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PubMed1996

Deformyldistamycin-DNA interaction; DNA conformational changes as revealed by titration rotational viscometry.

The conformational changes of a natural DNA species on binding of deformyl-distamycin (dDst) have been analysed, at 22 degrees C and 7.6 degrees C, in terms of changes of apparent persistence length (a) and of apparent contour length (L), by means of titration rotational viscometry with both high and low molar mass calf thymus (ct) DNA molecules. Next to ligand binding mediated alterations in DNA stiffness, changes of a are the result of helix bending and also of unbending of intrinsic helix bends. A test for the latter are viscosity measurements at different temperatures. Changes of L, on binding of non-intercalating ligands, are interpreted as the result of changes in the intrinsic solenoidal structure components of the natural eukaryotic DNA. Such tertiary-structure components do exist if base sequence dependent helix bends of (nucleosomal) DNA are phased with the helix screw [Drew & Travers, JMB 186, 773 (1985); Reinert et al., JBSD 9, 537 (1991)]. Hence, the measured very small changes of L at ligand/DNA-P ratios r < 0.02 are mainly understood as a partial abolition of intrinsic tertiary structure components and the following negative ones as a respective reinforcement of such structures by dDst binding to AT rich binding sites. Several r-intervals with different slope of the viscosity changes could be resolved at r < 0.05. The resolution of more than four modes of dDst interaction with ctDNA at very low r values is comparable to DNA interaction of Nt and several other ligands but not of distamycin. Advanced titration rotational DNA-viscometry is again able to resolve subtle quantitative details of ligand mediated DNA conformational changes of high stereochemical relevance.

Animals↗
PubMed2025

Next-generation sequencing in breast cancer: current clinical applications and future directions.

INTRODUCTION: Breast cancer is a heterogeneous disease that claims 670,000 lives by 2022. Omic technologies, particularly next generation sequencing (NGS) offers promising avenues for precision medicine. American Society of Clinical Oncology (ASCO) outlines genomic testing's utility, emphasizing prognostic and diagnostic potential. OBJECTIVES: This review succinctly explores NGS's evolution and clinical applications of NGS in breast cancer, thereby guiding future research to enhance patient care. METHODS: Comprehensive literature searches were conducted using databases such as PubMed, Google Scholar, and ResearchGate, focusing on keywords including breast cancer, HER-2 low breast cancer, circulating tumour DNA, single-cell RNA sequencing, and next-generation sequencing. Peer-reviewed, high-quality articles published in English were selected for inclusion. RESULTS: Previous studies have explored the evolution of NGS technology and its clinical applications in breast cancer, including genomic and transcriptomic characterization, treatment guidance, and resistance prediction. Molecular profiling of challenging entities such as early-onset breast cancer and HER-2 low tumours was summarized, with key findings highlighted. This review also discusses emerging technologies, including circulating DNA and single-cell sequencing, as promising avenues for discovery. CONCLUSION: NGS has revealed the genomic and transcriptomic diversity of breast cancer, identifying actionable alterations associated with chemotherapy response and resistance to therapies such as trastuzumab, TKIs, and CDK4/6 inhibitors. Circulating tumour DNA (ctDNA) shows potential for diagnosis, prediction, prognosis, and monitoring, despite tumour heterogeneity. Single-cell analysis enables exploration of individual cell transcriptomes, though high costs and low throughput remain barriers to widespread adoption. HER2-low tumours continue to pose significant research challenges.

Humans↗
PubMed1998

Mechanisms of DNA damage by chromium(V) carcinogens.

Reactions of bis(2-ethyl-2-hydroxy-butanato)oxochromate(V) with pUC19 DNA, single-stranded calf thymus DNA (ss-ctDNA), a synthetic oligonucleotide, 5'-GATCTATGGACTTACTTCAAGGCCGGGTAATGCTA-3' (35mer), deoxyguanosine and guanine were carried out in Bis-Tris buffer at pH 7.0. The plasmid DNA was only nicked, whereas the single-stranded DNA suffered extensive damage due to oxidation of the ribose moiety. The primary oxidation product was characterized as 5-methylene-2-furanone. Although all four bases (A, C, G and T) were released during the oxidation process, the concentration of guanine exceeds the other three. Orthophosphate and 3'-phosphates were also detected in this reaction. Likewise, the synthetic oliogomer exhibits cleavage at all bases with a higher frequecncy at G sites. This increased cleavage at G sites was more apparent after treating the primary oxidation products with piperidine, which may indicate base oxidation as well. DNA oxidation is shown to proceed through a Cr(V)-DNA intermediate in which chromium(V) is coordinated through the phosphodiester moiety. Two alternative mechanisms for DNA oxidation by oxochromate(V) are proposed to account for formation of 5-methylene-2-furanone, based on hydrogen abstraction or hydride transfer from the C1' site of the ribose followed by hydration and two successive beta-eliminations. It appears that phosphate coordination is a prerequisite for DNA oxidation, since no reactions between chromium(V) and deoxyguanosine or guanine were observed. Two other additional pathways, hydrogen abstraction from C4' and guanine base oxidation, are also discussed.

