Scanning electrochemical microscopy imaging of DNA microarrays using methylene blue as a redox-active intercalator

Scanning electrochemical microscopy (SECM) has been employed in the imaging of DNA microarrays fabricated on gold substrates using methylene blue (MB) as a redox-active intercalator and ferrocyanide as the SECM mediator in solution. MB intercalated between base pairs of immobilized ds-DNA is electrochemically reduced via electron transfer from the underlying gold substrate, and the product is reoxidized in solution by SECM tip-generated ferricyanide. The resulting feedback current allows a heterogeneous electron-transfer rate constant for the MB-intercalated DNA to be deduced. Moreover, DNA microarray spots can be imaged at a detection level of 14 fmol/spot for ds-DNA consisting of 15 base pairs. Microarrays prepared using 20 microM DNA solutions are easily visualized, and the feasibility of detecting base pair mismatches is also demonstrated.

Double-mismatched siRNAs enhance selective gene silencing of a mutant ALS-causing allele

AIM

Our previous study demonstrated an siRNA-mediated, allele-specific silencing of mutant genes that cause amyotrophic lateral sclerosis. To improve siRNA design for better therapeutic use of RNA interference, we systematically tested the base-pairing mismatch strategy in the design of asymmetric siRNA.

METHODS

A naturally symmetric siRNA that targets the human Cu Zn superoxide dismutase G85R mutant allele was modified by placing either 1 or 2 mismatches at the end of the siRNA from position 1 to 4 at each time. The target preference and silencing efficacy of modified siRNA were measured using a modified dual luciferase system.

RESULTS

The modification of single base-pairing mismatch successfully achieved the conversion of the siRNA that was originally favored to the antisense of the mutant allele to the one that was favored to the sense strand of the gene. Compared to the single-mismatched siRNA, those with double-mismatch at one end demonstrated an increased asymmetry, and thus, an enhanced specificity and efficacy of gene silencing. In addition, the siRNA with double-mismatch at both ends remained in symmetry.

CONCLUSION

Our results suggest the effectiveness of converting a symmetric siRNA to an asymmetric one by introducing mismatches into its structure, and the superiority of double-mismatched siRNA to single-mismatched siRNA in producing selective gene silencing resulting from the disruption of siRNA symmetry. The double-mismatch strategy is an improvement of the single-mismatch method and could be useful in the design of effective siRNAs for the treatment of diseases caused by dominant, gain-of-function gene mutations, such as ALS.

Population structure of Cicada barbara Stål (Hemiptera, Cicadoidea) from the Iberian Peninsula and Morocco based on mitochondrial DNA analysis

We assess the genetic history and population structure of Cicada barbara in Morocco and the Iberian Peninsula, based on analysis of the mitochondrial cytochrome b gene. The divergence between Morocco and the Iberian Peninsula populations was strongly corroborated by the molecular data, suggesting genetically isolated populations with a low level of gene flow. The Ceuta population from Spanish North Africa was more similar to the Iberian populations than the surrounding Moroccan populations, suggesting that the Strait of Gibraltar has not been acting as a strict barrier to dispersal while the Rif Mountains have. The Iberian Peninsula specimens showed a signature of demographic expansion before that which occurred in Morocco, but some of the assumptions related to the demographic parameters should be considered with caution due to the small genetic variation found. The high haplotype diversity found in Morocco implies higher demographic stability than in the Iberian Peninsula populations. These results do not, however, suggest a Moroccan origin for Iberian cicadas; but the most northwest region in Africa, such as Ceuta, might have acted as a southern refuge for Iberian cicadas during the most severe climatic conditions, from where they could expand north when climate improved. The separation of two subspecies within C. barbara (C. barbara lusitanica and C. barbara barbara) finds support with these results.

