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PMID: 3786147 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Analysis of nuclear factor I binding to DNA using degenerate oligonucleotides.

Nucleic acids research ·Vol. 14 ·No. 22 ·1986-11-25 ·Pages 9117-32

Gronostajski RM

Abstract

Nuclear factor I (NFI) binds tightly to DNA containing the consensus sequence TGG(N)6-7GCCAA. To study the role of the spacing between the TGG and GCCAA motifs, oligonucleotides homologous to the NFI binding site FIB-2 were synthesized and used for binding assays in vitro. The wild-type site (FIB-2.6) has a 6bp spacer region and binds tightly to NFI. When the size of this spacer was altered by +/- 1 or 2bp the binding to NFI was abolished. To further assess the role of the spacer and bases flanking the motifs, two oligonucleotide libraries were synthesized. Each member of these libraries had intact TGG and GCCAA motifs, but the sequence of the spacer and the 3bp next to each motif was degenerate. The library with a 6bp spacer bound to NFI to 40-50% the level of FIB-2.6. The library with a 7bp spacer bound to NFI to only 4% the level of FIB-2.6 and some of this binding was weaker than that of FIB-2.6 DNA. This novel use of degenerate DNA libraries has shown that: 1) the structural requirements for FIB sites with a 7bp spacer are more stringent than for sites with a 6bp spacer and 2) a limited number of DNA structural features can prevent the binding of NFI to sites with intact motifs and a 6bp spacer region.

