitive clinical targets for HDAC inhibitor therapy. ..
  25. Kanekura T, Miyauchi T, Tashiro M, Muramatsu T. Basigin, a new member of the immunoglobulin superfamily: genes in different mammalian species, glycosylation changes in the molecule from adult organs and possible variation in the N-terminal sequences. Cell Struct Funct. 1991;16:23-30 pubmed
    ..Another source of heterogeneity of basigin may be differences in N-terminal sequences, since cDNA clones with different 5' coding sequences were identified. ..
  26. Lyons K, Stein J, Smithies O. Length polymorphisms in human proline-rich protein genes generated by intragenic unequal crossing over. Genetics. 1988;120:267-78 pubmed
    ..These differences suggest that the larger number of length variants in PRB genes is related to their greater ease of homologous but unequal pairing compared to PRH genes. ..
  27. Velazquez E, Trujillo M, Peix A, Palomo J, García Benavides P, Mateos P, et al. Stable low molecular weight RNA analyzed by staircase electrophoresis, a molecular signature for both prokaryotic and eukaryotic microorganisms. Syst Appl Microbiol. 2001;24:490-9 pubmed
  28. Ludin C, Hofstetter H, Sarfati M, Levy C, Suter U, Alaimo D, et al. Cloning and expression of the cDNA coding for a human lymphocyte IgE receptor. EMBO J. 1987;6:109-14 pubmed
    ..A computer search with the translated amino acid sequence of the Fc epsilon R revealed a domain of 120 amino acids having striking homology to the human asialoglycoprotein receptors. ..
  29. Manseau L, Ganetzky B, Craig E. Molecular and genetic characterization of the Drosophila melanogaster 87E actin gene region. Genetics. 1988;119:407-20 pubmed
    ..The implications of the failure to identify recessive lethal mutations in the actin gene are discussed in reference to studies of other conserved multigene families and other muscle protein mutations. ..
  30. Kolton M, Meller Harel Y, Pasternak Z, Graber E, Elad Y, Cytryn E. Impact of biochar application to soil on the root-associated bacterial community structure of fully developed greenhouse pepper plants. Appl Environ Microbiol. 2011;77:4924-30 pubmed publisher
    ..We hypothesize that these biochar-augmented genera may be at least partially responsible for the beneficial effect of biochar amendment on plant growth and viability. ..
  31. Szewczak L. In vivo analysis of ribonucleoprotein complexes using nucleotide analog interference mapping. Methods Mol Biol. 2008;488:153-66 pubmed publisher
    ..Functional group analysis of complexes assembled in vivo provides predictive models for further investigation either in vivo or in vitro as well as benchmarks for evaluating and refining biochemical and structural models. ..
  32. Lefevre F, La Bonnardiere C. Molecular cloning and sequencing of a gene encoding biologically active porcine alpha-interferon. J Interferon Res. 1986;6:349-60 pubmed
    ..As expected, it contained no introns and encoded a 189-amino-acid-long preprotein with a putative signal peptide of 23 residues. The homology to human (Hu)IFN-alpha 1 was 78.5% at the nucleotide level and 64% at the amino acid level. ..
  33. Pon C, Calogero R, Gualerzi C. Identification, cloning, nucleotide sequence and chromosomal map location of hns, the structural gene for Escherichia coli DNA-binding protein H-NS. Mol Gen Genet. 1988;212:199-202 pubmed
    ..1 min on the E. coli chromosome, just before an IS30 insertion element. ..
  34. Vengrova S, Dalgaard J. High-resolution mapping of points of site-specific replication stalling. Methods Mol Biol. 2009;521:215-27 pubmed publisher
    ..The data obtained using this method allow determining the position of the 3'-end of the nascent strand at a stalled fork with a one-nucleotide resolution. ..
  35. Schrewe H, Thompson J, Bona M, Hefta L, Maruya A, Hassauer M, et al. Cloning of the complete gene for carcinoembryonic antigen: analysis of its promoter indicates a region conveying cell type-specific expression. Mol Cell Biol. 1990;10:2738-48 pubmed
    ..This indicates that cis-acting sequences which convey cell type-specific expression of the CEA gene are contained within this region. ..
  36. Andrianopoulos A, Hynes M. Sequence and functional analysis of the positively acting regulatory gene amdR from Aspergillus nidulans. Mol Cell Biol. 1990;10:3194-203 pubmed
    ..The amdR6c missense mutation occurs in the middle of the gene, and it is suggested that it results in an altered protein which activates gene expression efficiently in the absence of an inducer. ..
  37. Vlcek C, Kozmik Z, Paces V, Schirm S, Schwyzer M. Pseudorabies virus immediate-early gene overlaps with an oppositely oriented open reading frame: characterization of their promoter and enhancer regions. Virology. 1990;179:365-77 pubmed
    ..The PRV IE gene product repressed transcription from its own promoter and activated the SV40 early promoter. The transactivating virion protein Vmw65 of HSV1 had an opposite effect on these promoters. ..
  38. Thomann H, Schmutzler C, Hüdepohl U, Blow M, Gross H. Genes, variant genes and pseudogenes of the human tRNA(Val) gene family. Expression and pre-tRNA maturation in vitro. J Mol Biol. 1989;209:505-23 pubmed
    ..Finally, precursors encoded by the genes that carry mutations affecting the tRNA tertiary structure are completely resistant to 5' and 3' processing. ..
