E M Southern

Summary

Affiliation: University of Oxford
Country: UK

Publications

  1. ncbi DNA chips: analysing sequence by hybridization to oligonucleotides on a large scale
    E M Southern
    Department of Biochemistry, University of Oxford, UK
    Trends Genet 12:110-5. 1996
  2. ncbi Molecular interactions on microarrays
    E Southern
    Department of Biochemistry, University of Oxford, UK
    Nat Genet 21:5-9. 1999
  3. ncbi Steric factors influencing hybridisation of nucleic acids to oligonucleotide arrays
    M S Shchepinov
    Department of Biochemistry, University of Oxford, South Parks Road Oxford OX1 3QU, UK
    Nucleic Acids Res 25:1155-61. 1997
  4. ncbi Effects of base mismatches on joining of short oligodeoxynucleotides by DNA ligases
    C E Pritchard
    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
    Nucleic Acids Res 25:3403-7. 1997
  5. ncbi The folding of large RNAs studied by hybridization to arrays of complementary oligonucleotides
    M Sohail
    Department of Biochemistry, University of Oxford, England, United Kingdom
    RNA 5:646-55. 1999
  6. ncbi Hybridization of antisense reagents to RNA
    M Sohail
    University of Oxford, Department of Biochemistry, South Parks Road, Oxford OX1 3QU, UK
    Curr Opin Mol Ther 2:264-71. 2000
  7. ncbi Sequence variation in genes and genomic DNA: methods for large-scale analysis
    K U Mir
    Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
    Annu Rev Genomics Hum Genet 1:329-60. 2000
  8. ncbi Fidelity of DNA ligation: a novel experimental approach based on the polymerisation of libraries of oligonucleotides
    J N Housby
    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
    Nucleic Acids Res 26:4259-66. 1998
  9. ncbi Antisense oligonucleotides selected by hybridisation to scanning arrays are effective reagents in vivo
    M Sohail
    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
    Nucleic Acids Res 29:2041-51. 2001
  10. ncbi Oligonucleotide dendrimers: stable nano-structures
    M S Shchepinov
    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK and
    Nucleic Acids Res 27:3035-41. 1999

