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PubMedDate not supplied

Synthesis of 125I-labeled oligonucleotides from tributylstannylbenzamide conjugates.

A rapid and efficient method for the synthesis of 125I-labeled oligodeoxynucleotides ([125I]ODNs) is described. The key intermediates are tributylstannylbenzamide-modified ODNs (Sn-ODNs). Reaction conditions are described for the preparation of 5'-modified Sn-ODNs. Treatment with NaI and chloramine T gave conversion to the desired I-ODN, which was easily isolated by reversed phase chromatography. Thermal denaturation (Tm) studies showed that hybridization properties were not disturbed by the 4-iodobenzamide modification. An [125I]ODN was prepared and characterized by hybridization to 32P-labeled DNA targets. Sequence specific cleavage of the target DNA strand by 125I was measured.

Base Sequence↗
PubMed1993

Sterol carrier protein 2: a role in steroid hormone synthesis?

The intracellular movement of cholesterol is an important regulated step in the process of steroidogenesis. However, the molecular mechanisms by which cholesterol is translocated to key organelles, including the mitochondria, remains poorly understood. Lipid transfer proteins may have an important function in this process. One candidate lipid transfer protein is sterol carrier protein 2 (SCP2). This 13.2 kDa protein enhances the movement of cholesterol between vesicles and isolated mitochondria. It also stimulates mitochondrial pregnenolone synthesis. When introduced into intact cells, anti-SCP2 antibodies reduce steroid secretion. Moreover, expression of SCP2 in COS cells engineered to produce progestins increases steroid formation. SCP2 is abundant in steroidogenic glands and the pattern of SCP2 gene expression is consistent with a role for the protein in hormone synthesis: SCP2 transcripts are more prominent in the most steroidogenic compartments of the ovary and tropic hormones that stimulate steroidogenesis increase SCP2 gene expression. Other evidence that suggests that SCP2 plays important roles in cellular function includes a remarkable conservation of primary structure across species. The mechanisms by which SCP2 promotes intracellular sterol movement have not been elucidated. The protein appears to bind sterols and is synthesized with a 20 amino acid N-terminal "pro-" sequence that may serve to target SCP2 to mitochondria. In addition, the C-terminus of SCP2 contains a peroxisome-targeting sequence. SCP2 is derived from a large gene that encodes transcripts that are translated into larger proteins of 30 and 58 kDa. The 58 kDa protein, which has some structural homologies with thiolases, seems to be specifically targeted to peroxisomes whereas SCP2 has a broader subcellular distribution. The significance of the peroxisome association of SCP2 and steroidogenesis has not been disclosed. However, diseases of peroxisome function, including adrenoleukodystrophy and Zellweger syndrome, have notable deficits in steroid and bile acid metabolism, thus linking peroxisomes and steroidogenesis. SCP2 is deficient in fibroblasts of patients with these diseases.

Animals↗
PubMed2000

Specific regulatory inhibition of transfected HepG(2) with HCV 5'NCR by antisense phosphorothioate oligodeoxynucleotides.

OBJECTIVE: To screen efficient and specific new drugs against hepatitis C virus (HCV) and find the best target sequence of antisense oligodeoxynucleotides (ASODNs) targeting at HCV gene. METHODS: Fifteen S-ASODNs targeting at the 5'NCR and start AUG of HCV RNA were designed and synthesized according to the predicted RNA secondary structure of the HCV 5'NCR and the adjacent AUG region. HepG(2) cells were co-transfected with pHCV-neo4 and S-ASODN. The inhibitory effects of S-ASODNs on gene expression controlled by HCV 5'NCR were determined by the assay of luciferase activity. RESULTS: Five S-ASODNs, i.e. HCV65, HCV279, HCV363, HCV349 and HCV352, showed sequence-specific and dose-dependent inhibitory activities with an inhibition rate of more than 80% at a concentration of 100 nmol/L. According to 50% inhibitory concentrations, the inhibitory activity of HCV363 was the best. On the other hand, ASODNs had only little non-specific effect by negative control trials. In addition, the results also indicated that there were some coordinate effects between ASODNs at different targets. CONCLUSION: Stem-loop 2a and 3d of HCV 5'NCR and the start AUG of polyprotein precursor are candidate targets of S-ASODNs.