Animals↗
PubMed1995

Early iron deficiency stress response in leaves of sugar beet.

Iron nutrient deficiency was investigated in leaves of hydroponically grown sugar beets (Beta vulgaris) to determine how ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) gene expression is affected when thylakoid components of photosynthesis are diminished. Rubisco polypeptide content was reduced by 60% in severely iron-stressed leaves, and the reduction was directly correlated to chlorophyll content. The concentration of Rubisco protein in iron-stressed leaves was found to be regulated by availability of mRNAs, and CO2 fixation by Rubisco was reduced from 45 mumol CO2 m-2 s-1 in extracts from iron-sufficient leaves to 20 mumol CO2 m-2 s-1 in extracts from severely stressed leaves. The rate of CO2 fixation was directly correlated to leaf chlorophyll content. Rubisco in iron-sufficient control leaves was 59% activated, whereas in severely stressed leaves grown under the same light, Rubisco was 43% activated. RNA synthesis was reduced by about 50% in iron-deficient leaves, but 16S and 25S rRNA and ctDNA were essentially unaffected by iron stress.

Base Sequence↗
PubMed1978

Physicochemical characterization of mitochondrial DNA from soybean.

Mitochondrial DNA (mtDNA) of soybean (Glycine max L.) was isolated and its buoyant density was contrasted with that of nuclear (nDNA) and chloroplast (ctDNA) DNA. Each of the three DNAs banded at a single, characteristic buoyant density when centrifuged to equilibrium in a CsCl gradient. Buoyant densities were 1.694 g/cm(3) for nDNA and 1.706 g/cm(3) for mtDNA. These values correspond to G-C contents of 34.7 and 46.9%, respectively. Covalently closed, circular mtDNA molecules were isolated from soybean hypocotyls by ethidium bromide-cesium chloride density gradient centrifugation. Considerable variation in mtDNA circle size was observed by electron microscopy. There were seven apparent size classes with mean lengths of 5.9 mum (class 1), 10 mum (class 2), 12.9 mum (class 3), 16.6 mum (class 4), 20.4 mum (class 5), 24.5 mum (class 6), and 29.9 mum (class 7). In addition, minicircles were observed in all preparations. Partially denatured, circular mtDNA molecules with at least one representative from six of the seven observed size classes were mapped. In class 4, there appear to be at least three distinct denaturation patterns, indicating heterogeneity within this class. It is proposed that the mitochondrial genome of soybean is distributed among the different size circular molecules, several copies of the genome are contained within these classes and that the majority of the various size molecules may be a result of recombination events between circular molecules.

Journal Article↗
PubMed1982

Extranuclear DNA of a Marine Chromophytic Alga : RESTRICTION ENDONUCLEASE ANALYSIS.

Two extranuclear DNA species have been isolated from the marine alga Olisthodiscus luteus. Rapid lysis of cells followed by the immediate addition of CsCl to the lysate was critical to the preservation of these satellite DNA species. Restriction endonuclease analysis demonstrates a molecular weight of 99 x 10(6) for chloroplast DNA and 23 x 10(6) for a second satellite species. The origin of the second satellite is not known. However, this smaller satellite DNA which originates from a nonnuclear, DNAse insensitive cellular component, displays no sequence homology with ctDNA by hybridization experiments. Constancy of restriction endonuclease fragment patterns of chloroplast and second satellite species during all phases of the growth cycle, whether cultures were maintained synchronously or asynchronously, was demonstrated.

Journal Article↗
PubMed1994

Characterisation and mode of in vitro replication of pea chloroplast OriA sequences.