MeSH Terms
Base Sequence CCAAT-Enhancer-Binding Proteins Cell Nucleus/metabolism DNA/metabolism DNA-Binding Proteins/metabolism HeLa Cells/metabolism Humans Kinetics NFI Transcription Factors Nuclear Proteins Oligodeoxyribonucleotides/chemical synthesis,metabolism Protein Binding Structure-Activity Relationship Transcription Factors Y-Box-Binding Protein 1
Chemicals
CCAAT-Enhancer-Binding Proteins DNA-Binding Proteins NFI Transcription Factors Nuclear Proteins Oligodeoxyribonucleotides Transcription Factors Y-Box-Binding Protein 1 YBX1 protein, human DNA
Authors & Affiliations
1 authors, click to expand affiliations / ORCID
Gronostajski R M
References (49)
49 references, click to expand
  1. Lac repressor-operator interaction. I. Equilibrium studies.
    J Mol Biol. 1970 Feb 28;48(1):67-83 PMID: 4915295
  2. Studies on transformation of Escherichia coli with plasmids.
    J Mol Biol. 1983 Jun 5;166(4):557-80 PMID: 6345791
  3. Interaction of int protein with specific sites on lambda att DNA.
    Cell. 1979 Oct;18(2):297-307 PMID: 159130
  4. Sequencing end-labeled DNA with base-specific chemical cleavages.
    Methods Enzymol. 1980;65(1):499-560 PMID: 6246368
  5. Adenovirus DNA replication in vitro: characterization of a protein covalently linked to nascent DNA strands.
    Proc Natl Acad Sci U S A. 1980 Sep;77(9):5105-9 PMID: 6933548
  6. Formation of a covalent complex between the 80,000-dalton adenovirus terminal protein and 5'-dCMP in vitro.
    Proc Natl Acad Sci U S A. 1981 May;78(5):2678-82 PMID: 6942401
  7. Eukaryotic DNA replication: viral and plasmid model systems.
    Annu Rev Biochem. 1982;51:901-34 PMID: 7051968
  8. Separation of the adenovirus terminal protein precursor from its associated DNA polymerase: role of both proteins in the initiation of adenovirus DNA replication.
    Proc Natl Acad Sci U S A. 1982 Sep;79(17):5225-9 PMID: 6957861
  9. Adenovirus DNA replication in vitro: synthesis of full-length DNA with purified proteins.
    Proc Natl Acad Sci U S A. 1983 Jul;80(14):4266-70 PMID: 6308611
  10. Specific binding of a cellular DNA replication protein to the origin of replication of adenovirus DNA.
    Proc Natl Acad Sci U S A. 1983 Oct;80(20):6177-81 PMID: 6336326
  11. Energetics of B-to-Z transition in DNA.
    Proc Natl Acad Sci U S A. 1983 Oct;80(20):6206-10 PMID: 6578505
  12. The replication of adenovirus DNA with purified proteins.
    Cell. 1983 Nov;35(1):7-9 PMID: 6313228
  13. A perfectly symmetric lac operator binds the lac repressor very tightly.
    Proc Natl Acad Sci U S A. 1983 Nov;80(22):6785-9 PMID: 6316325
  14. DNA-protein interaction at the origin of DNA replication of the plasmid pSC101.
    Cell. 1983 Dec;35(2 Pt 1):495-502 PMID: 6317193
  15. A Drosophila RNA polymerase II transcription factor contains a promoter-region-specific DNA-binding activity.
    Cell. 1984 Feb;36(2):357-69 PMID: 6537904
  16. The interaction of Escherichia coli replication factor Y with complementary strand origins of DNA replication. Contact points revealed by DNase footprinting and protection from methylation.
    J Biol Chem. 1984 Feb 25;259(4):2594-601 PMID: 6142045
  17. Structure and function of the adenovirus origin of replication.
    Cell. 1984 May;37(1):309-19 PMID: 6722875
  18. Chromatin structure and protein binding in the putative regulatory region of the c-myc gene in Burkitt lymphoma.
    Cell. 1984 Jun;37(2):381-91 PMID: 6327064
  19. The TGGCA-binding protein: a eukaryotic nuclear protein recognizing a symmetrical sequence on double-stranded linear DNA.
    Nucleic Acids Res. 1984 May 25;12(10):4295-311 PMID: 6328417
  20. DNA sequences required for the in vitro replication of adenovirus DNA.
    Proc Natl Acad Sci U S A. 1984 May;81(10):3069-73 PMID: 6587341
  21. Isolation of human DNA sequences that bind to nuclear factor I, a host protein involved in adenovirus DNA replication.
    Proc Natl Acad Sci U S A. 1984 Jul;81(13):4013-7 PMID: 6588377
  22. A protein binds to a satellite DNA repeat at three specific sites that would be brought into mutual proximity by DNA folding in the nucleosome.
    Cell. 1984 Jul;37(3):889-901 PMID: 6540146
  23. The in vitro replication of adenovirus DNA.
    Curr Top Microbiol Immunol. 1984;110:221-55 PMID: 6478857
  24. DNAase I hypersensitive sites may be correlated with genomic regions of large structural variation.
