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EMBO J
1989 Jun 01;86:1809-17. doi: 10.1002/j.1460-2075.1989.tb03575.x.
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The DNA binding site of the Xenopus transcription factor IIIA has a non-B-form structure.
Fairall L
,
Martin S
,
Rhodes D
.
Abstract
On the basis of nuclease digestion studies we proposed that the DNA binding site of transcription factor IIIA (TFIIIA) may have an overall structure with A-type rather than B-type characteristics. This proposal was substantiated by the crystal structure of a part of the TFIIIA binding site. Recently, however, it has been reported that the binding site for TFIIIA is B-form in solution, thus implying that the conformation present in crystals is not the structure in solution. We have carried out a study using comparative circular dichroism (CD) spectroscopy of a number of double stranded deoxyoligonucleotides of different sequence, and known crystal structure. The correlation we have found between CD characteristics and certain structural parameters indicates that the solution and crystal structures of the TFIIIA binding site are closely related. This structure may be classed as an intermediate type, between A-form and B-form DNA.
Aboul-ela,
The TFIIIA recognition fragment d(GGATGGGAG).d(CTCCCATCC) is B-form in solution.
1988, Pubmed
Aboul-ela,
The TFIIIA recognition fragment d(GGATGGGAG).d(CTCCCATCC) is B-form in solution.
1988,
Pubmed
Aggarwal,
Recognition of a DNA operator by the repressor of phage 434: a view at high resolution.
1988,
Pubmed
Baase,
Circular dichroism and DNA secondary structure.
1979,
Pubmed
Bram,
Polynucleotide polymorphism in solution.
1971,
Pubmed
Brown,
How a simple animal gene works.
,
Pubmed
,
Xenbase
Calladine,
A base-centred explanation of the B-to-A transition in DNA.
1984,
Pubmed
Dickerson,
The effect of crystal packing on oligonucleotide double helix structure.
1987,
Pubmed
Diekmann,
Temperature and salt dependence of the gel migration anomaly of curved DNA fragments.
1987,
Pubmed
Drew,
Structure of a B-DNA dodecamer: conformation and dynamics.
1981,
Pubmed
Drew,
Recent studies of DNA in the crystal.
1988,
Pubmed
Drew,
DNA structural variations in the E. coli tyrT promoter.
1984,
Pubmed
Drew,
Negative supercoiling induces spontaneous unwinding of a bacterial promoter.
1985,
Pubmed
Fairall,
Mapping of the sites of protection on a 5 S RNA gene by the Xenopus transcription factor IIIA. A model for the interaction.
1986,
Pubmed
,
Xenbase
Fratini,
Reversible bending and helix geometry in a B-DNA dodecamer: CGCGAATTBrCGCG.
1982,
Pubmed
Frederick,
Kinked DNA in crystalline complex with EcoRI endonuclease.
,
Pubmed
Gottesfeld,
DNA sequence-directed nucleosome reconstitution on 5S RNA genes of Xenopus laevis.
1987,
Pubmed
,
Xenbase
Gottesfeld,
The 5S gene internal control region is B-form both free in solution and in a complex with TFIIIA.
,
Pubmed
,
Xenbase
Gray,
The circular dichroism and X-ray diffraction of DNA condensed from ethanolic solutions.
1979,
Pubmed
Hanas,
Xenopus transcription factor A requires zinc for binding to the 5 S RNA gene.
1983,
Pubmed
,
Xenbase
Heinemann,
Crystal structure analysis of an A-DNA fragment at 1.8 A resolution: d(GCCCGGGC).
1987,
Pubmed
Hillen,
Circular dichroism studies of the B goes to A conformational transition in seven small DNA restriction fragments containing the Escherichia coli lactose control region.
1980,
Pubmed
Hunter,
Crystallization and preliminary analysis of the deoxyoligonucleotide d(CGTAGATCTACG).
1988,
Pubmed
Ivanov,
Different conformations of double-stranded nucleic acid in solution as revealed by circular dichroism.
1973,
Pubmed
Jain,
The potentially Z-DNA-forming sequence d(GTGTACAC) crystallizes as A-DNA.
1987,
Pubmed
Johnson,
Correlations between deoxyribonucleic acid structural parameters and calculated circular dichroism spectra.
1981,
Pubmed
Jordan,
Structure of the lambda complex at 2.5 A resolution: details of the repressor-operator interactions.
1988,
Pubmed
Klug,
A hypothesis on a specific sequence-dependent conformation of DNA and its relation to the binding of the lac-repressor protein.
1979,
Pubmed
Lauble,
Three-dimensional structure of d(GGGATCCC) in the crystalline state.
1988,
Pubmed
Leslie,
Polymorphism of DNA double helices.
1980,
Pubmed
Lomonossoff,
Sequence-dependent variation in the conformation of DNA.
1981,
Pubmed
McCall,
The crystal structure of d(G-G-G-G-C-C-C-C). A model for poly(dG).poly(dC).
1985,
Pubmed
McCall,
The crystal structure of d(GGATGGGAG): an essential part of the binding site for transcription factor IIIA.
,
Pubmed
Miller,
Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes.
1985,
Pubmed
,
Xenbase
Moore,
Origins of the differences between the circular dichroism of DNA and RNA: theoretical calculations.
1973,
Pubmed
Nelson,
The structure of an oligo(dA).oligo(dT) tract and its biological implications.
,
Pubmed
Nilsson,
Structure refinement of oligonucleotides by molecular dynamics with nuclear Overhauser effect interproton distance restraints: application to 5' d(C-G-T-A-C-G)2.
1986,
Pubmed
Nishimura,
Salt induced B----A transition of poly(dG).poly(dC) and the stabilization of A form by its methylation.
1986,
Pubmed
Otwinowski,
Crystal structure of trp repressor/operator complex at atomic resolution.
1988,
Pubmed
Peck,
Sequence dependence of the helical repeat of DNA in solution.
1981,
Pubmed
Picard,
Isolation of a 7S particle from Xenopus laevis oocytes: a 5S RNA-protein complex.
1979,
Pubmed
,
Xenbase
Rhodes,
Helical periodicity of DNA determined by enzyme digestion.
1980,
Pubmed
Rhodes,
Sequence-dependent helical periodicity of DNA.
1981,
Pubmed
Rhodes,
Structural analysis of a triple complex between the histone octamer, a Xenopus gene for 5S RNA and transcription factor IIIA.
1985,
Pubmed
,
Xenbase
Rhodes,
An underlying repeat in some transcriptional control sequences corresponding to half a double helical turn of DNA.
1986,
Pubmed
,
Xenbase
Shakked,
Sequence-dependent conformation of an A-DNA double helix. The crystal structure of the octamer d(G-G-T-A-T-A-C-C).
1983,
Pubmed
Sprecher,
Conformation and circular dichroism of DNA.
1979,
Pubmed
Srinivasan,
Nucleic acid model building: the multiple backbone solutions associated with a given base morphology.
1987,
Pubmed
Tunis-Schneider,
Circular dichroism spectra of oriented and unoriented deoxyribonucleic acid films--a preliminary study.
1970,
Pubmed
Wang,
Molecular structure of r(GCG)d(TATACGC): a DNA--RNA hybrid helix joined to double helical DNA.
1982,
Pubmed
Wells,
Physicochemical studies on polydeoxyribonucleotides containing defined repeating nucleotide sequences.
1970,
Pubmed
Yoon,
Structure of an alternating-B DNA helix and its relationship to A-tract DNA.
1988,
Pubmed