5' Untranslated Regions↗
PubMed2024

Sex differences in MAGEL2 gene promoter methylation in high functioning autism - trends from a pilot study using nanopore Cas9 targeted long read sequencing.

BACKGROUND: MAGEL2 is an autism susceptibility gene whose deficiency has been associated with autism-related behaviors in animal models and in syndromic human autism spectrum disorders (ASDs) such as Schaaf-Yang syndrome, but has not been studied in the broader autism spectrum. Given the capabilities of long-read sequencing technologies, this pilot study used a targeted nanopore sequencing approach to simultaneously examine MAGEL2 DNA sequence and methylation in adults with high-functioning autism (HFA) compared to neurotypical controls (NC). METHODS: Using DNA extracted from peripheral blood, Cas9-targeted nanopore DNA sequencing was used to analyze MAGEL2, including its entire regulatory construct (chr15:23639316-23651466), for sequence variation and 5-methyl-cytosine (5mC) modification in a cohort of adults with HFA compared to sex- and age-matched NC. Given the known sex differences in ASD and MAGEL2 KO animal models, results were further analyzed by sex. RESULTS: 20 adults with HFA (10 males, 10 females) and 20 NC were included. While there were no overall differences in MAGEL2 DNA sequence and 5mC modification between HFA and NC, we found a significant difference in MAGEL2 gene promoter methylation between males and females with HFA and NC of both sexes, with HFA males tending to show hypomethylation in a 300 bp long differentially methylated region (chr15:23647640-23647939) around the MAGEL2 transcription start site. CONCLUSIONS: In this pilot study utilizing nanopore Cas9 targeted DNA sequencing, significant sex-specific differences in MAGEL2 gene promoter methylation were identified in male adults with HFA in comparison to control groups, suggesting the potential for sex-specific epigenetic differences. However, further replication in larger cohorts is required to validate these findings.

Humans↗
PubMed1992

Multiple copies of SUC4 regulatory regions may cause partial de-repression of invertase synthesis in Saccharomyces cerevisiae.

Transformation to generate multiple copies of regulatory DNA sequences has been used to study the interactions between regulatory proteins and their target sequences, since a high copy number of these sequences may titrate trans-acting regulatory proteins. We have analyzed the synthesis of invertase in yeast strains carrying different SUC genes transformed with the multiple-copy plasmid pSH143, a derivative of pJDB207 containing the promoter and upstream regulatory sequences of SUC4. The results obtained seem to be strain dependent. Under repressing conditions a high copy number of SUC4 promoter regions may cause increased expression of the invertase genes resulting in the synthesis of external glycosylated protein. A similar result was obtained under de-repressing conditions since transformants from some strains showed higher levels of activity. These results suggest that transcriptional regulatory (negative) factors may become limiting when the copy number of their target DNA sequences is increased. This effect may depend on the amount of active repressor molecules as well as on their affinity for SUC4 upstream sequences. This is discussed on the basis of the nucleotide sequences of SUC promoters.

Base Sequence↗
PubMed1992

Age differences in short-term memory: organization or internal noise?

Older and young adults' letter search performances were examined on a short-term memory (STM) task where subjects compared a five-letter target sequence stored in short-term memory to a subsequently presented five-letter probe sequence. The same five letters were always presented on target and probe portions of a given trial, but on half of the trials, two letters were transposed in the first chunk, second chunk, or between the first and second chunks of the probe sequence ("No" trials). On the remaining half of the trials, the target and probe sequences were identical ("Yes" trials). Both young and older adults showed increases in reaction time (RT) when the chunk boundary for "yes" trials was different for the target and probe sequences of a given trial. This finding indicated that both age groups were organizing the sequences in STM in the same qualitative manner. However, older adults showed a relatively greater increase in RT and errors than young adults for second-chunk transpositions than for first-chunk or between-chunk transpositions, and this finding suggested that an age difference in task complexity could not account for this effect. We propose, though, that these data are consistent with an internal noise model.

