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PubMed1998

Multimode interaction of Hoechst 33258 with eukaryotic DNA; quantitative analysis of the DNA conformational changes.

The interaction of the minor groove binding ligand Hoechst 33258 (Hoe) with natural DNA was investigated by high resolution titration rotational viscometry. Analysis of the concomitant DNA conformational changes was performed with two DNA samples of sufficiently different molar mass M, at 4 degrees C, 22 degrees C and 40 degrees C, for Hoe/DNA-P ratios below r = 0.02. In this narrow r range several interaction modes could be resolved. The measured conformational changes were quantified in terms of relative changes of both apparent DNA persistence length, delta a/a, and hydrodynamically operative DNA contour length, deltaL/L. Delta a/a(r) primarily is a measure of ligand-induced DNA helix stiffening, but both, delta a/a(r) and deltaL/L(r), generally depend also on ligand binding induced DNA bending or DNA unbending. The essential difference obviously is that delta a/a(r) is influenced by the randomly distributed helix bends and deltaL/L(r) by phased ones. The measurements performed at different temperatures deliver informations about existence and temperature dependent abolition of intrinsic helix curvature. Both Hoe and netropsin (Nt) prefer binding to AT rich DNA segments, which are candidates for intrinsic DNA helix bends. But our data for Hoe interaction with calf thymus DNA (ctDNA) show characteristic differences to those for Nt-ctDNA interaction. Especially for Hoe, the mode of highest affinity is saturated already at a ligand concentration of roughly 1 nM (r approximately = 0.0015 Hoe/DNA-P). It exhibits an unusually strong temperature dependence of the conformational DNA response. A Hoe-Nt competition experiment shows that Hoe binding to the sites of the very first Hoe mode is almost unaffected by bound Nt. But Hoe binding to the sites of the following Hoe modes does not occur due to the competition with Nt. Thus this mode of strongest Hoe-DNA interaction reflects a unique mechanism, possibly of high relevance for gene regulatory systems.

Animals↗
PubMed2026

The next-generation biomarkers in early-stage triple negative breast cancer.

PURPOSE OF REVIEW: Despite maximal neoadjuvant chemoimmunotherapy, nearly 40% of early-stage triple-negative breast cancer (TNBC) patients fail to achieve pathological complete response, underscoring an urgent need for biomarkers capable of guiding treatment modulation. This review summarizes recent advances in tumor-infiltrating lymphocytes (TILs), circulating tumor DNA (ctDNA), and genomic signatures, exploring their potential integration into clinical decision-making. RECENT FINDINGS: TILs remain the most validated, cost-effective prognostic biomarker, although standardized scoring is still needed to overcome interobserver variability. ctDNA has emerged as a dynamic, real-time prognostic tool, with postneoadjuvant detection strongly predicting relapse and worse outcomes. Nonetheless, optimal sampling timing remains undefined. Genomic signatures, particularly TNBC-DX, provide standardized, reproducible prognostic information by integrating immune and proliferative gene expression. Emerging data suggest that combining these biomarkers may offer a complementary and synergistic effect. SUMMARY: Multibiomarker integration, supported by prospective validation and automated models, represents a promising approach to personalize treatment algorithms in early-stage TNBC, balancing efficacy and toxicity while guiding escalation and de-escalation strategies.

artificial intelligence↗
PubMed1979

Transcription activity of a DNA-protein complex isolated from spinach plastids.

A DNA . protein complex of about 150 S is isolated from purified spinach chloroplasts by Sepharose 4B gel filtration. A DNA-dependent RNA polymerase activity is found associated with the complex. This DNA protein complex is able to initiate RNA chains in vitro. The RNA synthesis is more dependent on CTP than other nucleoside triphosphates. 50% of the activity is still present with 0.6 M KCl. The temperature optimum occurs between 30 degrees C and 35 degrees C. Rifampicin and rifamycin SV have no inhibitory effect. TNA products have been characterized by gel filtration and by hybridization with chloroplast DNA (ctDNA). At the beginning of transcription DNA products are linked to the transcription complex and are later detached. The molecular weight of the product ranges between 0.07 X 10(6) and 2 X 10(6). A part of the product (3--4%) has a molecular weight higher than 2 X 10(6). No endogenous RNase activity was present during the molecular weight determinations experiments. Hybridization experiments show that at least 75% of the RNA products are hybridizable with ctDNA and that 40% of these products are composed of chloroplast ribosomal RNA, showing that rDNA is preferentially transcribed.