Altering DNA base excision repair: use of nuclear and mitochondrial-targeted N-methylpurine DNA glycosylase to sensitize astroglia to chemotherapeutic agents

Primary astrocyte cultures were used to investigate the modulation of DNA repair as a tool for sensitizing astrocytes to genotoxic agents. Base excision repair (BER) is the principal mechanism by which mammalian cells repair alkylation damage to DNA and involves the processing of relatively nontoxic DNA adducts through a series of cytotoxic intermediates during the course of restoring normal DNA integrity. An adenoviral expression system was employed to target high levels of the BER pathway initiator, N-methylpurine glycosylase (MPG), to either the mitochondria or nucleus of primary astrocytes to test the hypothesis that an alteration in BER results in increased alkylation sensitivity. Increasing MPG activity significantly increased BER kinetics in both the mitochondria and nuclei. Although modulating MPG activity in mitochondria appeared to have little effect on alkylation sensitivity, increased nuclear MPG activity resulted in cell death in astrocyte cultures treated with methylnitrosourea (MNU). Caspase-3 cleavage was not detected, thus indicating that these alkylation sensitive astrocytes do not undergo a typical programmed cell death in response to MNU. Astrocytes were found to express relatively high levels of antiapoptotic Bcl-2 and Bcl-XL and very low levels of proapoptotic Bad and Bid suggesting that the mitochondrial pathway of apoptosis may be blocked making astrocytes less vulnerable to proapoptotic stimuli compared with other cell types. Consequently, this unique characteristic of astrocytes may be responsible, in part, for resistance of astrocytomas to chemotherapeutic agents.

[Study on the germline mutation of MSH6 gene in Chinese hereditary nonpolyposis colorectal cancer pedigrees using PCR based sequencing]

OBJECTIVE

To detect the germline mutation of mismatch repair gene (MSH6) in hereditary nonpolyposis colorectal cancer (HNPCC) kindreds fulfilling different clinical criteria.

METHODS

The germline mutations of MSH6 gene were detected by PCR based DNA sequencing in 39 unrelated HNPCC probands fulfilling different clinical criteria in which MSH2 and MLH1 mutations were excluded. The exons with missense mutations were analyzed using PCR sequencing in the germline genomic DNA of 137 healthy persons. The expression of MSH6 protein was detected by Envision immunohistochemistry staining in the tumor tissues of the mutational probands.

RESULTS

Six germline mutations of MSH6 gene were detected in 39 probands of Chinese HNPCC kindreds, and the mutations distributed in the exon 4, 6, 9 and 10. Four out of six mutations were missense mutation, one was nonsense mutation and the remaining one was insertion mutation in splice site. The results of sequecing for the exons with above four missense mutations in 137 healthy persons' genomic DNA showed that 5 of 137 persons had the missense mutation of c.3488 A to T at codon 1163 of the 6th exon. The mutational rate was approximately 3.65% (5/137), so the mutation could be a single nucleotide polymorphism (SNP). The remaining missense mutations were not found in any germline genomic DNA of 137 healthy persons. Positive expression of MSH6 protein had been identified in the tumor of the SNP proband while the tumors had negative MSH6 protein expression in the rest probands of germline mutation MSH6 gene. The types of mutations and their potential significance were determined by comparing the following databases: http://www.ncbi.nlm.nih.gov/, http://www.ensembl.org/homo-sapies, and http://www.insight-group.org. Five out of the six mutations had not been reported previously and they were new pathological mutations, the rest one was a new SNP.

CONCLUSION

Germline mutations of MSH6 gene may play an important role in Chinese HNPCC kindreds fulfilling different clinical criteria. It is necessary to analyze the germline mutations of MSH6 gene using sequencing to identify HNPCC families in the probands in which MSH2 and MLH1 mutation were excluded.

Population structure and gene flow among wild populations of the black muntjac (Muntiacus crinifrons) based on mitochondrial DNA control region sequences

The black muntjac (Muntiacus crinifrons) is a rare species endemic to China and its current distribution is confined to partial mountain ranges in eastern China. To assess the population structure and gene flow among the extant populations, we sequenced a portion of the mitochondrial control region (424 bp) for 47 samples collected from its current three large populations (Huangshan, Tiammushan and Suichang). A total of 18 unique haplotypes were defined based on 22 polymorphic sites. Of these haplotypes, 15 ones were population-specific and only one haplotype was shared among the three populations. Significant genetic differentiation was detected between Suichang and Huangshan populations (ø(ST)=0.1677, P<0.001) or between Suichang and Tianmushan populations (ø(ST)=0.2002, P<0.001), indicating that the Suichang population may be spatially structured from other two populations along matriline. The Mantel test revealed that this significant differentiation was not driven by geographic distance (P=0.14), implying that genetic divergence of Suichang population might result from recent human disturbances. Phylogenetic analyses suggested the mitochondrial control region haplotypes were split into two well divergent clades (Clade I and Clade II). Interestingly, the two distinct haplotype clades were found to coexist in Suichang area. The nested clade analysis revealed a significant phylogeographic structure among the black muntjac populations (total cladogram: chi2=18.68; P<0.001), which was inferred to result from past fragmentation followed by range expansion. The population expansion was supported by the analysis of mismatch distribution and the tests of neutrality. Therefore, we suggest that the coexistence of distinct haplotypes in Suichang population was induced by historical population expansion after fragmentation and that the current genetic differentiation should be attributed to the reduction of female-mediated gene flow due to recent habitat fragmentation and subsequent loss.