Adolescent↗
PubMed2000

Roles of adeno-associated virus Rep protein and human chromosome 19 in site-specific recombination.

Adeno-associated virus type 2 (AAV) is the only known eucaryotic virus capable of targeted integration in human cells. AAV integrates preferentially into human chromosome (ch) 19q13.3qter. The nonstructural proteins of AAV-2, Rep78 and Rep68, are essential for targeted integration. Rep78 and Rep68 are multifunctional proteins with diverse biochemical activities, including site-specific binding to AAV and ch-19 target sequences, helicase activity, and strand-specific, site-specific endonuclease activities. Both a Rep DNA binding element (RBE) and a nicking site essential for AAV replication present within the viral terminal repeats are also located on ch-19. Recently, identical RBE sequences have been identified at other locations in the human genome. This fact raises numerous questions concerning AAV targeted integration; specifically, how many RBE sequences are in the human genome? How does Rep discriminate between these and the ch-19 RBE sequence? Does Rep interact with all sites and, if so, how is targeted integration within a fixed time frame facilitated? To better characterize the role of Rep in targeted integration, we established a Rep-dependent filter DNA binding assay using a highly purified Rep-68 fusion protein. Electron microscopy (EM) analysis was also performed to determine the characteristics of the Rep-RBE interaction. Our results determined that the Rep affinity for ch-19 is not distinct compared to other RBEs in the human genome when utilizing naked DNA. In fact, a minimum-binding site (GAGYGAGC) efficiently associated with Rep, suggesting that as many as 2 x 10(5) sites may exist. In addition, such sites also exist frequently in nonprimate mammalian genomes, although AAV integrates site specifically into primate genomes. EM analysis demonstrated that only one Rep-DNA complex was formed on ch-19 target DNA. Surprisingly, identically sized complexes were observed on all substrates containing a RBE sequence, but never on DNA lacking an RBE. Rep-DNA complexes involved a multimeric protein structure that spanned ca. 60 bp. Immunoprecipitation of AAV latently infected cells determined that 1,000 to 4,000 copies of Rep78 and Rep68 protein are expressed per cell. Comparison of the Rep association constant with those of established DNA binding proteins indicates that sufficient molecules of Rep are present to interact with all potential RBE sites. Moreover, Rep expression in the absence of AAV cis-acting substrate resulted in Rep-dependent amplification and rearrangement of the target sequence in ch-19. This result suggests that this locus is a hot spot for Rep-dependent recombination. Finally, we engineered mice to carry a single 2.7-kb human ch-19 insertion containing the AAV ch-19 target locus. Using cells derived from these mice, we demonstrated that this sequence was sufficient for site-specific recombination after infection with transducing vectors expressing Rep. This result indicates that any host factors required for targeting are conserved between human and mouse. Furthermore, the human ch-19 cis sequences and chromatin structure required for site-specific recombination are contained within this fragment. Overall, these results indicate that the specificity of targeted recombination to human ch-19 is not dictated by differential Rep affinities for RBE sites. Instead, specificity is likely dictated by human ch-19 sequences that serve as a Rep protein-mediated origin of replication, thus facilitating viral targeting through Rep-Rep interactions and host enzymes, resulting in site-specific recombination. Control of specificity is clearly dictated by the ch-19 sequences, since transfer of these sequences into the mouse genome are sufficient to achieve Rep-dependent site-specific integration.

Animals↗
PubMed2001

DNA binding and cleavage selectivity of the Escherichia coli DNA G:T-mismatch endonuclease (vsr protein).

