Unprecedented C-selective interstrand cross-linking through in situ oxidation of Furan-Modified Oligodeoxynucleotides

Chemical reagents that form interstrand cross-links have been used for a long time in cancer therapy. They covalently link two strands of DNA, thereby blocking transcription. Cross-link repair enzymes, however, can restore the transcription processes, causing resistance to certain anti-cancer drugs. The mechanism of these cross-link repair processes has not yet been fully revealed. One of the obstacles in this study is the lack of sufficient amounts of well-defined, stable, cross-linked duplexes to study the pathways of cross-link repair enzymes. Our group has developed a cross-link strategy where a furan moiety is incorporated into oligodeoxynucleotides (ODNs). These furan-modified nucleic acids can form interstrand cross-links upon selective furan oxidation with N-bromosuccinimide. We here report on the incorporation of the furan moiety at the 2'-position of a uridine through an amido or ureido linker. The resulting modified ODNs display an unprecedented selectivity for cross-linking toward a cytidine opposite the modified residue, forming one specific cross-linked duplex, which could be isolated in good yield. Furthermore, the structure of the formed cross-linked duplexes could be unambiguously characterized

Large-scale copy number analysis reveals variations in genes not previously associated with malignant pleural mesothelioma

Malignant pleural mesothelioma (MPM) is an aggressive tumor that is often causally associated with asbestos exposure. Comparative genomic hybridization techniques and arrays demonstrated a complex set of copy number variations (CNVs) in the MPM-genome. These techniques however have a limited resolution, throughput and flexibility compared to next-generation sequencing platforms. In this study, the presence of CNVs in the MPM-genome was investigated using an MPM-cohort (N = 85) for which genomic microarray data are available through 'The Cancer Genome Atlas' (TCGA). To validate these results, the genomes of MPMs and matched normal samples (N = 21) were analyzed using low-pass whole genome sequencing on an 'Illumina HiSeq' platform. CNVs were detected using in-house developed analysis pipelines and frequencies of copy number loss and gain were calculated. In both datasets, losses on chromosomes 1, 3, 4, 6, 9, 13 and 22 and gains on chromosomes 1, 5, 7 and 17 were found in at least 25% and 15% of MPMs, respectively. Besides the well-known MPM-associated genes, CDKN2A, NF2 and BAP1, other interesting cancer-associated genes were listed as frequently involved in a copy number loss (e.g. EP300, SETD2 and PBRM1). Moreover, four cancer-associated genes showed a high frequency of copy number gain in

Birds of a Feather Flock Together: Experience-Driven Formation of Visual Object Categories in Human Ventral Temporal Cortex

The present functional magnetic resonance imaging study provides direct evidence on visual object-category formation in the human brain. Although brain imaging has demonstrated object-category specific representations in the occipitotemporal cortex, the crucial question of how the brain acquires this knowledge has remained unresolved. We designed a stimulus set consisting of six highly similar bird types that can hardly be distinguished without training. All bird types were morphed with one another to create different exemplars of each category. After visual training, fMRI showed that responses in the right fusiform gyrus were larger for bird types for which a discrete category-boundary was established as compared with not-trained bird types. Importantly, compared with not-trained bird types, right fusiform responses were smaller for visually similar birds to which subjects were exposed during training but for which no category-boundary was learned. These data provide evidence for experience-induced shaping of occipitotemporal responses that are involved in category learning in the human brain

Sequence specific DNA cross-linking triggered by visible light

A new biocompatible strategy for photoinduced DNA interstrand cross-linking is presented. Methylene blue induced O-1(2) formation triggers furan oxidation; the resulting aldehyde then rapidly reacts with complementary A or C with formation of stable adducts. Easily accessible furan modified nucleosides, a commercially available photosensitizer, and visible light irradiation constitute the necessary tools to achieve selective duplex interstrand cross-linkin