Analysis of sequence conservation at nucleotide resolution

One of the major goals of comparative genomics is to understand the evolutionary history of each nucleotide in the human genome sequence, and the degree to which it is under selective pressure. Ascertainment of selective constraint at nucleotide resolution is particularly important for predicting the functional significance of human genetic variation and for analyzing the sequence substructure of cis-regulatory sequences and other functional elements. Current methods for analysis of sequence conservation are focused on delineation of conserved regions comprising tens or even hundreds of consecutive nucleotides. We therefore developed a novel computational approach designed specifically for scoring evolutionary conservation at individual base-pair resolution. Our approach estimates the rate at which each nucleotide position is evolving, computes the probability of neutrality given this rate estimate, and summarizes the result in a Sequence CONservation Evaluation (SCONE) score. We computed SCONE scores in a continuous fashion across 1% of the human genome for which high-quality sequence information from up to 23 genomes are available. We show that SCONE scores are clearly correlated with the allele frequency of human polymorphisms in both coding and noncoding regions. We find that the majority of noncoding conserved nucleotides lie outside of longer conserved elements predicted by other conservation analyses, and are experiencing ongoing selection in modern humans as evident from the allele frequency spectrum of human polymorphism. We also applied SCONE to analyze the distribution of conserved nucleotides within functional regions. These regions are markedly enriched in individually conserved positions and short (<15 bp) conserved “chunks.” Our results collectively suggest that the majority of functionally important noncoding conserved positions are highly fragmented and reside outside of canonically defined long conserved noncoding sequences. A small subset of these fragmented positions may be identified with high confidence.

The structure of the human genome remains largely unknown, including which parts of the genome are functionally relevant and which parts are “junk.” The availability of genomic sequence from a large number of mammals allows a more detailed exploration of this structure, using comparison of related sequences from different species to identify portions of the genome that have remained unchanged, conserved by the action of natural selection, and thus likely to be functionally significant. To date, most efforts focused on localizing the functional fraction of the human genome have been based on identifying contiguous stretches of positions conserved in multiple species. Here, we present an analysis that is based instead on a single-position measure of conservation called SCONE. Our analysis suggests that the majority of conserved and putatively functional positions are highly fragmented and lie outside contiguous regions of conserved sequence. A subset of these fragmented positions may be identified based on local clustering.

The number of genes having different alleles between rice cultivars estimated by SNP analysis

Identification of single nucleotide polymorphisms (SNPs) in a large number of genes will enable estimation of the number of genes having different alleles in a population. In the present study, SNPs between 21 rice cultivars including 17 Japanese cultivars, one upland rice, and three indica cultivars were analyzed by PCR-RF-SSCP. PCR-RF-SSCP analysis was found to be a more efficient method for detecting SNPs than mismatch-cleavage analysis, though both PCR-RF-SSCP and mismatch-cleavage are useful for screening SNPs. The number of DNA fragments showing polymorphism between Japanese cultivars was 134 in the 1,036 genes analyzed. In 137 genes, 638 DNA polymorphisms were identified. Out of 52 genes having polymorphisms in the exons, one had a frame-shift mutation, three had polymorphism causing amino acid insertions or deletions, and 16 genes had missense polymorphisms. The number of genes having frame-shift mutations and missense polymorphisms between the 17 Japanese cultivars was estimated to be 41 and 677 on average, respectively, and those between japonica and indica to be 425 and 6,977, respectively. Chromosomal regions of cultivars selected in rice breeding processes were identified by SNP analysis of genes.