The Escherichia coli vsr endonuclease recognises T:G base-pair mismatches in double-stranded DNA and initiates a repair pathway by hydrolysing the phosphate group 5' to the incorrectly paired T. The gene encoding the vsr endonuclease is next to the gene specifying the E. coli dcm DNA-methyltransferase; an enzyme that adds CH3 groups to the first dC within its target sequence CC[A/T]GG, giving C5MeC[A/T]GG. Deamination of the d5MeC results in CT[A/T]GG in which the first T is mis-paired with dG and it is believed that the endonuclease preferentially recognises T:G mismatches within the dcm recognition site. Here, the preference of the vsr endonuclease for bases surrounding the T:G mismatch has been evaluated. Determination of specificity constant (kst/KD; kst = rate constant for single turnover, KD = equilibrium dissociation constant) confirms vsr's preference for a T:G mismatch within a dcm sequence i.e. CT[A/T]GG (the underlined T being mis-paired with dG) is the best substrate. However, the enzyme is capable of binding and hydrolysing sequences that differ from the dcm target site by a single base-pair (dcm star sites). Individual alteration of any of the four bases surrounding the mismatched T gives a substrate, albeit with reduced binding affinity and slowed turnover rates. The vsr endonuclease has a much lower selectivity for the dcm sequence than type II restriction endonucleases have for their target sites. The results are discussed in the light of the known crystal structure of the vsr protein and its possible physiological role.

Base Pair Mismatch↗
PubMed2001

Non-LTR retrotransposons encoding a restriction enzyme-like endonuclease in vertebrates.

All autonomous non-long terminal repeat (non-LTR) retrotransposons reported to date in vertebrates encode an apurinic/apyrimidinic endonuclease-like enzyme necessary for target sequence cleavage and subsequent target-primed reverse transcription. We describe here vertebrate non-LTR retrotransposons encoding another type of endonuclease more related to type IIS restriction enzymes. Such retrotransposons have been detected until now only in trypanosomes, nematodes, and arthropods. The retrotransposon Rex6 was identified in the genome of several teleost fish including Xiphophorus maculatus (platyfish), Oryzias latipes (medakafish), Oreochromis niloticus (Nile tilapia), and Fugu rubripes (Japanese pufferfish). Rex6 encodes a reverse transcriptase and a putative restriction enzyme-like endonuclease and is a member of the R4 family of non-LTR retrotransposons containing the Dong and R4 elements found in nematodes and insects. Rex6 was active in many species during teleost evolution and underwent several bursts of retrotransposition (some of them being relatively recent) leading to a high copy number of Rex6 in the genome of numerous fish. Extremely truncated Rex6-related sequences were detected by database screening in reptiles, including the snake Trimeresus flavoviridis and the lizard Anolis carolinensis, but not in sequences from the human genome project, suggesting that this element might have been lost from certain vertebrate lineages.

Amino Acid Sequence↗
PubMed2001

Characterization of the manganese-containing superoxide dismutase and its gene regulation in stress response of Schizosaccharomyces pombe.

Fission yeast Schizosaccharomyces pombe contains two superoxide dismutases (SODs), one in the cytosol and the other in mitochondria. The sod2+ gene encoding putative mitochondrial superoxide dismutase containing manganese (MnSOD) has been isolated. Purification and analysis of the sod2+ gene product revealed that it contained only manganese as a cofactor, thus verified to be a genuine MnSOD. It was localized in mitochondria as expected. Its N-terminal amino acid sequence indicated that the mitochondrial targeting sequence of 21 amino acids was removed. The native form consisted of two identical subunits. The sod2+ expression was induced by external stresses, such as treatments with superoxide generators, high osmolarity, and heat. The induction by these stress treatments depended on Wis1-Spc1 MAPK signal transduction pathway being independent of transcription factors Atf1 or Pap1. The sod2 disruption rendered cells sensitive to various superoxide-generators, heat, and high osmolarity, suggesting that the mitochondrial MnSOD acts as a general defense agent against multiple stresses.

Amino Acid Sequence↗
PubMed1994

Studies on excision of conjugative transposons in enterococci: evidence for joint sequences composed of strands with unequal numbers of nucleotides.

