Effect of methylation on the pyrimidine-pyrimidine stacking interaction studied by 1H NMR chemical shift

Aradi, Ferenc

doi:10.1016/0301-4622(94)00115-z

Cited by 11 publications

(29 citation statements)

References 21 publications

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“…These results suggest that at low concentrations, when the stacks of sunset yellow are generally short, i.e. less than around 100 monomer units, 22 There are a number of reports in the literature describing aromatic stacking interactions between molecules with similar structures such as pyrimidines and purines, 45,46 purine and indoles, 47 and caffeine and adenosine. 28 Several of these studies employ more sophisticated versions of the isodesmic model, 28 incorporating …”

Section: Diffusion Behaviourmentioning

confidence: 87%

NMR Investigations of the Interaction Between the Azo-Dye Sunset Yellow and Fluorophenol

Katz

Day

2013

J. Phys. Chem. B

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Copyright and reuse:Sussex Research Online is a digital repository of the research output of the University.Copyright and all moral rights to the version of the paper presented here belong to the individual author(s) and/or other copyright owners. To the extent reasonable and practicable, the material made available in SRO has been checked for eligibility before being made available.Copies of full text items generally can be reproduced, displayed or performed and given to third parties in any format or medium for personal research or study, educational, or not-for-profit purposes without prior permission or charge, provided that the authors, title and full bibliographic details are credited, a hyperlink and/or URL is given for the original metadata page and the content is not changed in any way. [Abstract word count: 134]

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Section: Diffusion Behaviourmentioning

confidence: 87%

NMR Investigations of the Interaction Between the Azo-Dye Sunset Yellow and Fluorophenol

Katz

Day

2013

J. Phys. Chem. B

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“…It is therefore likely that DAMD enriches for differential DNA methylation on the basis of the increase in T m caused by methylated cytosine, and this conclusion is supported by the highly increased density of CpG methylation at DAMD-positive loci as determined by bisulfite sequence analysis. It has been hypothesized that the increase in the stability of duplex DNA caused by cytosine methylation is a result of changes in base-base stacking interactions (35). This effect of methylated cytosine on duplex DNA has previously been used to detect methylation patterns of specific loci by using denaturing gradient gel electrophoresis (36), but this technique is not amenable to genomewide studies.…”

Section: Discussionmentioning

confidence: 99%

DNA methylation of developmental genes in pediatric medulloblastomas identified by denaturation analysis of methylation differences

Diede

Guenthoer

Geng

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

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DNA methylation might have a significant role in preventing normal differentiation in pediatric cancers. We used a genomewide method for detecting regions of CpG methylation on the basis of the increased melting temperature of methylated DNA, termed denaturation analysis of methylation differences (DAMD). Using the DAMD assay, we find common regions of cancer-specific methylation changes in primary medulloblastomas in critical developmental regulatory pathways, including Sonic hedgehog (Shh), Wingless (Wnt), retinoic acid receptor (RAR), and bone morphogenetic protein (BMP). One of the commonly methylated loci is the PTCH1-1C promoter, a negative regulator of the Shh pathway that is methylated in both primary patient samples and human medulloblastoma cell lines. Treatment with the DNA methyltransferase inhibitor 5-aza-2′-deoxycytidine (5-aza-dC) increases the expression of PTCH1 and other methylated loci. Whereas genetic mutations in PTCH1 have previously been shown to lead to medulloblastoma, our study indicates that epigenetic silencing of PTCH1, and other critical developmental loci, by DNA methylation is a fundamental process of pediatric medulloblastoma formation. This finding warrants strong consideration for DNA demethylating agents in future clinical trials for children with this disease.hereas cancer is widely viewed as a genetic disease, the role of epigenetic modifications, especially cytosine methylation in the promoter regions of genes, has been a major research focus in attempting to delineate the mechanisms leading to the formation of cancer, as well as for biomarker discovery (1). Genomic DNA of cancer cells is generally hypomethylated compared to DNA of normal cells, but displays a striking hypermethylation in the promoter regions of a subset of genes. This DNA hypermethylation has been correlated with transcriptional repression, indicating that epigenetic silencing of tumor suppressor genes may be an early step in the process of carcinogenesis (2).In this report, we describe a genomewide DNA methylation assay that identifies CpG methylation on the basis of the biophysical property that 5-methylcytosine increases the melting temperature (T m ) of DNA. We show that this denaturation analysis of methylation differences method detects differentially methylated loci with high CpG density. Assessment of differential methylation in pediatric medulloblastomas compared to normal cerebellum DNA identifies cancer-specific methylation of genes associated with developmental processes. Of particular interest is cancer-specific methylation of the PTCH1-1C promoter, a negative regulator of the Sonic hedgehog (Shh) pathway. Whereas genetic mutations in PTCH1 have been described in human medulloblastomas, this demonstrates that epigenetic silencing by DNA methylation of PTCH1 contributes to the formation of this childhood cancer and suggests the use of DNA demethylating agents as a potential strategy for therapy. Results An Assay to Detect Palindrome Formation Enriches for CpG Methylation.Earlier work from our l...