Immunohistochemical staining for mismatch repair proteins, and its relevance in the diagnosis of hereditary non-polyposis colorectal cancer

BACKGROUND

Hereditary non-polyposis colorectal cancer (HNPCC) arises mostly from germline mutations of the mismatch repair genes MSH2 and MLH1. The diagnosis of HNPCC is based on a set of clinical criteria that may be too restrictive to identify all affected patients. Immunohistochemical staining (IHC) for the mismatch repair proteins, MutS homologue 2 (MSH2) and MutL homologue 1 (MLH1), reliably identifies the microsatellite instability phenotype. This study evaluated the ability of IHC to detect germline mutations in an unselected group of patients with colorectal cancer (CRC).

METHODS

All patients with CRC operated on between July 2000 and March 2003, and demonstrating a loss of protein, were contacted. Following informed consent, searchs for germline mutation and methylation of the promoter were performed on normal and tumoral DNA.

RESULTS

Thirty patients agreed to participate, four of whom fulfilled the Amsterdam II criteria. Loss of expression of MLH1 was found in 20 patients, and loss of expression of MSH2 in ten patients. Four of the MLH1-deficient patients had a germline MLH1 point mutation (positive predictive value (PPV) 20 (95 per cent confidence interval (c.i.) 2 to 38 per cent) and 11 had promoter methylation. Seven of the MSH2-deficient patients had a germline MSH2 point mutation (PPV 70 (95 per cent c.i. 54 to 96 per cent), and none showed promoter methylation.

CONCLUSION

MLH1-deficient patients who are young or have a positive family history of cancer should be referred for genetic testing and counselling, whereas MSH2-deficient patients should be counselled in the same way as patients with HNPCC.

Model-P: a basecalling method for resequencing microarrays of diploid samples

MOTIVATION

Basecalling is a critical step of the analysis of DNA resequencing microarray data for single nucleotide polymorphism discovery and genotyping. For microarrays hybridized with DNA derived from diploid organisms, basecalling with high accuracy at high call rates is a challenging task. Current methods sometimes do not produce satisfactory results.

RESULTS

We explored using physical models based on the sequences of the probe and the target to predict feature intensities in resequencing microarrays. Based on these intensity-predicting models, a new basecalling method (Model-P), which takes into consideration the expected feature intensities for different potential genotypes, was developed. Model-P is shown to have better performance at high call rates compared with ABACUS, the current state-of-the-art method, on a test dataset and on relatively AT-rich regions.

AVAILABILITY

Model-P is available upon request.

A nucleotide substitution model with nearest-neighbour interactions

MOTIVATION

It is well known that neighbouring nucleotides in DNA sequences do not mutate independently of each other. In this paper, we introduce a context-dependent substitution model and derive an algorithm to calculate the likelihood of sequences evolving under this model. We use this algorithm to estimate neighbour-dependent substitution rates, as well as rates for dinucleotide substitutions, using a Bayesian sampling procedure. The model is irreversible, giving an arrow to time, and allowing the position of the root between a pair of sequences to be inferred without using out-groups.

RESULTS

We applied the model upon aligned human-mouse non-coding data. Clear neighbour dependencies were observed, including 17-18-fold increased CpG to TpG/CpA rates compared with other substitutions. Root inference positioned the root halfway the mouse and human tips, suggesting an approximately clock-like behaviour of the irreversible part of the substitution process.

Highly efficient somatic-mutation identification using Escherichia coli mismatch-repair detection

The discovery of somatic mutations in cancer tissue is extremely laborious, time-consuming and costly. In an evaluation comparing mismatch repair detection (MRD) against Sanger sequencing for somatic-mutation detection, we found that MRD had a specificity of 96% and a sensitivity of 92%. Our results showed that MRD is a robust and cost-effective alternative to Sanger sequencing for identifying somatic mutations in human tumors.

Mutational analysis of bacterial NAD+-dependent DNA ligase: role of motif IV in ligation catalysis

The bacterial DNA ligase as a multiple domain protein is involved in DNA replication, repair and recombination. Its catalysis of ligation can be divided into three steps. To delineate the roles of amino acid residues in motif IV in ligation catalysis, site-directed mutants were constructed in a bacterial NAD+-dependent DNA ligase from Thermus sp. TAK16D. It was shown that four conserved residues (D286, G287, V289 and K291) in motif IV had significant roles on the overall ligation. Under single turnover conditions, the observed apparent rates of D286E, G287A, V289I and K291R mutants were clearly reduced compared with that of WT ligase on both match and mismatch nicked substrates. The effects of D286E mutation on overall ligation may not only be ascribed to the third step. The G287A mutation has a major effect on the second step. The effects of V289I and K291R mutation on overall ligation are not on the third step, perhaps other aspects, such as conformation change of ligase protein in ligation catalysis, are involved. Moreover, the amino acid substitutions of above four residues were more sensitive on mismatch nicked substrate, indicating an enhanced ligation fidelity.

