Chemical probing of homopurine-homopyrimidine mirror repeats in supercoiled DNA

Voloshin, Oleg N.; Mirkin, Sergei M.; Lyamichev, Victor I.; Belotserkovskii, Boris P.; Frank‐Kamenetskii, Maxim D.

doi:10.1038/333475a0

Cited by 174 publications

(116 citation statements)

References 12 publications

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“…More rigorous proof for the formation of slipped structures has been presented for the adenovirus late promoter (55). Another possibility is that this homopyrimidine-homopurine stretch of DNA forms a triplehelical or triplex structure (28,49).…”

Section: -mentioning

confidence: 99%

Modulation of epidermal growth factor receptor proto-oncogene transcription by a promoter site sensitive to S1 nuclease.

1988

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The epidermal growth factor (EGF) receptor is the functional target of the mitogen EGF and the cellular homolog of the avian erythroblastosis virus erbB oncogene product. Regulation of expression of the proto-oncogene encoding the EGF receptor can be elucidated by studying the structure and function of the gene promoter outside the confines of the cell. Previously, we reported the isolation of the human EGF receptor gene promoter. The promoter is highly GC rich, contains no TATA or CAAT box, and has multiple transcription start sites. An Si nuclease-sensitive site has now been found 80 to 110 base pairs (bp) upstream from the maijor in vivo transcription initiation site. Two sets of direct repeat sequences were found in this area; both conform to the motif TCCTCCTCC. When deletion mutations were made in this region of the promoter by using either Bal 31 exonuclease or S1 nuclease, we found that in vivo activity dropped three-to fivefold, on the basis of transient-transfection analysis. Examination of nuclear protein binding to normal and mutated promoter DNAs by gel retardation analysis and DNase I footprinting revealed that two specific factors bind to the direct repeat region but cannot bind to the S1 nuclease-mutated promoter. One of the specific factors is the transcription factor Spl. The results suggest that these nuclear trans-acting factors interact with the S1 nuclease-sensitive region of the EGF receptor gene promoter and either directly or indirectly stimulate transcription.The epidermal growth factor (EGF) is a potent mitogen capable of stimulating protein and RNA synthesis, DNA replication, and, ultimately, cellular proliferation (5,19,30). It elicits these cellular responses by binding to the Nterminus of a 170-kilodalton cell surface glycoprotein, the EGF receptor. The receptor possesses a very active tyrosine kinase at its C-terminus and is capable of phosphorylating itself and other substrates upon EGF binding (4). By virtue of its extensive homology to the erbB oncogene product of the avian erythroblastosis virus, the EGF receptor is considered the cellular erbB proto-oncogene (7,33,47,53). This proto-oncogene has been found to be overexpressed and occasionally amplified in a variety of malignant cell types (6,27,31,37,38,54 Promoter regions of active genes are frequently hypersensitive to the endonucleases DNase I and S1 (10,29,50). This sensitivity is thought to be the result of changes in the structure of the active chromatin, possibly because of the differential dissociation of nucleosomes and local alteration in DNA superhelicity (29,50). Isolated eucaryotic promoter regions cloned into plasmid vectors maintain sensitivity to S1 nuclease, provided the plasmid is supercoiled (12,14,34,35,40,44,55 (#1) is designated by the bent arrow at position -258. Heavy arrows underscore the location of the four sequences making up two sets of direct repeats (designated A and B). The cross-hatched box marks the general region sensitive to Si nuclease. The underlined sequences are those deleted by S1 nuc...

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Section: -mentioning

confidence: 99%

Modulation of epidermal growth factor receptor proto-oncogene transcription by a promoter site sensitive to S1 nuclease.

1988

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“…These include the left-handed Z-DNA, cruciform and protonated structures [1][2][3]. The interest aroused by such alternative structures in supercoiled covalently closed DNA (ccDNA) is largely associated with their possible role in the functioning of DNA.…”

Section: Introductionmentioning

confidence: 99%

Localization of melted regions in supercoiled DNA

Voloshin¹,

Shlyakhtenko²,

Lyubchenko³

1989

FEBS Letters

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Diethyl pyrocarbonate (DEPC) was used as a probe of local denatured regions in CCDNA pAO3 plasmid. It was found that in native ccDNA molecules only adenosine residues in the loop of the cruciform structure react with DEPC. Denaturation of ccDNA is accompanied by the appearance of two short regions (20 bp long) at both borders of the cruciform structure. Further increase in the denaturation process is associated with considerable expansion of the region located to the left of the cruciform, while the cruciform structure itself and the denatured region located to the right of it disappear.

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“…The sequence-specific recognition of DNA duplexes by a third strand (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12), has implications in gene-regulation and site specific cleavage of genomic DNA (13)(14)(15). There have been several NMR studies on the structural characterization of pyrimidine(Y).purine(R):pyrimidine(Y) DNA triplexes (throughout this paper, Watson and Crick base pairs are represented as R:Y, Hoogsteen as YR and mismatch as R-Y).…”

Section: Introductionmentioning

confidence: 99%

NMR characterisation of a triple stranded complex formed by homo-purine and homo-pyrimidine DNA strands at 1:1 molar ratio and acidic pH

Bhaumik¹,

Chary²,

Govil³

et al. 1995

Nucl Acids Res

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Homo-purine (d-TGAGGAAAGAAGGT) and homopyrimidine (d-CTCCT TI CTTCC) oligomers have been designed such that they are complementary in parallel orientation. When mixed in a 1:1 molar ratio, the system adopts an antiparallel duplex at neutral pH with three mismatched base pairs. On lowering the pH below 5.5, a new complex is formed. The NMR results show the coexistence of a intermolecular pyrimidine.purine:pyrimidine DNA triplex and a single stranded oligopurine at this pH.

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Chemical probing of homopurine-homopyrimidine mirror repeats in supercoiled DNA

Cited by 174 publications

References 12 publications

Modulation of epidermal growth factor receptor proto-oncogene transcription by a promoter site sensitive to S1 nuclease.

Modulation of epidermal growth factor receptor proto-oncogene transcription by a promoter site sensitive to S1 nuclease.

Localization of melted regions in supercoiled DNA

NMR characterisation of a triple stranded complex formed by homo-purine and homo-pyrimidine DNA strands at 1:1 molar ratio and acidic pH

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