A partially purified replicative system of pea chloroplast that replicates recombinant DNAs containing pea chloroplast origin sequences has been characterised. Polymerisation by this system is very fast and insensitive to chain terminators like dideoxynucleotides, arabinosylcytosine 5'-triphosphate, etc. Both strands of template DNA are synthesized and single-stranded DNA templates undergo more than one round of replication. When sequences of either of the two chloroplast origins of replication (OriA or OriB) are used as templates, the replicative intermediates are found to have sigma structures. Electron microscopic analysis of the sigma structures restricted with various enzymes reveals that the initiation site of in vitro replication maps near the displacement-loop regions where replication initiates also in vivo. Although the observed replication initiation in the OriA recombinant template is chloroplast-DNA-specific, the mode of replication is different from that observed in vivo with intact ctDNA. However, when the template DNA contains both the OriA and OriB sequences, the in vitro replication proceeds in the theta mode, the mode of replication usually observed in vivo.

Chloroplasts↗
PubMed2004

Chloroplast and nuclear DNA variation in common wheat: insight into the origin and evolution of common wheat.

To understand the origin and evolution of common wheat, chloroplast (ct) and nuclear DNA variations were studied in five hexaploid and three tetraploid wheat subspecies. Based on chloroplast simple sequence repeats at 24 loci, they were classified into two major plastogroups. Plastogroup I consisted of 11 plastotypes, including the major plastotype H10 that occurred at the highest frequency (59%) in common wheat. Plastogroup II consisted of five plastotypes and occurred in eight out of 27 accessions of T. aestivum ssp. spelta and one accession of ssp. aestivum. As for nuclear DNA variations, AFLP data using 10 primer sets revealed two major clades of a phylogenetic tree constructed by UPGMA (unweighted pair-group method with arithmetic mean), one consisting of common wheat and the other of emmer wheat. The clade of common wheat was further divided into two major and six minor subclades. One of the major subclades consisted only of non-free-threshing ssp. spelta accessions, which were grouped into two clusters, one consisting only of accessions with plastogroup I ctDNA and the other with both plastogroups I and II. T. aestivum ssp. macha, another non-free-threshing common wheat, formed the other cluster. Taken together, our data indicate the existence of at least two maternal lineages in common wheat and support the hypothesis that European spela wheat originated in Europe separately from other groups of common wheat.

Biological Evolution↗
PubMed2025

MRDtarget: A heuristic Gaussian approach for optimizing targeted capture regions to enhance Minimal Residual Disease detection.

Molecular residual disease (MRD) detection, initially developed for hematologic malignancies, has become a critical biomarker for monitoring solid tumors. MRD detection primarily relies on circulating tumor DNA (ctDNA) analysis using next-generation sequencing, offering high sensitivity and broad genomic coverage. However, challenges remain in designing cost-effective panels that maximize mutation detection while maintaining biological relevance. Fixed panels often lack sufficient patient-specific mutation coverage, while WES-based personalized MRD assays, despite their high sensitivity, are costly and less accessible. We developed a tumor comprehensive genomic profiling (CGP)-informed personalized MRD assay to detect tumor-derived mutations, which allowed us to design patient-specific personalized panels and meanwhile, provide a cost-effective alternative to whole exome sequencing (WES). To address these limitations, we developed MRDtarget, a heuristic multivariate Gaussian model-based targeted capture region selection method. By expanding beyond traditional hotspot regions, MRDtarget optimizes variant tracking for MRD detection, significantly improving sensitivity. Using a Bayesian inference-based heuristic approach, MRDtarget integrates multi-feature informativeness rates to identify optimal genomic regions for capture. Experimental results demonstrate that MRDtarget enables the detection of more variants per patient. This study underscores the importance of rational panel design to improve MRD sensitivity and provides a novel approach to enhance precision diagnostics and treatment for solid tumor patients.

Humans↗
PubMed2007

Electrochemical studies oxidation of ciprofloxacin at nano-SnO2/PVS modified electrode and its interaction with calf thymus DNA.

In pH 6.0 phosphate buffer solutions (PBS), a glassy carbon electrode (GCE) modifying by nano-tin oxide/polyvinyl sulfonic potassium (nano-SnO2/PVS) exhibited an enhanced effectiveness for the oxidation of ciprofloxacin (CFX), which compared with a bare GCE or a nano-SnO2 modified electrode. In addition we also investigated the electrooxidation mechanism of the fluoroquinolone antibiotics (utilizing ciprofloxacin, ofloxacin, sparfloxacin and lomefloxacin) at the modified electrode. Furthermore, gel electrophoresis coupled with electrochemistry and spectra techniques were used to study the interaction of CFX and calf thymus DNA (ctDNA). These acquired data showed that the binding mode of CFX and DNA was mainly an intercalation mechanism.

Anti-Bacterial Agents↗
PubMed2026

Epigenetic profiling of circulating cell-free DNA for early detection and minimal residual disease assessment in lung cancer: a focus on DNA methylation.