Folding of a DNA hairpin loop structure in explicit solvent using replica-exchange molecular dynamics simulations

Hairpin loop structures are common motifs in folded nucleic acids. The 5'-GCGCAGC sequence in DNA forms a characteristic and stable trinucleotide hairpin loop flanked by a two basepair stem helix. To better understand the structure formation of this hairpin loop motif in atomic detail, we employed replica-exchange molecular dynamics (RexMD) simulations starting from a single-stranded DNA conformation. In two independent 36 ns RexMD simulations, conformations in very close agreement with the experimental hairpin structure were sampled as dominant conformations (lowest free energy state) during the final phase of the RexMDs ( approximately 35% at the lowest temperature replica). Simultaneous compaction and accumulation of folded structures were observed. Comparison of the GCA trinucleotides from early stages of the simulations with the folded topology indicated a variety of central loop conformations, but arrangements close to experiment that are sampled before the fully folded structure also appeared. Most of these intermediates included a stacking of the C(2) and G(3) bases, which was further stabilized by hydrogen bonding to the A(5) base and a strongly bound water molecule bridging the C(2) and A(5) in the DNA minor groove. The simulations suggest a folding mechanism where these intermediates can rapidly proceed toward the fully folded hairpin and emphasize the importance of loop and stem nucleotide interactions for hairpin folding. In one simulation, a loop motif with G(3) in syn conformation (dihedral flip at N-glycosidic bond) accumulated, resulting in a misfolded hairpin. Such conformations may correspond to long-lived trapped states that have been postulated to account for the folding kinetics of nucleic acid hairpins that are slower than expected for a semiflexible polymer of the same size.

A new variant database for mismatch repair genes associated with Lynch syndrome

Mutations in some mismatch repair (MMR) genes are associated with Lynch syndrome (LS; also called hereditary nonpolyposis colorectal cancer [HNPCC]), an autosomal dominant cancer susceptibility syndrome. Colorectal cancer (CRC) is the most frequent cancer observed in LS. However, tumors occur at a variety of extracolonic sites and individuals may have multiple primary cancers. LS is the most common hereditary form of CRC, accounting for approximately 1% of all CRC. Since the first account of mutations in MSH2 causing this cancer susceptibility syndrome in 1993, mutations in three additional MMR genes, MLH1, MSH6, and PMS2, have been shown to cause LS. More than 1,500 different variants have been identified in these four genes and approximately 80% of the alterations have been identified in MLH1 and MSH2. There have been a few previous attempts to systematically record MMR variants associated with LS patients; however, they were not complete nor were they continuously updated. Thus, it was our goal to generate and maintain a comprehensive catalogue of MMR variants from genes known to be mutated in LS (http://www.med.mun.ca/MMRvariants; last accessed 8 February 2007). Providing such a resource should aid investigators in understanding the significance of the variants.

NMR investigation of primer-template models: structural effect of sequence downstream of a thymine template on mutagenesis in DNA replication

Misaligned structures can occur in primer-templates during DNA replication, which can be bypassed and extended by low-fidelity polymerases and ultimately lead to mutations. In this study, we have investigated how the nucleotide downstream of a thymine template affects the primer-template structures upon misincorporation of dNTPs. The base pair structures at the replicating sites of a set of primer-template models containing either a G or an A downstream of the thymine template have been determined using NMR spectroscopy. Incorporation of dCTP and dTTP opposite 5'-GT and 5'-AT templates, respectively, can result in misaligned structures with a T-bulge. Depending on the downstream sequence, subsequent extension of the primers may stabilize the misaligned structures or cause the formation of mismatched structures. These results provide alternative pathways for base substitution and deletion errors during DNA replication by low-fidelity polymerases.