    J Mol Biol. 1984 Aug 25;177(4):591-607 PMID: 6090673
  25. The dnaA protein complex with the E. coli chromosomal replication origin (oriC) and other DNA sites.
    Cell. 1984 Oct;38(3):889-900 PMID: 6091903
  26. Mechanism of strand cleavage and exchange in the Cre-lox site-specific recombination system.
    J Mol Biol. 1985 Feb 5;181(3):351-62 PMID: 3856690
  27. High-affinity binding site for a specific nuclear protein in the human IgM gene.
    Nature. 1985 Mar 21-27;314(6008):289-92 PMID: 3920528
  28. Site-specific DNA binding of nuclear factor I: analyses of cellular binding sites.
    Mol Cell Biol. 1985 May;5(5):964-71 PMID: 4039788
  29. The TGGCA protein binds to the MMTV-LTR, the adenovirus origin of replication, and the BK virus enhancer.
    Nucleic Acids Res. 1985 Mar 25;13(6):2045-61 PMID: 2987840
  30. The origin of adenovirus DNA replication: minimal DNA sequence requirement in vivo.
    EMBO J. 1985 Feb;4(2):421-6 PMID: 4018031
  31. Adenovirus DNA replication in vitro: site-directed mutagenesis of the nuclear factor I binding site of the Ad2 origin.
    Nucleic Acids Res. 1985 Jul 11;13(13):4935-52 PMID: 4040630
  32. Adenovirus sequences required for replication in vivo.
    Nucleic Acids Res. 1985 Jul 25;13(14):5173-87 PMID: 2991857
  33. Recognition site of nuclear factor I, a sequence-specific DNA-binding protein from HeLa cells that stimulates adenovirus DNA replication.
    EMBO J. 1985 Jun;4(6):1515-21 PMID: 4040852
  34. Control of eukaryotic messenger RNA synthesis by sequence-specific DNA-binding proteins.
    Nature. 1985 Aug 29-Sep 4;316(6031):774-8 PMID: 4041012
  35. In vitro replication of duplex circular DNA containing the simian virus 40 DNA origin site.
    Proc Natl Acad Sci U S A. 1985 Sep;82(17):5710-4 PMID: 2994044
  36. Determination of DNA sequences essential for FLP-mediated recombination by a novel method.
    J Biol Chem. 1985 Oct 5;260(22):12320-7 PMID: 2995371
  37. Sequence-induced DNA curvature at the bacteriophage lambda origin of replication.
    Nature. 1985 Oct 3-9;317(6036):451-3 PMID: 2995831
  38. D1 protein of Drosophila melanogaster. Purification and AT-DNA binding properties.
    J Biol Chem. 1985 Nov 15;260(26):14311-8 PMID: 2997203
  39. Homologous recognition of a promoter domain common to the MSV LTR and the HSV tk gene.
    Cell. 1986 Feb 28;44(4):565-76 PMID: 3004739
  40. Specific interaction between a transcription factor and the upstream element of the adenovirus-2 major late promoter.
    EMBO J. 1985 Dec 16;4(13A):3563-70 PMID: 4092688
  41. A sensitive and rapid gel retention assay for nuclear factor I and other DNA-binding proteins in crude nuclear extracts.
    Nucleic Acids Res. 1986 Feb 11;14(3):1303-17 PMID: 3513122
  42. Curved DNA: design, synthesis, and circularization.
    Proc Natl Acad Sci U S A. 1986 Feb;83(4):862-6 PMID: 3456570
  43. DNA bending at adenine . thymine tracts.
    Nature. 1986 Apr 10-16;320(6062):501-6 PMID: 3960133
  44. Nuclear factor 1 interacts with five DNA elements in the promoter region of the human cytomegalovirus major immediate early gene.
    EMBO J. 1986 Jun;5(6):1367-71 PMID: 3015602
  45. Adenovirus DNA replication in vitro: identification of a host factor that stimulates synthesis of the preterminal protein-dCMP complex.
    Proc Natl Acad Sci U S A. 1982 Nov;79(21):6438-42 PMID: 6216480
  46. Mechanics of sequence-dependent stacking of bases in B-DNA.
    J Mol Biol. 1982 Oct 25;161(2):343-52 PMID: 7154084
  47. Purification of an adenovirus-coded DNA polymerase that is required for initiation of DNA replication.
    Cell. 1982 Dec;31(3 Pt 2):613-23 PMID: 6297776
  48. Base sequence and helix structure variation in B and A DNA.
    J Mol Biol. 1983 May 25;166(3):419-41 PMID: 6854650
  49. Evidence for a function of the adenovirus DNA-binding protein in initiation in DNA synthesis as well as in elongation of nascent DNA chains.
    Virology. 1977 Jul 1;80(1):98-110 PMID: 878318
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
0305-1048
DOI
10.1093/nar/14.22.9117
Published
1986-11-25
Pages
9117-32
Language
English
Region
England
NLM ID
0411011
PMCID
PMC311933
Subset
IM
Databases
GENBANK
M11237, M15899
External Links
PubMed source DOI: 10.1093/nar/14.22.9117 PMC Full Text View journal details
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