We determined the nucleotide sequence of polymerase chain reaction products resulting from amplification of joint regions created after excision of transposons Tn5381 and Tn916 from a single site within plasmid pAD1. For both transposons, two joint sequences were observed. One (ATAGAT) was six nucleotides in length and identical to one of the junction sequences flanking the integrated transposon. This sequence also represents the original target sequence within pAD1. The other (TATGT (Tn5381) or TAGTT (Tn916)) was five nucleotides in length and identical to the junction sequence at the other end of the integrated transposons. These results suggest that excision of conjugative transposons from some insertion sites in gram-positive bacteria results in the formation of a joint region heteroduplex mismatched in nucleotide number as well as complementarity.

Base Sequence↗
PubMed1998

Centromere 3 specific tandem repeat from Chironomus pallidivittatus.

A 155-bp tandem repeat was previously reported to be present in all centromeric regions of the dipteran Chironomus pallidivittatus. We have now isolated a second centromere specific tandem repeat, 375 bp long. Two blocks were found of the new unit, differing in size, probably representing allelic forms. The repeat is present only in chromosome 3, bordering 155-bp repeat arrays. There are about 100 repeats per genome, compared to 1300 units for the 155-bp repeat. The two units contain an identical 9-bp sequence which can form target-site duplications flanking a short mobile element, Cp1. An inversion within the tandem array was isolated, the breakpoint of which is within the 9-bp target sequence. Another short shared motif, 10-bp long, is also present at the insertion site for a mobile element. The two repeat units are similar in having long regions with more than 80% AT and an overall high AT content.

Animals↗
PubMed1989

Studies on the biogenesis of the mammalian ATP synthase complex: isolation and characterization of a full-length cDNA encoding the rat F1-beta-subunit.

Screening a rat cDNA library with a fragment of the gene encoding the corresponding bovine protein, we have isolated cDNA clones encoding the complete precursor to the rat F1-beta-subunit. Comparison with other mammalian beta-subunit sequences reveals a 5' untranslated sequence of 27 bp, a targeting sequence of 48 amino acid residues, a 480 amino acid long mature polypeptide and a 3' untranslated region of approximately 150 bp. In vitro translation of F1-beta mRNA reveals the synthesis of multiple fragments of the protein. Preliminary characterization of intron-containing cDNA isolates indicates that the gene encoding the rat F1-beta subunit contains at least two introns.

Amino Acid Sequence↗
PubMed2005

Subgingival distribution of Campylobacter rectus and Tannerella forsythensis in healthy children with primary dentition.

OBJECTIVE: It is important to know how many subgingival plaque samples should be assayed from a child to ascertain infection with a periodontal pathogen. Plaque samples from several sites may fail to detect some important bacteria if only a limited number of gingival sites are sampled. The purpose of this study was to evaluate the detection of periodontal pathogens in a large number of subgingival sites in the same children in order to determine the number of samples necessary. METHODS: Ten children, aged 4-6 years, with complete primary dentition were enrolled in this study. Plaque samples from the mesio-buccal aspect of each erupted tooth were first collected by gently inserting a sterile paper point for 10s. Purified genomic DNA from all plaque samples was prepared for polymerase chain reaction. The primers for species-specific 16S ribosomal RNA sequence were selected as the target sequence. Standard strains of Campylobacter rectus and Tannerella forsythensis (formerly Bacteroides forsythus) were used as control strains. RESULTS: All subjects were found positive for C. rectus and T. forsythensis with the mean of positive sites at 17.6 +/- 2.4 (range: 12-20 sites) for C. rectus and 9.3 +/- 5.0 (range: 1-19) for T. forsythensis. The mean number of positive sites was 1.7 +/- 0.8 for C. rectus and 6.5 +/- 4.9 for T. forsythensis, with a confidence ratio of 95%. CONCLUSIONS: We concluded that two or more random sites for C. rectus and seven or more random sites for T. forsythensis from children to detect those bacteria at 95% probability.

Aggressive Periodontitis↗
PubMed1995

The potential of ribozymes as antiviral agents.