Collaborators

Detail Information

Publications16

  1. ncbi DNA chips: analysing sequence by hybridization to oligonucleotides on a large scale
    E M Southern
    Department of Biochemistry, University of Oxford, UK
    Trends Genet 12:110-5. 1996
    ..Oligonucleotide arrays, or 'DNA chips', are miniature, parallel analytical devices, which could bring to sequence analysis and molecular genetics many of the advantages that semiconductor devices brought to computing...
  2. ncbi Molecular interactions on microarrays
    E Southern
    Department of Biochemistry, University of Oxford, UK
    Nat Genet 21:5-9. 1999
    ..We discuss how arrays of oligonucleotides provide powerful tools to study the molecular basis of these interactions on a scale which is impossible using conventional analysis...
  3. ncbi Steric factors influencing hybridisation of nucleic acids to oligonucleotide arrays
    M S Shchepinov
    Department of Biochemistry, University of Oxford, South Parks Road Oxford OX1 3QU, UK
    Nucleic Acids Res 25:1155-61. 1997
    ..Surface coverage was varied using a combination of cleavable and stable linkers, giving the highest hybridisation yields for surfaces containing approximately 50% of the maximum concentration of oligonucleotides...
  4. ncbi Effects of base mismatches on joining of short oligodeoxynucleotides by DNA ligases
    C E Pritchard
    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
    Nucleic Acids Res 25:3403-7. 1997
    ..In the case of Tth DNA ligase, mismatches at the seventh and eighth position 5'to the nick completely inhibit the ligation of octamers. The results are relevant to mechanisms of ligation...
  5. ncbi The folding of large RNAs studied by hybridization to arrays of complementary oligonucleotides
    M Sohail
    Department of Biochemistry, University of Oxford, England, United Kingdom
    RNA 5:646-55. 1999
    ..The method here described helps in identifying regions in the transcripts that take part in long-range interactions...
  6. ncbi Hybridization of antisense reagents to RNA
    M Sohail
    University of Oxford, Department of Biochemistry, South Parks Road, Oxford OX1 3QU, UK
    Curr Opin Mol Ther 2:264-71. 2000
    ..Empirical approaches appear more successful. Of notable interest, and reviewed here, are 'global' methods based on DNA arrays and on mapping of transcripts with RNase H...
  7. ncbi Sequence variation in genes and genomic DNA: methods for large-scale analysis
    K U Mir
    Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
    Annu Rev Genomics Hum Genet 1:329-60. 2000
    ..The problem of large-scale amplification is addressed, and emerging technologies for present and future needs are indicated...
  8. ncbi Fidelity of DNA ligation: a novel experimental approach based on the polymerisation of libraries of oligonucleotides
    J N Housby
    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
    Nucleic Acids Res 26:4259-66. 1998
    ..We suggest that sequence selection was imposed by the ligase and not just by base pairing interactions. The ligase directs polymerisation in the 3' to 5' direction which we propose is linked to its role in lagging strand DNA replication...
  9. ncbi Antisense oligonucleotides selected by hybridisation to scanning arrays are effective reagents in vivo
    M Sohail
    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
    Nucleic Acids Res 29:2041-51. 2001
    ..Excellent correlation was found between antisense potency and affinity of oligonucleotides for the cyclin transcripts as measured by the array, despite the complexity of the cellular environment...
  10. ncbi Oligonucleotide dendrimers: stable nano-structures
    M S Shchepinov
    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK and
    Nucleic Acids Res 27:3035-41. 1999
    ..These features also suggest applications in oligonucleotide array/DNA chip technology when higher hybridisation temperatures are required, for example, to melt secon-dary structure in the target...
  11. ncbi Determining the influence of structure on hybridization using oligonucleotide arrays
    K U Mir
    Department of Biochemistry, University of Oxford, South Parks Rd, Oxford OX1 3QU UK
    Nat Biotechnol 17:788-92. 1999
    ..The study is relevant to duplex formation on oligonucleotide microarrays and to antisense technologies...
  12. ncbi Selecting optimal antisense reagents
    M Sohail
    Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU, Oxford, UK
    Adv Drug Deliv Rev 44:23-34. 2000
    ..Of notable significance are the 'global' methods based on mapping of transcripts with the endoribonuclease H (RNase H) and oligonucleotide scanning arrays...
  13. ncbi Oligonucleotide dendrimers: synthesis and use as polylabelled DNA probes
    M S Shchepinov
    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
    Nucleic Acids Res 25:4447-54. 1997
    ..The strand bearing the dendrimer was resistant to degradation by T7 Gene 6 exonuclease making it easy to convert the double-stranded product of the PCR to a multiply-labelled, single-stranded probe...
  14. ncbi Optimised ligation of oligonucleotides by thermal ligases: comparison of Thermus scotoductus and Rhodothermus marinus DNA ligases to other thermophilic ligases
    J N Housby
    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
    Nucleic Acids Res 28:E10. 2000
    ..We compared the rates of ligation between the four ligases using an octanucleotide library as substrate. By this criterion, the Ts and Rm ligases are far more active compared to the more commonly available thermostable ligases...
  15. ncbi Oligonucleotide scanning arrays: application to high-throughput screening for effective antisense reagents and the study of nucleic acid interactions
    M Sohail
    University of Oxford, Department of Biochemistry, England, UK
    Adv Biochem Eng Biotechnol 77:43-56. 2002
    ..In this article, we discuss the format of these arrays, the technology used to fabricate and to read them, and their applications...
  16. ncbi Analysing genetic information with DNA arrays
    S C Case-Green
    Department of Biochemistry, University of Oxford, UK
    Curr Opin Chem Biol 2:404-10. 1998
    ..Rapid application of the technology to genotyping, antisense oligonucleotide selection and gene expression analysis has illustrated the general power of this approach...