Mutation in mouse hei10, an e3 ubiquitin ligase, disrupts meiotic crossing over

Crossing over during meiotic prophase I is required for sexual reproduction in mice and contributes to genome-wide genetic diversity. Here we report on the characterization of an N-ethyl-N-nitrosourea-induced, recessive allele called mei4, which causes sterility in both sexes owing to meiotic defects. In mutant spermatocytes, chromosomes fail to congress properly at the metaphase plate, leading to arrest and apoptosis before the first meiotic division. Mutant oocytes have a similar chromosomal phenotype but in vitro can undergo meiotic divisions and fertilization before arresting. During late meiotic prophase in mei4 mutant males, absence of cyclin dependent kinase 2 and mismatch repair protein association from chromosome cores is correlated with the premature separation of bivalents at diplonema owing to lack of chiasmata. We have identified the causative mutation, a transversion in the 5′ splice donor site of exon 1 in the mouse ortholog of Human Enhancer of Invasion 10 (Hei10; also known as Gm288 in mouse and CCNB1IP1 in human), a putative B-type cyclin E3 ubiquitin ligase. Importantly, orthologs of Hei10 are found exclusively in deuterostomes and not in more ancestral protostomes such as yeast, worms, or flies. The cloning and characterization of the mei4 allele of Hei10 demonstrates a novel link between cell cycle regulation and mismatch repair during prophase I.

Human infertility and reproductive complications have devastating social and monetary costs. Errors in meiosis during reproduction may lead to birth defects, spontaneous abortion, or infertility. Many of the genes essential for meiosis function in DNA repair and mutations in several of these genes have been shown to contribute to cancer. The identification of the genes necessary for normal meiosis is an important goal and will potentially influence the fields of reproductive and cancer biology. In this study, genetic screens in mice have generated the mutation mei4. mei4 causes male and female sterility by disrupting meiosis and altering the function of the DNA repair system known as mismatch repair. We have identified the causative mutation behind the mei4 phenotype in a gene called Human Enhancer of Invasion 10 or Hei10. This work demonstrates that Hei10 is essential for the completion of meiosis and that it functions to coordinate the DNA repair system and the progression of the cell cycle during meiosis.

Biallelic germline mutations of mismatch-repair genes: a possible cause for multiple pediatric malignancies

BACKGROUND

Heterozygous defects in mismatch-repair (MMR) genes cause hereditary nonpolyposis colorectal cancer (HNPCC). In this syndrome, tumors typically arise from age 25 years onward. Case reports have shown that homozygosity or compound heterozygosity for MMR gene mutations can cause multiple tumors in childhood, sometimes combined with neurofibromatosis type I (NF1)-like features. Therefore, the authors studied the role of homozygosity or compound heterozygosity (CZ) for MMR gene defects in children with multiple primary tumors.

METHODS

A database that contained all pediatric oncology patients who were seen between 1982 and 2003 at the author's institution was queried to identify patients aged <16 years with more than 1 tumor for whom tissue of at least 1 tumor was available. On isolated DNA, microsatellite instability (MSI) and immunohistochemistry of MMR proteins were assessed.

RESULTS

In total, 15 patients with more than 1 tumor were identified. Abnormal test results were obtained in 2 of them, including 1 patient who was diagnosed at age 4 years with a glioblastoma (MSI-stable; no human mutL homolog 1 [MLH1] or postmeiotic segregation increased, Saccharomyces cerevisiae 2 [PMS2] expression) and a Wilms tumor (high MSI; no MLH1 or PMS2 expression). Apart from >6 cafe-au-lait spots, he had no other signs of NF1. The patient had CZ identified for a pathogenic MLH1 mutation (593delAG frameshift) and an unclassified MLH1 variant (Met35Asn). There was strong evidence that this unclassified variant was a pathogenic mutation. The second patient was diagnosed with a non-Hodgkin lymphoma (no tissue available) and an anaplastic oligodendroglioma (low MSI; no MSH6 expression) at age 4 years and 6 years, respectively. His brother had died of a medulloblastoma at age 6 years (low MSI, no MSH6 expression). Both boys had cafe-au-lait spots. Further genetic testing was not possible.

CONCLUSIONS

Carriage of biallelic MMR gene defects can be associated with multiple malignancies in childhood that may differ from the standard spectrum of HNPCC tumor types. In 15 pediatric patients with multiple malignancies, the authors identified 1 clear case and 1 possible case of biallelic MMR gene defect. Recognition of the inherited nature of the tumors in these patients is important for counseling these patients and their families.