Lung Cancer (LC) continues to be the biggest cause of cancer-related deaths around the world, mostly because of delayed diagnosis. Even if tissue biopsies and circulating tumor DNA (ctDNA) tests have revolutionized clinical management of LC patients, their effectiveness is restricted in settings with lower tumor burden, molecular heterogeneity, and bias in sampling approaches. In this scenario, the epigenetic profiling of cell-free DNA (cfDNA) stands out as a promising, less invasive approach, accurately detect cancer traces. Evidence from stage I-II disease and CT-detected pulmonary nodules supports the diagnostic potential of cfDNA methylation, although further validation in prospective screening cohorts remains necessary. Beyond genomic alterations, cfDNA epigenetic changes, including DNA methylation, chromatin organization, nucleosome positioning, and fragmentation patterns, reflect multi-dimensional complexity of tumor biology. These properties convey both the functional status and the origin of the circulating DNA fragments, accelerating for tumor integrating genomic analysis. Within this group, DNA methylation is the biologically robust and clinically well-established epigenetic marker, as alterations in methylation linked to cancer often occur in the early stages of tumorigenesis and are commonly found across different cancer cell types. Here, we explored the biological and clinical relevance of the epigenetic landscape of cfDNA in LC patients, particularly focusing on DNA methylation-based biomarkers and their evolving applications towards early diagnosis and post-surgical monitoring of minimal residual disease (MRD). We aimed to comprehensively overview analytical approaches for cfDNA methylation analysis, including targeted and genome-wide profiling strategies, and discuss their integration with machine learning (ML) and multi-omics frameworks in order to improve diagnostic performance and clinical applicability in LC management.

DNA methylation↗
PubMed2026

Integrating Radiogenomics and CSF-Based Liquid Biopsy Sequencing for Precision Neuro-Oncology.

Glioblastoma and diffuse gliomas pose major therapeutic challenges due to marked intratumoral heterogeneity, limited tissue accessibility, and the blood-brain barrier. Tissue-based next-generation sequencing (NGS) remains essential for WHO CNS5 molecular classification, yet it is invasive and poorly suited to serial monitoring. Two complementary non- or minimally invasive approaches have advanced rapidly: radiogenomics, which correlates multiparametric MRI features with genomic alterations, and cerebrospinal fluid (CSF) liquid biopsy sequencing, which detects circulating tumor DNA with high tissue concordance. This review examines the independent progress and synergistic integration of radiogenomics and CSF-NGS. Imaging signatures can non-invasively predict key drivers (IDH1/2, EGFR, TERT, PTEN, TP53) and molecular subtypes, while CSF-ctDNA sequencing enables real-time assessment of clonal evolution, therapy resistance (including post-temozolomide hypermutation), and residual disease. We discuss technical considerations, performance metrics, multimodal artificial-intelligence fusion, and emerging clinical applications for diagnosis, prognosis, treatment selection, and longitudinal surveillance. Critical challenges, standardization, prospective validation, and workflow integration are highlighted. By combining the spatial phenotypic information of radiogenomics with the temporal genomic resolution of CSF sequencing, this multimodal strategy offers a promising path toward precision neuro-oncology and reduced reliance on repeated invasive sampling.

Humans↗
PubMed2003

[Review on genetic diversity in Pinus].

The ways of probing genetic diversity of pines involve many aspects, such as morphology, chromosome, isozyme, DNA, etc. The phenotypic characteristics in pines vary widely and the differences of inheritability(h2) are obvious among characteristics and among species. Up to now,isozyme is still the most common means to measure genetic diversity of pines. Generally,there are high allozyme diversity within populations and low differentiation coefficient among populations, but differences exist between species in Pinus. The variations of chromosome among pines are very low and the karyotypes of pines are consentaneous,but the genomes of pines in cell nucleus are much larger than that of broadleaves. Diversity of pines are abundant at nucleus DNA level but are poor at plastid DNA level, such as ctDNA. There are many factors that will affect genetic diversity of pines, in which mating system and environment are two main factors. Finally,we reviewed the research on origin of Pinus and conservation strategy of genetic diversity,etc.

English Abstract↗
PubMed2004

[Studies on application and mechanism of energy transfer system of acridine orange (AO)-rhodamine B (RB) dimer in the determination of DNA].

