Photochemical probing of the B–A conformational transition in a linearized pUC19 DNA and its polylinker region

Nejedlý, Karel; Chládková, Jana; Kypr, Jaroslav

doi:10.1016/j.bpc.2006.08.007

Cited by 2 publications

(1 citation statement)

References 56 publications

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“…(dT) 50 ) and AT-rich cruciform-forming sequence d(AT) 34 (more details in S1 Table). Formation of non-B DNA structures in different superhelical plasmids was checked by several techniques (S3 Fig): S1 nuclease treatment, OsO 4 -bipy modification detected by specific antibody against OsO 4 -bipy-DNA adducts [48] (S3F Fig) and OsO 4 -bipy modification on the sequencing level [47, 49] (S3G Fig). The H-DNAs formed in plasmids pBA50 and pA69 were also visualized by AFM (Fig 3A and S5 Fig).…”

Section: Resultsmentioning

confidence: 99%

p53 Specifically Binds Triplex DNA In Vitro and in Cells

et al. 2016

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Triplex DNA is implicated in a wide range of biological activities, including regulation of gene expression and genomic instability leading to cancer. The tumor suppressor p53 is a central regulator of cell fate in response to different type of insults. Sequence and structure specific modes of DNA recognition are core attributes of the p53 protein. The focus of this work is the structure-specific binding of p53 to DNA containing triplex-forming sequences in vitro and in cells and the effect on p53-driven transcription. This is the first DNA binding study of full-length p53 and its deletion variants to both intermolecular and intramolecular T.A.T triplexes. We demonstrate that the interaction of p53 with intermolecular T.A.T triplex is comparable to the recognition of CTG-hairpin non-B DNA structure. Using deletion mutants we determined the C-terminal DNA binding domain of p53 to be crucial for triplex recognition. Furthermore, strong p53 recognition of intramolecular T.A.T triplexes (H-DNA), stabilized by negative superhelicity in plasmid DNA, was detected by competition and immunoprecipitation experiments, and visualized by AFM. Moreover, chromatin immunoprecipitation revealed p53 binding T.A.T forming sequence in vivo. Enhanced reporter transactivation by p53 on insertion of triplex forming sequence into plasmid with p53 consensus sequence was observed by luciferase reporter assays. In-silico scan of human regulatory regions for the simultaneous presence of both consensus sequence and T.A.T motifs identified a set of candidate p53 target genes and p53-dependent activation of several of them (ABCG5, ENOX1, INSR, MCC, NFAT5) was confirmed by RT-qPCR. Our results show that T.A.T triplex comprises a new class of p53 binding sites targeted by p53 in a DNA structure-dependent mode in vitro and in cells. The contribution of p53 DNA structure-dependent binding to the regulation of transcription is discussed.

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Section: Resultsmentioning

confidence: 99%

p53 Specifically Binds Triplex DNA In Vitro and in Cells

et al. 2016

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Single-molecule portrait of DNA and RNA double helices

Arias-González

2014

Integr. Biol.

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The composition and geometry of the genetic information carriers were described as double-stranded right helices sixty years ago. The flexibility of their sugar-phosphate backbones and the chemistry of their nucleotide subunits, which give rise to the RNA and DNA polymers, were soon reported to generate two main structural duplex states with biological relevance: the so-called A and B forms. Double-stranded (ds) RNA adopts the former whereas dsDNA is stable in the latter. The presence of flexural and torsional stresses in combination with environmental conditions in the cell or in the event of specific sequences in the genome can, however, stabilize other conformations. Single-molecule manipulation, besides affording the investigation of the elastic response of these polymers, can test the stability of their structural states and transition models. This approach is uniquely suited to understanding the basic features of protein binding molecules, the dynamics of molecular motors and to shedding more light on the biological relevance of the information blocks of life. Here, we provide a comprehensive single-molecule analysis of DNA and RNA double helices in the context of their structural polymorphism to set a rigorous interpretation of their material response both inside and outside the cell. From early knowledge of static structures to current dynamic investigations, we review their phase transitions and mechanochemical behaviour and harness this fundamental knowledge not only through biological sciences, but also for Nanotechnology and Nanomedicine.

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Photochemical probing of the B–A conformational transition in a linearized pUC19 DNA and its polylinker region

Cited by 2 publications

References 56 publications

p53 Specifically Binds Triplex DNA In Vitro and in Cells

p53 Specifically Binds Triplex DNA In Vitro and in Cells

Single-molecule portrait of DNA and RNA double helices

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