Chloroplasts↗
PubMed2026

RAS Pathway Activation and Microenvironmental Adaptation as Hallmarks of Myeloid Sarcoma.

UNLABELLED: Myeloid sarcoma, an aggressive extramedullary subtype of acute myeloid leukemia (AML), occurs in approximately 20% of patients and remains strikingly understudied in large-scale genomic and multiomic investigations. The key drivers of its tumor evolution are largely unknown; timely detection in asymptomatic patients poses a clinical challenge, and effective treatment options are limited, as patients are often excluded from clinical trials, rendering it a largely neglected disease entity. In this study, we demonstrate that myeloid sarcoma evolves from medullary AML but exhibits distinct site-specific clonal evolution. This is supported by unique transcriptional signatures of myeloid sarcoma, reflecting adaptation to the extramedullary microenvironment. We establish a proof of concept that circulating tumor DNA (ctDNA) sequencing captures the molecular composition of myeloid sarcoma, offering a potential noninvasive approach for molecular profiling of extramedullary AML. Our findings highlight marked differences between medullary AML and myeloid sarcoma, including universal molecular evolution and RAS pathway activation as disease hallmarks. SIGNIFICANCE: We provide a comprehensive multiomic characterization of myeloid sarcoma, identifying key molecular pathways that contribute to its development, and suggest ctDNA as a noninvasive method of detection. We identify RAS pathway activation and transcriptional adaptation to the solid tissue microenvironment as cardinal features of myeloid sarcoma, suggesting novel therapeutic avenues.

Sarcoma, Myeloid↗
PubMed2026

MRD-2 in the GHSG HD21 trial assessed by a validated circulating tumor DNA sequencing assay.

Beyond cure, major goals in patients with Hodgkin lymphoma (HL) are tailoring treatment to a patient's individual risk for relapse to reduce acute and late toxicities, identifying candidates for early incorporation of novel agents, and making treatment affordable on a global level. Minimal residual disease (MRD) assessment by circulating tumor DNA (ctDNA) sequencing emerged as a promising strategy to achieve these goals; however, previous studies differed in sampling time points, assay validation, and definitions for MRD negativity. Here, we applied LymphoVista, a validated ctDNA sequencing assay for genotyping and MRD monitoring in lymphoma, to samples obtained from the German Hodgkin Study Group (GHSG) HD21 trial after 2 cycles of treatment (MRD-2) using a case-cohort design. Patients with positive MRD-2 result were at higher risk for relapse, progression, or death compared with MRD-2-negative patients (4-year progression-free survival [PFS], 36.7% vs 82.2%; hazard ratio, 5.3; 95% confidence interval, 2.0-13.8; P = .0008). After inverse probability weighting accounting for the number of events in the full reference set, patients with positive and negative MRD-2 results had 4-year PFS rates of 72.2% vs 95.3%. Combining MRD-2 with positron emission tomography after 2 cycles of BrECADD/eBEACOPP (PET-2) can identify patients at very low and patients at very high risk of relapse, progression, or death. In summary, these results suggest that MRD-2 assessment by LymphoVista allows for early outcome prognostication in patients with HL and could be used as a tool to improve treatment guidance on its own or in conjunction with PET-2.

Humans↗
PubMed2001

Efficient photocleavage of DNA by cationic porphyrin-acridine hybrids with the effective length of diamino alkyl linkage.