[Recognition of congenital endometrial carcinoma: the importance of family history and investigation of microsatellite instability in the tumour]

Endometrial cancer diagnosed at a relatively young age or in a patient with a medical history of colorectal cancer may be indicative of Lynch syndrome. Four women, aged 43, 60, 41 and 54 respectively, with a family history of endometrial or colorectal neoplasm were examined for microsatellite instability (MSI) in tumour tissue with positive results. Subsequently, a mutation was found in one of the DNA mismatch repair genes. Lynch syndrome, also known as hereditary non-polyposis colorectal cancer (HNPCC), is caused by a germline mutation in a mismatch repair gene and is an autosomal dominant disorder that is characterized by the development of carcinoma of the endometrium and colorectum at a relatively young age. Until recently, recognition of Lynch syndrome was mainly based on an, often incomplete, family history, but today the presence of MSI in tumour tissue can be used to identify patients at risk for Lynch syndrome. A pathologist can contribute to identifying a patient at risk for Lynch syndrome by initiating MSI testing when: (a) endometrial cancer is diagnosed under the age of 50, (b) a combination of endometrial cancer and colorectal cancer is diagnosed under the age of 70.

DNA base mismatch detection with bulky rhodium intercalators: synthesis and applications

This protocol describes the syntheses and applications of two metallointercalators, Rh(bpy)2(chrysi)3+ and Rh(bpy)2(phzi)3+, that target single base mismatches in DNA. The complexes bind mismatched DNA sites specifically and, upon photoactivation, promote strand scission neighboring the mismatch. Owing to their high specificity and sequence context independence, targeting mismatches with these complexes offers an attractive alternative to current mismatch- and SNP-detection methodologies. This protocol also describes the synthesis of these complexes and their use in marking mismatched sites. Irradiation of 32P-labeled duplex DNA with either intercalator followed by denaturing PAGE allows the detection of mismatches in oligonucleotides. The protocol also outlines a method for efficient detection of single nucleotide polymorphisms (SNPs) in larger genes or plasmids. Pooled genes are denatured and re-annealed to form heteroduplexes; they are then incubated with either complex, irradiated and analyzed using capillary electrophoresis to probe for mismatches (SNP sites). The synthesis of the metallointercalators requires approximately 5-7 d. The mismatch- and SNP-detection experiments each require approximately 3 d.

Single-molecule observation of DNA charge transfer

DNA charge transfer highly depends on the electronic interaction between base pairs and reflects the difference in the base composition and sequence. For the purpose of investigating the charge transfer process of individual DNA molecules and the optical readout of DNA information at the single-molecule level, we performed single-molecule observation of the DNA charge transfer process by using single-molecule fluorescence spectroscopy. The DNA charge transfer process, leading to the oxidation of the fluorescent dye, was explored by monitoring the on-off signal of the dye after the charge injection by the excitation of a photosensitizer. The photobleaching efficiency of the dyes by the DNA charge transfer specifically depended on the base sequence and mismatch base pair, demonstrating the discrimination of the individual DNA information. Based on this approach, the optical readout of a single-base mismatch contained in a target DNA was performed at the single-molecule level.

Characterization of mismatch and high-signal intensity probes associated with Affymetrix genechips

MOTIVATION

For Affymetrix microarray platforms, gene expression is determined by computing the difference in signal intensities between perfect match (PM) and mismatch (MM) probesets. Although the use of PM is not controversial, MM probesets have been associated with variance and ultimately inaccurate gene expression calls. A principal focus of this study was to investigate the nature of the MM signal intensities and demonstrate its contribution to the experimental results.

