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As imaging techniques rapidly evolve to probe nanoscale genome organization at higher resolution, it is critical to consider how the reagents and procedures involved in sample preparation affect chromatin at the relevant length scales. Here, we investigate the effects of fluorescent labeling of DNA sequences within chromatin using the gold standard technique of three-dimensional fluorescence in situ hybridization (3D FISH). The chemical reagents involved in the 3D FISH protocol, specifically formamide, cause significant alterations to the sub-200 nm (sub-Mbp) chromatin structure. Alternatively, two labeling methods that do not rely on formamide denaturation, resolution after single-strand exonuclease resection (RASER)-FISH and clustered regularly interspaced short palindromic repeats (CRISPR)-Sirius, had minimal impact on the three-dimensional organization of chromatin. We present a polymer physics-based analysis of these protocols with guidelines for their interpretation when assessing chromatin structure using currently available techniques., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Shim et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

In the current study, four novel mononuclear Cu(ii) complexes with terpyridine (L) and different co-ligands (phen, bipy, and imd) were synthesized and characterized in detail, where L is 4'-(3,4,5-trimethoxyphenyl)-2,2':6',2''-terpyridine. The identity and purity of all complexes were determined by elemental analysis, spectroscopic techniques (UV-vis, FTIR, ESI-MS, and EPR) and CV, including single crystal X-ray determination of three complexes ([Cu(L)(phen)](ClO4)2 (C-I), [Cu(L)2](ClO4)2 (C-II) and [Cu(L)(imd)(ClO4)](ClO4) (C-IV). DNA binding studies were performed using fluorescence assay and the binding constants were calculated using the Stern-Volmer equation and the modified Stern-Volmer equation. The magnitude of Kapp of all complexes was 105 M-1, indicating moderate intercalative binding between CT-DNA and the complexes. Agarose gel electrophoresis clearly reflected their ability to cleave a double stranded pET-28b plasmid in the presence of an external reducing agent (3-mercapto propionic acid). Steady-state fluorescence quenching was performed to understand their interactions with BSA. The studies suggested a mixed quenching mechanism with an initial static process. Furthermore, the antiproliferative activity of the complexes was evaluated against lung cancer A549 cells and primary mice splenocytes. Interestingly, the complexes show 25-200 fold greater toxicity towards the A549 cells than primary splenocytes, indicating their selectivity towards the former. The good binding behavior of all four complexes towards DNA and BSA and their cytotoxicity render these compounds promising potent anticancer drugs.

Reported herein the binding affinity between Human Serum Albumin and the DNA binding and cleavage activity of three copper(II) complexes, [Cu(phen)(o-van)ClO 4 ] (1), [Cu(phen)(gly)]ClO 4 (2) and [Cu(L 1 ) 2 (H 2 O) 2 ] (3) wherein 1 and 2 are synthesized with 1,10-phenanthroline (phen) and co-ligands (o-van: o-vanillin; gly: glycine) and 3 with a ligand 2-hydroxy-3-methoxybenzylidene-4H-1,2,4-triazol-4-amine (H 1 L 1 ). Complex 2 crystallizes in monoclinic (P21/n) space group shows square pyramidal geometry. The complex 3 crystallizes in monoclinic (P21/a) space group. All the three complexes exhibit binding affinity towards the transport protein Human Serum albumin (HSA). Quantitative evaluation of the thermodynamics of interaction and the results obtained from fluorescence spectroscopy suggest that metal coordinated glycynate, o-vanillin and perchlorate groups have a major role to play in the binding process, the latter two being stronger in the binding of complex 1. The coordinated water in complex 3 also plays an important role in the binding, which makes binding of complex 3 with HSA stronger than that of complex 2. Experimental results indicate that the binding affinity of the complexes towards CT-DNA is in the order 1>3>2 implying that complex 1 binds stronger than complex 3 and 2.The DNA cleaving activity of all the three complexes was explored in the presence of reactive oxygen compound, H 2 O 2 . All the three complexes have primarily shown the DNA cleaving activity., (Copyright © 2017. Published by Elsevier B.V.)

Eukaryotic transcriptional factors (TFs) typically recognize short genomic sequences alone or together with other proteins to modulate gene expression. Mapping of TF-DNA interactions in the genome is crucial for understanding the gene regulatory programs in cells. While chromatin immunoprecipitation followed by sequencing (ChIP-Seq) is commonly used for this purpose, its application is severely limited by the availability of suitable antibodies for TFs. To overcome this limitation, we developed an efficient and scalable strategy named cmChIP-Seq that combines the clustered regularly interspaced short palindromic repeats (CRISPR) technology with microhomology mediated end joining (MMEJ) to genetically engineer a TF with an epitope tag. We demonstrated the utility of this tool by applying it to four TFs in a human colorectal cancer cell line. The highly scalable procedure makes this strategy ideal for ChIP-Seq analysis of TFs in diverse species and cell types.