Positively charged porphyrins bearing an acridine with various lengths of diamino alkyl linkage, 5-[4-[(6-chloro-2-methoxy-9-acridyl)aminoalkylaminocarbonyl]phenyl]-10,15,20-tris(4-N-methylpyridiniumyl)porphine triiodide, alkyl=ethyl, butyl, hexyl, or octyl, were synthesized. They exhibited more enhanced photocleavage activity of pUC18 plasmid DNA than TMPyP, meso-tetrakis(4-N-methylpyridiniumyl)porphine, which is well known to bind to DNA tightly and to cleave DNA effectively; the hybrid linked with the hexamethylene chain showed particularly high activity. An equilibrium dialysis experiment demonstrated that the binding ability of the hybrids to calf thymus (CT) DNA correlated quantitatively with the photocleavage activity. The lack of the substantial red-shift of the Soret maxima of the hybrids through the titration with CTDNA denied the intercalative binding of the porphyrin part. In their circular dichroism (CD) spectral change on binding to CTDNA, two negative peaks appeared at 275 nm and at 285-290 nm in the UV range. The latter negative peak was observed for hybrids, but not for TMPyP, and thus we assigned it to induced CD (ICD) derived from intercalation of acridine chromophore. In the visible range, the hybrids showed only a positive peak around their Soret maxima, and this feature suggested the porphyrin moiety lay in the DNA groove. In addition, the length of the linker markedly influenced the ellipticity of their visible ICD, suggesting that the proximity of the porphyrin moiety to DNA was greatly affected by the linker.

Acridines↗
PubMed2002

Estimation of biologically damaging UV levels in marine surface waters with DNA and viral dosimeters.

We have surveyed the biologically harmful radiation penetrating the water column along a transect in the western Gulf of Mexico using dosimeters consisting of intact viruses or naked calf-thymus DNA (ctDNA). The indigenous marine bacteriophage PWH3a-P1, which lytically infects the heterotrophic bacterium Vibrio natriegens (strain PWH3a), displayed decay rates for infectivity approaching 1.0 h(-1) in surface waters when deployed in a seawater-based dosimeter. The accumulation of pyrimidine dimers in ctDNA dosimeters provided a strong correlation to these results, with pyrimidine dimers representing more than 0.3% (up to ca 3800 dimers Mb(-1) DNA) of the total DNA in dosimeters exposed to sea surface levels of solar radiation. The results demonstrate a strong correlation between the dimer formation in the DNA dosimeters, the decay rates of viral infectivity and the penetration of UVB radiation into the water column. The decay of viral infectivity attenuated with depth in a manner similar to the decay of solar radiation and was still significant at 10 m in offshore oligotrophic water and at dimer frequencies less than 0.1% (ca 200-300 dimers Mb(-1) DNA).

Animals↗
PubMed2006

Electrochemical characteristics of gatifloxacin and its interaction with DNA.

The electrochemical behavior of gatifloxacin (GTFX) and its interaction with natural calf thymus DNA (ctDNA) is investigated by differential pulse voltammetry (DPV) on a carbon paraffined electrode. According to the suggested electrochemical equation, a binding constant of 1.7058 x 10(5) (mol L(-1))(-1) and binding sizes s = 3.09 (base pairs) of GTFX with ctDNA are obtained by nonlinear fit analysis of electrochemical data. The results demonstrate that GTFX has the properties of an intercalative binder.

Animals↗
PubMed2006

Nucleic acids analysis with nano-Ag-Tb(III) by a resonance light scattering technique.

The nano-Ag-terbium(III)-mucleic acids system was observed by a resonance light scattering (RLS) technique for the first time, and the quantitative analysis of nucleic acids at nanogram levels was established. Studies showed that the RLS intensity of the nano-Ag-terbium(III) system can be obviously enhanced by nucleic acid, which was characterized by the RLS spectrum and the UV-Vis spectrum. In this system, the nanoparticles were only of a definite size and in a limited particle concentration region. Further research indicated that under the optimum conditions, the enhanced intensity of RLS is in proportion to the concentration of nucleic acids in the ranges of 7.0 x 10(-9) g ml(-1) to 8.0 x 10(-6) g ml(-1) for calf thymus DNA (ctDNA), 2.0 x 10(-8) g ml(-1) to 1.0 x 10(-6) g ml(-1) for fish sperm DNA (fsDNA) and 1.0 x 10(-9) g ml(-1) to 1.0 x 10(-7) g ml(-1) for yeast RNA (yRNA). The detection limits were 1.4 ng ml(-1) for ctDNA, 1.2 ng ml(-1) for fsDNA and 0.85 ng ml(-1) for yRNA, respectively. Synthetic and real samples were determined satisfactorily.