RESULTS

While most MM intensities were likely associated with random noise, a subset of approximately 20% (99,485) of the MM probes displayed relatively high signal intensities to the corresponding PM probes (MM > PM) in a non-random fashion; 13,440 of these probes demonstrated exceptionally high 'outlier' intensities. About 15,938 PM probes also demonstrated exceptionally high outlier intensities consistently across all hybridizations. About 92% of the MM > PM probes had either a dThymidine (dT) or a dCytidine (dC) at the 13th position of the probe sequence. MM and PM probes displaying extremely high outlier intensities contained high dC rich nucleotides, and low dA contents at other nucleotides positions along the 25mer probe sequence. Differentially expressed genes generated using Genechip Operating System (GCOS) or modified PM-only methods were also examined. Of those candidate genes identified in the PM-only method, 157 of them were designated by GCOS as absent across all datasets and many others contained probes with MM > PM signal intensities. Our data suggests that MM intensity from PM signal can be a major source of error analysis, leading to fewer potentially biologically important candidate genes.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

OMA Browser--exploring orthologous relations across 352 complete genomes

MOTIVATION

Inference of the evolutionary relation between proteins, in particular the identification of orthologs, is a central problem in comparative genomics. Several large-scale efforts with various methodologies and scope tackle this problem, including OMA (the Orthologous MAtrix project).

RESULTS

Based on the results of the OMA project, we introduce here the OMA Browser, a web-based tool allowing the exploration of orthologous relations over 352 complete genomes. Orthologs can be viewed as groups across species, but also at the level of sequence pairs, allowing the distinction among one-to-one, one-to-many and many-to-many orthologs.

AVAILABILITY

http://omabrowser.org.

Comprehensive study of interactions between DNA and new electroactive Schiff base ligandsApplication to the detection of singly mismatched Helicobacter pylori sequences

N,N'-Bis(3,4-dihydroxybenzylidene)-1,2-diaminobenzene (3,4-DHS) and N,N'-bis(2,5-dihydroxybenzylidene)-1,2-diaminobenzene (2,5-DHS) have been used as electrochemical probes in DNA sensing. These ligands, containing ortho and para quinone functional groups, respectively, as well as planar aromatic domains, are capable of binding to double stranded DNA (ds-DNA) more efficiently than to single stranded DNA (ss-DNA). Emphasis has been placed on the elucidation of the nature of the interaction by combining spectroscopic and electrochemical techniques. From spectrophotometric titration experiments, the binding constants of 3,4-DHS and 2,5-DHS with ds-DNA were found to be (9.0+/-0.3) x 10(3) and (3.3+/-0.2) x 10(3)M(-1), respectively. These values are consistent with a binding mode dominated by interactions with the minor groove of ds-DNA. The electroactivity of the quinone moiety in 3,4-DHS bound to DNA could be employed as an electrochemical indicator to detect hybridization events in DNA biosensors. These biosensors have been constructed by immobilization of a thiolated capture probe sequence from Helicobacter pylori onto gold electrodes. After hybridization with the complementary target sequence, 3,4-DHS was accumulated within the double stranded DNA layer. Electrochemical detection was performed by differential pulse voltammetry over the potential range where the quinone moiety is redox active. Using this approach, complementary target sequences of H. pylori can be quantified over the range of 8.9-22.2 microM with a detection limit of 8.3+/-0.4 microM and a linear correlation coefficient of 0.989. In addition this approach is capable of detecting hybridization of complementary sequences containing a single mismatch.

Identifying highly mutated IGHD genes in the junctions of rearranged human immunoglobulin heavy chain genes

The reliable identification of IGHD genes within human immunoglobulin heavy chains is challenging with up to one third of rearrangements having no identifiable IGHD gene. The short, mutated IGHD genes are generally assumed to be indistinguishable from the N-REGIONS of non-template encoded nucleotides that surround them. In this study we have characterised N-REGIONS, demonstrating the importance of nucleotide composition biases in the addition process, including the formation of homopolymer tracts. We then use a simulation approach to determine the likelihood of misidentification of highly mutated IGHD genes among the JUNCTION nucleotides. These likelihoods provide general rules for the identification of mutated D-REGIONs, and suggest that longer D-REGIONs (>25 nucleotides) with as many as ten mutations can be identified with a low risk of error. Shorter D-REGIONs (>16 nucleotides) with as many as four mutations are also identifiable. The reliability of different alignments is dependent upon the junction length (combined N-REGIONs and D-REGION). Data is presented that can guide the alignment of sequences with junction lengths from 5 to 50 nucleotides, including explicit selection between two D-REGION possibilities. The use of such a statistically-based approach to the alignment of IGHD genes will improve the reliability of the partitioning of immunoglobulin sequences, and this in turn will facilitate the study of the many processes that contribute to the diversity of the immunoglobulin repertoire.