  39. Schatz D, Leberman R, Eckstein F. Interaction of Escherichia coli tRNA(Ser) with its cognate aminoacyl-tRNA synthetase as determined by footprinting with phosphorothioate-containing tRNA transcripts. Proc Natl Acad Sci U S A. 1991;88:6132-6 pubmed
    ..It is suggested that these regions of the tRNA interact with the helical arm of the synthetase. ..
  40. Dolci S, Grimaldi P, Geremia R, Pesce M, Rossi P. Identification of a promoter region generating Sry circular transcripts both in germ cells from male adult mice and in male mouse embryonal gonads. Biol Reprod. 1997;57:1128-35 pubmed
    ..5 and 13.5 days postcoitum, immediately after the expression of the linear transcript starting from the unique region. ..
  41. Kurosaki T, Ushiro H, Mitsuuchi Y, Suzuki S, Matsuda M, Matsuda Y, et al. Primary structure of human poly(ADP-ribose) synthetase as deduced from cDNA sequence. J Biol Chem. 1987;262:15990-7 pubmed
    ..These facts suggest the possibility that the physiological function of poly(ADP-ribose) synthetase lies in its ability to bind to DNA and to control transformation of living eukaryotic cells like the cases of those oncogene products. ..
  42. Schott D, East P, Paigen K. Characterization of the AdhSL regulatory mutation in Drosophila melanogaster. Genetics. 1988;119:631-7 pubmed
    ..The AdhSL allele carries a 4.5-kb insert approximately 3 kb 5' to the distal promoter. This new insertion may be responsible for the regulatory phenotype of AdhSL. ..
  43. Snutch T, Heschl M, Baillie D. The Caenorhabditis elegans hsp70 gene family: a molecular genetic characterization. Gene. 1988;64:241-55 pubmed
    ..Finally, utilizing strain-specific restriction fragment length differences, we have mapped the chromosomal position of hsp70A to the far right of chromosome IV. ..
  44. Huang C, Guizzo M, Kikuchi M, Blumenfeld O. Molecular genetic analysis of a hybrid gene encoding Sta glycophorin of the human erythrocyte membrane. Blood. 1989;74:836-43 pubmed
    ..The Sta gene is similar in overall structure to another delta-alpha hybrid gene, Dantu, but differs from it in junction structure, copy number, gene linkage, and antigen specificity. ..
  45. Strobel S. Ribozyme chemogenetics. Biopolymers. 1998;48:65-81 pubmed
    ..The model includes a functionally important monovalent metal ion binding site, a wobble-wobble receptor motif for helix-helix packing interactions, and a minor groove triple helix. ..
  46. Reitsma P, Bertina R, Ploos van Amstel J, Riemens A, Briet E. The putative factor IX gene promoter in hemophilia B Leyden. Blood. 1988;72:1074-6 pubmed
    ..The results indicate that the two Dutch kindreds are related and point to the functional significance of the -20 position for the expression of the human factor IX gene. ..
  47. Tanaka T, Har El R, Tanzer M. Partial structure of the gene for chicken cartilage proteoglycan core protein. J Biol Chem. 1988;263:15831-5 pubmed
    ..The dispersed distribution and relatively small size of the exons, if representative of the entire gene, suggest that the complete gene which codes for the core protein may be quite sizable. ..
  48. Schwaninger R, Dumermuth E, Schweingruber M. Effects of seven different mutations in the pho1 gene on enzymatic activity, glycosylation and secretion of acid phosphatase in Schizosaccharomyces pombe. Mol Gen Genet. 1990;221:403-10 pubmed
    ..These mutational lesions apparently block transport of acid phosphatase from the endoplasmic reticulum to the Golgi apparatus. ..
  49. Golden J, Mulligan M, Haselkorn R. Different recombination site specificity of two developmentally regulated genome rearrangements. Nature. 1987;327:526-9 pubmed
    ..We also show that the nifS gene is transcribed only from rearranged genomes. ..
  50. Yanicostas C, Vincent A, Lepesant J. Transcriptional and posttranscriptional regulation contributes to the sex-regulated expression of two sequence-related genes at the janus locus of Drosophila melanogaster. Mol Cell Biol. 1989;9:2526-35 pubmed
    ..The janA gene displayed a much more complex expression; one of the major mRNAs was found in both sexes and at all stages, whereas the two other janA transcripts were expressed only in males. ..
  51. Tzeng W, Frey T. Mapping the rubella virus subgenomic promoter. J Virol. 2002;76:3189-201 pubmed
  52. Elmgren A, Börjeson C, Svensson L, Rydberg L, Larson G. DNA sequencing and screening for point mutations in the human Lewis (FUT3) gene enables molecular genotyping of the human Lewis blood group system. Vox Sang. 1996;70:97-103 pubmed
    ..Of 21 Le(a-b+) and 4 Le(a+b-), 17 typed as LeLe and 7 as Lele202/314. A pedigree study of 8 Lewis-positive individuals showed that the mutations at nucleotides 202 and 314 were located on the same allele. ..
  53. Yan Y, Kunert C, Postlethwait J. Sequence homologies among the three yolk polypeptide (Yp) genes in Drosophila melanogaster. Nucleic Acids Res. 1987;15:67-85 pubmed
    ..These results identify sequences to mutate in order to define elements that regulate Yp gene expression and govern YP polypeptide function. ..