Calibration↗
PubMed2026

Epigenetic Profiling for Early Detection and Treatment Response Monitoring in Non-Small Cell Lung Cancer: Protocol for a Prospective Translational Biomarker Study.

BACKGROUND: Non-small cell lung cancer (NSCLC) is the leading cause of cancer-related mortality worldwide and continues to have poor survival outcomes, with most patients diagnosed at advanced stages of disease. In New Zealand, NSCLC contributes substantially to cancer inequities, with Māori communities experiencing disproportionately high incidence and mortality rates. Although low-dose computed tomography screening can improve early detection, major limitations remain, including false-positive findings, overdiagnosis, high infrastructure costs, and limited accessibility for rural and underserved populations. Liquid biopsy approaches using circulating tumor DNA (ctDNA), particularly DNA methylation profiling, have emerged as promising, minimally invasive strategies for improving cancer detection, treatment monitoring, and precision oncology. OBJECTIVE: This study aims to establish integrated genomic and epigenomic predictive and prognostic biomarkers using ctDNA, tumor tissue, and transcriptomic profiling to improve early detection, risk stratification, treatment selection and response prediction, and longitudinal monitoring, with particular emphasis on identifying molecular mechanisms associated with treatment resistance and disease progression. METHODS: This prospective observational translational biomarker study is being conducted through the University of Otago and associated respiratory and oncology services in New Zealand. The study will recruit participants with NSCLC (including squamous and nonsquamous subtypes), individuals referred to fast-track lung nodule assessment clinics, and nonmalignant respiratory controls. Serial peripheral blood sampling will be performed in selected participants at predefined clinical follow-up time points to evaluate treatment response and disease progression. The availability of formalin-fixed paraffin-embedded archival tissues will be recorded, but will not be mandatory for enrollment. Genome-scale DNA methylation profiling will be performed using cell-free reduced representation bisulfite sequencing (cfRRBS), while targeted genomic profiling and transcriptomic analyses will be conducted using targeted sequencing panels and RNA sequencing. Integrative bioinformatic analyses will be used to identify molecular biomarkers associated with early-stage disease, advanced disease, treatment response, and therapeutic resistance. RESULTS: Ethics approval for the study has been obtained from the New Zealand Health and Disability Ethics Committee (2022 EXP 12566). This study commenced in 2022, and recruitment and biospecimen collection are ongoing. The study aims to recruit approximately 450 participants, including patients with NSCLC, individuals referred through respiratory diagnostic pathways, and nonmalignant controls. As of July 31, 2026, 205 participants have been recruited, with recruitment continuing until the target sample size is reached. Molecular and data analyses are ongoing, with additional publications expected as the cohort matures. CONCLUSIONS: This study will generate one of the first integrated genomic, epigenomic, and transcriptomic liquid biopsy datasets for NSCLC in New Zealand. The findings are expected to support the development of sensitive, accessible, and equitable blood-based biomarkers for NSCLC detection and treatment monitoring while also contributing to improved precision oncology approaches and reducing NSCLC inequities among Māori populations.

Humans↗
PubMed2004

[Determination of deoxyribonucleic acids based on the enhanced effect of resonance light scattering of malachite green sensitized by cetyltrimethylammonium bromide].

A resonance light scattering (RLS) enhancement method was reported for the determination of deoxyribonucleic acids. The proposed method was based on the enhanced effect of deoxyribonucleic acid on the resonance light scattering of malachite green (MG) sensitized by cetyltrimethylammonium bromide (CTMAB). Alkaline medium was necessary for the experiment. Under optimal conditions, the linear ranges for both calf thymus DNA (ctDNA) and fish sperm DNA (fsDNA) were 0-1.5 microg x mL(-1), the detection limits were 0.05 microg x mL(-1) for ctDNA and 0.03 microg x mL(-1) for fsDNA. The measurement can be made on normal spectrofluorimeter. Mechanic studies show that MG probably aggregates on the molecular surface of single-chained DNA, and then interacts on CTMAB to form large particles, which produce strong RLS. This method was successfully applied to the determination of DNA in synthetic samples.