Ribozymes are promising tools for the specific inhibition of viral gene expression and replication. They represent one of the most attractive developments of antisense nucleic acids, which have been shown in the past few years to act as antiviral agents. Ribozymes not only complex with target sequences via complementary antisense sequences, but also hydrolyze the target site.

Animals↗
PubMed1997

Lysine-ketoglutarate reductase and saccharopine dehydrogenase from Arabidopsis thaliana: nucleotide sequence and characterization.

We isolated the gene encoding lysine-ketoglutarate reductase (LKR, EC 1.5.1.8) and saccharopine dehydrogenase (SDH, ED 1.5.1.9) from an Arabidopsis thaliana genomic DNA library based on the homology between the yeast biosynthetic genes encoding SDH (lysine-forming) or SDH (glutamate-forming) and Arabidopsis expressed sequence tags. A corresponding cDNA was isolated from total Arabidopsis RNA using RT-PCR and 5' and 3' Race. DNA sequencing revealed that the gene encodes a bifunctional protein with an amino domain homologous to SDH (lysine-forming), thus corresponding to LKR, and a carboxy domain homologous to SDH (glutamate-forming). Sequence comparison between the plant gene product and the yeast lysine-forming and glutamate-forming SDHs showed 25% and 37% sequence identity, respectively. No intracellular targeting sequence was found at the N-terminal or C-terminal of the protein. The gene is interrupted by 24 introns ranging in size from 68 to 352 bp and is present in Arabidopsis in a single copy. 5' sequence analysis revealed several conserved promoter sequence motifs, but did not reveal sequence homologies to either an Opaque 2 binding site or a Sph box. The 3'-flanking region does not contain a polyadenylation signal resembling the consensus sequence AATAAA. The plant SDH was expressed in Escherichia coli and exhibited similar biochemical characteristics to those reported for the purified enzyme from maize. This is the first report of the molecular cloning of a plant LKR-SDH genomic and cDNA sequence.

Amino Acid Sequence↗
PubMed2000

Characterization of RCI-1, a chloroplastic rice lipoxygenase whose synthesis is induced by chemical plant resistance activators.

A full-length lipoxygenase cDNA (RCI-1) has been cloned from rice (Oryza sativa) whose corresponding transcripts accumulate in response to treatment of the plants with chemical inducers of acquired resistance such as benzo(1,2,3)thiadiazole-7-carbothioic acid S-methyl ester (BTH), 2,6-dichloroisonicotinic acid (INA), and probenazole. In contrast, RCI-1 transcript levels did not increase after inoculation with compatible and incompatible races of the rice blast fungus Magnaporthe grisea and the nonhost pathogen Pseudomonas syringae pv. syringae. RCI-1 transcript levels also increased after exogenous application of jasmonic acid, but not upon wounding. Dose-response and time course experiments revealed a similar pattern of transcript accumulation and lipoxygenase activity in BTH-treated rice leaves. Enzymatic analysis of recombinant RCI-1 protein produced in Escherichia coli revealed that 13-hydroperoxy-octadecanoic acids were the predominant reaction products when either linoleic or linolenic acid used as a substrate. The RCI-1 sequence features a putative chloroplast targeting sequence at its N-terminus. Indeed, a protein consisting of the putative chloroplast transit peptide fused to green fluorescent protein was exclusively localized in chloroplasts, indicating that RCI-1 is a chloroplastic enzyme.

Amino Acid Sequence↗
PubMed1991

Transposon-facilitated DNA sequencing.

We describe here a transposon-based DNA sequencing strategy that allows the introduction of sequencing priming sites throughout a target sequence by bacterial mating. A miniplasmid was designed to select against transposon insertions into the vector. Sites of transposon insertion are mapped by the polymerase chain reaction with bacterial overnight cultures providing the templates. A small set of plasmids with transposons spaced several hundred base pairs apart can then be sequenced. Sequencing primers corresponding to the transposon ends allow sequencing in both directions. Thus, the entire sequence of both strands can be easily determined.

Base Sequence↗