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To study the molecular mechanism of DNA minor groove binding ligand as a radiaiton modulator

ABSTRACT: Radiation induced DNA damage initiates a complex series of overlapping responses responsible for the maintenance of genome integrity. The data reports the expression analysis in response to DNA minor groove binding ligand with an emphasis on its ability to afford better protection in cells exposed to ionizing radiation.

ORGANISM(S): Homo sapiens

PROVIDER: GSE22808 | GEO | 2010/11/01

SECONDARY ACCESSION(S): PRJNA127913

REPOSITORIES: GEO

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Molecular mechanism of DNA minor groove binding ligand as a radiation modulator

2011-08-01 | GSE30044 | GEO

Molecular mechanism of DNA minor groove binding ligand as a radiation modulator

Project description:Radiation-induced DNA damage initiates a complex series of overlapping responses responsible for the maintenance of genome integrity. This study reports the expression analysis in response to DNA minor groove binding ligand (DMA-5-(4-methylpiperazin-1-yl)-2-[2’-(3,4-dimethoxyphenyl)-5`-benzimidazolyl] benzimidazole, an analogue of Hoechst 33342), with an emphasis on its ability to afford better protection in cells exposed to ionizing radiation. Four different types of samples were employed in the analysis: Control (untreated) cells, 50µM ligand-treated cells, 2Gy radiation-treated cells, and cells treated with 50µM ligand one hour prior to 2Gy irradiation.

2011-07-31 | E-GEOD-30044 | biostudies-arrayexpress

To study the molecular mechanism of DNA minor groove binding ligand as a radiaiton modulator

Project description:Radiation induced DNA damage initiates a complex series of overlapping responses responsible for the maintenance of genome integrity. The data reports the expression analysis in response to DNA minor groove binding ligand with an emphasis on its ability to afford better protection in cells exposed to ionizing radiation. Four different types if samples were employed in analysis- Control i.e. untreated cells, 50ÂµM ligand treated cells, 2Gy radiation treated cells, cells treated with 50ÂµM ligand one hour prior to 2 Gy irradiation.

2010-11-01 | E-GEOD-22808 | biostudies-arrayexpress

Gene expression based, effect of DNA minor groove binding ligand on human cells in response to ionizing radiation

2010-11-01 | GSE18422 | GEO

Gene expression based, effect of DNA minor groove binding ligand on human cells in response to ionizing radiation

Project description:Radiation induced DNA damage initiates a complex series of overlapping responses responsible for the maintenance of genome integrity. The data reports the expression analysis in response to DNA minor groove binding ligand with an emphasis on its ability to afford better protection in cells exposed to ionizing radiation. Four different types if samples were employed in analysis- Control i.e. untreated cells, 50ÂµM ligand treated cells, 8.5Gy radiation treated cells, cells treated with 50ÂµM ligand one hour prior to irradiation.

2010-11-01 | E-GEOD-18422 | biostudies-arrayexpress

Differential gene expression after gamma radiation in bis-benzimidazole-treated human glioblastoma using microarray analysis

2011-08-01 | GSE30043 | GEO

Differential gene expression after gamma radiation in bis-benzimidazole-treated human glioblastoma using microarray analysis

Project description:Radiation-induced DNA damage initiates a complex series of overlapping responses responsible for the maintenance of genome integrity. This study reports the expression analysis in response to DNA minor groove binding ligand (DMA-5-(4-methylpiperazin-1-yl)-2-[2’-(3,4-dimethoxyphenyl)-5`-benzimidazolyl] benzimidazole, an analogue of Hoechst 33342), with an emphasis on its ability to afford better protection in cells exposed to ionizing radiation. Four different types of samples were employed in the analysis: Control (untreated) cells, 50µM ligand-treated cells, 8.5Gy radiation-treated cells, and cells treated with 50µM ligand one hour prior to irradiation.

2011-07-31 | E-GEOD-30043 | biostudies-arrayexpress

The HRP3 PWWP domain recognizes the minor groove of double-stranded DNA and recruits HRP3 to chromatin

Project description:HDGF-related protein 3 (HRP3, also known as HDGFL3) belongs to the family of HDGF-related proteins (HRPs) and plays an essential role in hepatocellular carcinoma pathogenesis. All HRPs have a PWWP domain at the N-terminus that binds both histone and DNA substrates. Despite previous advances in PWWP domains, the molecular basis by which HRP3 interacts with chromatin is unclear. In this study, we solved the crystal structures of the HRP3 PWWP domain in complex with various double-stranded DNAs with/without bound histone peptides. We found that HRP3 PWWP bound to the phosphate backbone of the DNA minor groove and showed a preference for DNA molecules bearing a narrow minor groove width. In addition, HRP3 PWWP preferentially bound to histone peptides bearing the H3K36me3/2 modification. HRP3 PWWP uses two adjacent surfaces to bind both DNA and histone substrates simultaneously, enabling us to generate a model illustrating the recruitment of PWWP to H3K36me3-containing nucleosomes. Cell-based analysis indicated that both DNA and histone binding by the HRP3 PWWP domain are important for HRP3 recruitment to chromatin in vivo. Our work establishes that HRP3 PWWP is a new family of minor groove-specific DNA binding proteins, which improves our understanding of HRP3 and other PWWP domain-containing proteins.

2019-04-11 | GSE120492 | GEO

A role for water molecules in DNA-ligand minor groove recognition.

Project description:Targeting the minor groove of DNA through binding to a small molecule has long been considered an important molecular-recognition strategy in biology. A wide range of synthetic heterocyclic molecules bind noncovalently in the minor groove of the double helix and are also effective against a number of human and animal diseases. A classic structural concept, the isohelicity principle, has guided much of this work: such heterocyclic molecules require a shape that complements the convex surface of the minor groove. Researchers have used this principle to design molecules that can read DNA sequences. This principle also predicts that molecules that lack the complementary shape requirement would only bind weakly to DNA. Recently, however, researchers have unexpectedly found that some essentially linear compounds, which do not have this feature, can have high DNA affinity. In this Account, we discuss an alternative recognition concept based on these new findings. We demonstrate that highly structured water molecules can play a key role in mediating between the ligand and DNA minor groove without loss of binding affinity. Combined structural and thermodynamic approaches to understanding the behavior of these molecules have shown that there are different categories of bound water in their DNA complexes. For example, application of this water-bridging concept to the phenylamidine platform has resulted in the discovery of molecules with high levels of biological activity and low nonspecific toxicity. Some of these molecules are now in advanced clinical trials.

| S-EPMC2668807 | biostudies-literature

Ranking ligand affinity for the DNA minor groove by experiment and simulation.

Project description:The structural and thermodynamic basis for the strength and selectivity of the interactions of minor groove binders (MGBs) with DNA is not fully understood. In 2003, we reported the first example of a thiazole-containing MGB that bound in a phase-shifted pattern that spanned six base pairs rather than the usual four (for tricyclic distamycin-like compounds). Since then, using DNA footprinting, NMR spectroscopy, isothermal titration calorimetry, and molecular dynamics, we have established that the flanking bases around the central four being read by the ligand have subtle effects on recognition. We have investigated the effect of these flanking sequences on binding and the reasons for the differences and established a computational method to rank ligand affinity against varying DNA sequences.

| S-EPMC4007966 | biostudies-literature

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