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“…The tendency to hetero-association was found to depend strongly on the type of substituents; for example, K h increases with methylation of purine and pyrimidine bases, which was interpreted in terms of either greater hydrophobic or van der Waals contribution to the thermodynamics of complexation [70,[83][84][85][86]98]. However, methylation also leads to alterations in the structures of 1:1 hetero-complexes due to the steric demands to accommodate the methyl group within the complex (an increase in distance and induction of partial overlap between the chromophores) [85,101].…”

Section: Hetero-association Of Derivatives Of Nucleic Acid Basesmentioning

confidence: 99%

“…However, methylation also leads to alterations in the structures of 1:1 hetero-complexes due to the steric demands to accommodate the methyl group within the complex (an increase in distance and induction of partial overlap between the chromophores) [85,101]. As a result of these observations, it was suggested that electrostatics plays an important role in International Reviews in Physical Chemistry 17 determining the structural features of the hetero-complexes [85,89] and was later suggested as a general feature of 'electrostatic complementarity' in aromatic stacking [12,102]. Similarly, 'structural complementarity' was also suggested as being important for the hetero-association of various tautomeric and isomeric forms of nitrogen bases in solution [70].…”

Section: Hetero-association Of Derivatives Of Nucleic Acid Basesmentioning

confidence: 99%

“…Quantitative parameters of the hetero-association in solution of various combinations of derivatives of nucleic acid bases have been reported for purine-purine, purine-pyrimidine and pyrimidine-pyrimidine interactions [27,70,71,[83][84][85][86][87][88][89]. Derivatives of nucleic acid bases tend to form stacking-type complexes in aqueous solutions with minor contribution, if any, from in-plane hydrogen-bonding (base-pairing), as deduced from the monotonic shift of aromatic protons to lower frequency in NMR [70,83,85,86,88,89] or the hypochromic effect in UV-vis spectroscopy [90][91][92] on increasing concentration or decreasing 16 M.P. Evstigneev temperature, and also supported by high-level quantum-chemical computations [93][94][95][96].…”

Section: Hetero-association Of Derivatives Of Nucleic Acid Basesmentioning

confidence: 99%

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Hetero-association of aromatic molecules in aqueous solution

Evstigneev

2014

International Reviews in Physical Chemistry

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Knowledge of the physical chemistry of small molecules complexation (the hetero-association) in aqueous solution is increasingly important in view of the rapidly emerging branch of supramolecular chemistry dealing with the formation of heterogeneous polymeric structures having specific functional roles. In this paper, the 50-year history of scientific studies of hetero-association of heterocyclic aromatic molecules in aqueous solution has been reviewed. Some important correlations of structural and thermodynamic parameters of complexation have been reported based on large data-set of hetero-association parameters accumulated to date. The fundamental problem of 'energetic composition' of π-stacking is extensively discussed. The review has shown that there are some gaps in our understanding of heteroassociation, which provides a challenge for further studies in this area.

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Effect of methylation on the pyrimidine-pyrimidine stacking interaction studied by 1H NMR chemical shift

Cited by 11 publications

References 21 publications

NMR Investigations of the Interaction Between the Azo-Dye Sunset Yellow and Fluorophenol

NMR Investigations of the Interaction Between the Azo-Dye Sunset Yellow and Fluorophenol

DNA methylation of developmental genes in pediatric medulloblastomas identified by denaturation analysis of methylation differences

Hetero-association of aromatic molecules in aqueous solution

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