Anti-Infective Agents, Local↗
PubMed2005

[Study on BS-12 as a new probe for the determination of DNA by resonance light scattering].

A new method has been developed for the determination of DNA by resonance light scattering with dodecyl dimethyl betaine (BS-12) in aqueous solution as a new probe. At pH 9.3, the interactions of BS-12 and DNA gave strong RLS signals at 388.0 nm. Linear relationships were found between the enhanced intensity of RLS and the concentration of DNAs in the range 0.25-12.0 microg x mL(-1) for fsDNA and 0.25-11.0 microg x mL(-1) for ctDNA. The limits of detection were 0.15 ng x mL(-1) and 0.16 ng x mL(-1) for fsDNA and ctDNA, respectively. The method was applied to the determination of synthetic samples with satisfactory results.

Animals↗
PubMed2006

[Fluorescence characteristic of terbium-ciprofloxacin complex and its application].

On binding to deoxyribonucleic acid, the complex of terbium-ciprofloxacin (Tb(3+)-CIP) increases its fluorescence quantum efficiency. Based on this, an easy, rapid and sensitive method for the determination of DNA was developed. Like ethidium bromide (EB), the complex can be intercalated into DNA bases, but it is non-poisonous. Determination can be made at pH 7.0, where the native structure of DNA is not disrupted. The maximum emission is at 545 nm with excitation at 325 nm. This method has good sensitivity (2.8 x 10(-9) mol x L(-1) of ctDNA), high selectivity and a wide linear range (4.3 x 10(-7)-3. 0 x 10(-5) mol x L(-1) of ctDNA). This complex was also employed for the clinical examination of DNA in whole blood of tumor patients. Ten tumor patients and 10 normal persons were enrolled in this study. It was showed that significant difference existed between control group and tumor group (p < 0.05).

Animals↗
PubMedDate not supplied

The inhibition of P338 lymphocytic leukemia DNA polymerase alpha activity by cis-diamminedichloroplatinum(II) and related derivatives.

Cis-platinum derivatives were observed to inhibit the activity of DNA polymerase alpha of P388 lymphocytic leukemia cells. A 600g nuclear preparation of the polymerase alpha was inhibited by cis-diamminedichloroplatinum(II) [cDDP], diamminemalonatoplatinum(II) [MAL], (1,2-diaminocyclohexane)-dichloroplatinum(II) [DACH-Pt-CL2], and (1,2-diaminocyclohexane)malonato-platinum(II) [DACH-Pt-MAL]. cDDP was a more potent inhibitor of the enzyme activity which was positively correlated with the observed inhibition of DNA synthesis of P388 cells in vivo and in vitro. The inhibition of the 600g preparation by cDDP could be partially reversed by the addition of exogenous ctDNA, but 35% inhibition was not retreivable by adding new template. Isolation of the P388 DNA polymerase alpha enzyme by DEAE column chromatography led to an enzyme with 100 fold purification, which was sensitive to N-ethyl maleimide at 0.1 mM concentration. cDDP inhibited the activity of this enzyme in a dose dependent manner. However, MAL, DACH-Pt-Cl2 and DACH-Pt-MAL afforded no inhibition, nor did the latter two derivatives bind to the enzyme. cDDP inhibition of the activity of purified enzyme was partially reversed by the addition of exogenous ctDNA and by the addition of dGTP, whereas addition of other d(NTP)s had no effect on the recovery of the enzyme activity. These studies suggest that cDDP inhibits DNA polymerase alpha activity and that the inhibition is not the sole mechanism of the action of the drug in suppression of DNA synthesis and cell death. Preliminary studies suggest that the drug may bind to the apoprotein of the enzyme in a competitive manner with dGTP.

Animals↗
PubMed2025

Liquid Biopsy in Hematologic Malignancies: Advances, Challenges, and Future Directions.