Not only dye monomer is the form of energy transfer but also dye dimer is the effective form of energy transfer. In this work, the energy transfer system of acridine orange (AO)-rhodamine B (RB) dimer was built for the determination of DNA as fluorescence probe. At the same time, the mechanism was also considered. Under the optimum experimental conditions, the linear range of this assay was 0.33-1.33 mg x L(-1) for fish sperm DNA and 0.33-3.33 mg x L(-1) for calf thymus DNA, the detection limit was 1.63 x 10(-3) mg x L(-1) for fish sperm DNA and 1.52 x 10(-3) mg x L(-1) for calf thymus DNA, respectively. The RSD for the determination of 1.00 mg x L(-1) DNA was 2.40% for fsDNA and 2.00% for ctDNA, respectively. The method was used for the determination of DNA in synthetic samples with satisfied results.

Acridine Orange↗
PubMed2004

[Determination of deoxyribonucleic acids at nanograms levels with toluidine blue by a resonance light-scattering method].

Resonance light scattering (RLS) spectra of toluidine blue (TB) with DNA was studied. The RLS of TB was greatly enhanced by DNA in the range of pH 10-11. A RLS peak at 350 nm was found, and the enhanced intensity of RLS at this wavelength was proportional to the concentration of DNA. The linear range of the calibration curve was 0-900 ng x mL(-1) with the detection limit of 6.75 ng x mL(-1) for the ctDNA, and for fsDNA the linear range was 0-900 ng x mL(-1) with the detection limit of 2.99 ng x mL(-1). Precision at 500 ng x mL(-1) for the two nucleic acids was 3.7% and 5.6%, respectively. Four synthetic samples were determined satisfactorily.

Calibration↗
PubMed2005

[Construction of tobacco chloroplast multicistron site integration expression vector and its transgene].

According to the published DNA sequence, a serial of elements for constructing the tobacco chloroplast multicistron site integrating expression vectors have been cloned by PCR technique, which include Prrn (a modified plastid ribosomal RNA operon promoter), psbA3' (the 3' region of the plastid psbA gene), aadA gene (encoding aminoglycoside 3'-adenylytransferase), man gene (encoding mannase), gfp gene (encoding green fluorescence protein) and tobacco chloroplast high-frequency homologous recombination ctDNA fragment (psaA/psbC, 3463 bp) (Fig.2). A tobacco chloroplast multicistron expression vector pLM4 (Fig.1) (-psaA-Prrn-SD-man-SD-gfp-SD-aadA-psbA3'- psbC-) was constructed with these elements. Then the tobacco leaves were bombarded 5 times with gold particles coated with the vector pLM4. After growing on the screening medium, the function of aadA gene was identified (Fig.3), and the function of gfp gene was confirmed by laser scanner (Fig.4), the expression of man was identified by Western blot (Fig.5). All these genes man, gfp and aadA being integrated in the tobacco chloroplast genome DNA were confirmed by PCR (Fig.6). And the multicistron expression cassette integrating in tobacco chloroplast genome DNA was confirmed by RFLP (Fig.7). All these showed that the three genes in the tomato vector pLM4 were expressed in tobacco chloroplast genome DNA.

Binding Sites↗
PubMed2006

[Determination of nucleic acids using toluidine blue as a fluorescence probe].

A new fluorimetric method has been developed for the determination of deoxyribonucleic acid (DNA) with toluidine blue (TB) as a fluorescence probe. It is based on the fluorescence quenching of toluidine blue in the presence of DNA. In Tris-HCl buffer solution (pH 8.5), the calibration graph was linear over the range 0.10-6.00 microg x mL(-1) for ctDNA, and the detection limit was 27 ng x mL(-1). The result of the determination of DNA of camphor tree's leaf by this method was satisfactory.

DNA↗
PubMed1989

[Photosystem II of rye. Nucleotide sequence of psbB and psbH genes, coding 47-kDa of chlorophyll(a)-binding and 10-kDa phosphorylated subunits].

Chloroplast DNA was isolated from rye seedlings by the non-aqueous method. The region of rye ctDNA which comprises two genes psbB and psbH encoding polypeptide subunits of photosystem II (47 kappa l) Chl alpha -binding protein (CP alpha -1) and 10 kD phosphoprotein, respectively) and two ORFs in the opposite strands in the psbB--psbH spacer region encoding hydrophobic peptides with strongly charged C-terminal segments was sequenced. The deduced amino acid sequences of polypeptide products of the genes were compared with those of different plant species (in case of the psbB product also with sequence of a cyano-bacterium Synechocystis) and revealed some highly conservative amino acid residues and regions of polypeptide chains, which apparently play essential role in the interaction with other PS II subunits and in the binding of chlorophyll molecules. Some speculations are made on the possible function of the peptides encoded by the two ORFs.

Amino Acid Sequence↗