Hematologic malignancies are cancers that affect the bone marrow, lymphatic system, and hematopoietic cells, resulting in various cancer subtypes and clinical manifestations. Currently, tissue biopsy in hematological malignancies is typically performed for genomic profiling and has limitations such as invasiveness, lengthy procedures, and high expense. On the other hand, liquid biopsy serves as an emerging tool used for examining the blood or other bodily fluids of patients, for the purpose of identifying genetic mutations, biomarkers, or cancer-related substances. Liquid biopsy biomarkers include circulating tumor DNA (ctDNA), microRNA (miRNA), and exosomes. In the context of hematological malignancies, these biomarkers offer valuable insights into disease etiology, enabling effective disease monitoring and guiding treatment decisions owing to their differential expression patterns. This review critically examines the recent advancements and effectiveness of liquid biopsy biomarkers in the areas of diagnosis, therapy, and monitoring. The challenges and future directions of liquid biopsy for hematological malignancies are also discussed.

Humans↗
PubMedDate not supplied

The sensitive determination of nucleic acids using a fluorescence-quenching method.

Experiments indicated that nucleic acids can quench the fluorescence of the Eu3+ -2-thenoyltrifluoroacetone (TTA)-1,10-phenanthroline (Phen) system. Based on this, a sensitive method for the determination of nucleic acids was proposed. The experiments indicated that under the optimum conditions, the quenched fluorescence intensity was in proportion to the concentration of nucleic acids in the range 1.0 x 10(-11)-1.0 x 10(-6) g/mL for yeast RNA (yRNA), 5.0 x 10(-11)-5.0 x 10(-7) g/mL for fish sperm (fsDNA) and 1.0 x 10(-10)-1.5 x 10(-6) g/mL for calf thymus DNA (ctDNA). Their detection limits were 3.0 x 10(-12), 4.0 x 10(-12) and 5.0 x 10(-11) g/mL, respectively. Therefore, the proposed method is one of the most sensitive methods available. The interaction between nucleic acids and Eu3+ -TTA-Phen is also discussed.

Europium↗
PubMed2003

Synthesis and biological activity of a platinum(II) 6-phenyl-2,2'-bipyridine complex and its dimeric analogue.

We have synthesized (pyridyl)-(6-phenyl-2,2'-bipyridine)platinum(II) hexafluorophosphate (1) and its corresponding dimer, micro-N,N'-bis(isonicotinyl)-1,6-hexanediamino bis-[6-phenyl-2,2'-bipyridine-platinum(II)] dichloride (2). The DNA binding constants of 1 and 2 at 20 degrees C were determined by absorption titration to be 2.25 x 10(4) M(-1) and 3.07 x 10(6) M(-1), respectively. Compound 1 showed an AT preference, while 2 had no base preference. The binding site sizes of 2 for [poly(dA-dT)](2), calf thymus DNA (ctDNA), and [poly(dG-dC)](2), as determined by fluorescence titration, were 6.6, 4.0, and 2.8 bp, respectively. Compound 2 probably bound to [poly(dA-dT)](2) through bisintercalation, and to [poly(dG-dC)](2) by monointercalation. Binding of DNA by both complexes is favorable, since the binding free energies of 1 and 2 were estimated to be -5.8 and -8.7 kcal mol(-1), respectively. The results of viscosity measurements and gel mobility shift assay demonstrated that binding of 1 and 2 caused DNA lengthening. The cytotoxicities of the complexes in various human cancer cell lines were determined by MTT assay. Complex 2 exhibited cytotoxicity comparable to that of cisplatin, and was more toxic than 1 by an order of magnitude.

Algorithms↗
PubMed1980

Comparative studies of chloroplastic and nuclear DNA repair abilities after ultraviolet irradiation of Euglena gracilis.

Studies of nuclear and chloroplastic-DNA repair after ultraviolet irradiation of Euglena gracilis show that photoreactivation is very efficient at both the nuclear and chloroplastic level. Liquid-holding or split-dose experiments and treatment with caffeine reveal, furthermore, that dark-repair is very efficient in nuclear DNA but not in chloroplastic DNA (ctDNA). The possibility of a chloroplastic dark-repair of restricted efficiency is discussed. Determination of chloroplastic DNA content by reassociation kinetics indicates that an important degradation follows UV irradiation during liquid holding in the dark.

Animals↗