In the current study, four novel mononuclear Cu(II) complexes with terpyridine (L) and different co-ligands (phen, bipy, and imd) were synthesized and characterized in detail, where L is 4′-(3,4,5-trimethoxyphenyl)-2,2′:6′,2′′-terpyridine. The identity and purity of all complexes were determined by elemental analysis, spectroscopic techniques (UV-vis, FTIR, ESI-MS, and EPR) and CV, including single crystal X-ray determination of three complexes ([Cu(L)(phen)](ClO4)2 (C-I), [Cu(L)2](ClO4)2 (C-II) and [Cu(L)(imd)(ClO4)](ClO4) (C-IV). DNA binding studies were performed using fluorescence assay and the binding constants were calculated using the Stern–Volmer equation and the modified Stern–Volmer equation. The magnitude of Kapp of all complexes was 105 M−1, indicating moderate intercalative binding between CT-DNA and the complexes. Agarose gel electrophoresis clearly reflected their ability to cleave a double stranded pET-28b plasmid in the presence of an external reducing agent (3-mercapto propionic acid). Steady-state fluorescence quenching was performed to understand their interactions with BSA. The studies suggested a mixed quenching mechanism with an initial static process. Furthermore, the antiproliferative activity of the complexes was evaluated against lung cancer A549 cells and primary mice splenocytes. Interestingly, the complexes show 25–200 fold greater toxicity towards the A549 cells than primary splenocytes, indicating their selectivity towards the former. The good binding behavior of all four complexes towards DNA and BSA and their cytotoxicity render these compounds promising potent anticancer drugs. [ABSTRACT FROM AUTHOR]

Hypermethylation of the glutathione S-transferase p 1 (GSTP1) gene promoter region has been reported to be a potential biomarker to distinguish hepatocellular carcinoma (HCC) from other liver diseases. However, reports regarding how specific a marker it is have ranged from 100% to 0%. We hypothesized that, to a large extent, the variation of specificity depends on the location of the CpG sites analyzed. To test this hypothesis, we compared the methylation status of the GSTP1 promoter region of the DNA isolated from HCC, cirrhosis, hepatitis, and normal liver tissues by bisulfite-PCR sequencing. We found that the 59 region of the position 248 nt from the transcription start site of the GSTP1 gene is selectively methylated in HCC, whereas the 39 region is methylated in all liver tissues examined, including normal liver and the HCC tissue. Interestingly, when DNA derived from fetal liver and 11 nonhepatic normal tissue was also examined by bisulfite-PCR sequencing, we found that methylation of the 39 region of the promoter appeared to be liver-specific. A methylation-specific PCR assay targeting the 59 region of the promoter was developed and used to quantify the methylated GSTP1 gene in various diseased liver tissues including HCC. When we used an assay targeting the 39 region, we found that the methylation of the 59-end of the GSTP1 promoter was significantly more specific than that of the 39-end (97.1% vs. 60%, p,0.0001 by Fisher's exact test) for distinguishing HCC (n = 120) from hepatitis (n = 35) and cirrhosis (n = 35). Encouragingly, 33.8% of the AFP-negative HCC contained the methylated GSTP1 gene. This study clearly demonstrates the importance of the location of CpG site methylation for HCC specificity and how liver-specific DNA methylation should be considered when an epigenetic DNA marker is studied for detection of HCC. [ABSTRACT FROM AUTHOR]

Research on development of novel metal based anti-cancer agents continues with its popularity among bioinorganic community. Benzothiazole, an important heterocyclic pharmacophore, was chosen as a valuable and useful scaffold for the synthesis of novel copper(II) complexes. Three new copper(II) complexes obtained from the synthesis of newly synthesized benzothiazole based N -(benzo d thiazol-2-ylmethyl)- N -methyl-2-(pyridin-2-yl)ethan-1-amine (btzpy) ligand with CuCl 2 [Cu(btzpy)Cl 2 (1), Cu(NCS) 2 [Cu(btzpy)(NCS) 2 (2), and Cu(NO 3) 2 [Cu(btzpy)(NO 3)(H 2 O)]NO 3 (3) were isolated and characterized by physical and spectroscopic measurements, including single-crystal X-ray structures. The interaction of complexes 1 and 3 with calf thymus (CT)-DNA was investigated using ethidium bromide fluorescence quenching assay and weak intercalation with K SV values of 9.8 × 102 M−1 and 8.2 × 102 M−1, respectively was observed. All three complexes have shown DNA cleavage of supercoiled plasmid DNA forming single nicked and double nicked forms in the presence of external reducing agents like 3-mercaptopropionic acid (3-MPA) and ascorbic acid. The water-soluble complexes 1 and 3 also show prominent hydrolytic DNA cleavage. From the DPPH (2,2-diphenyl-1-picrylhydrazyl) radical scavenging assay, it was observed that complex 2 also exhibits good antioxidant properties. The cytotoxicity of complexes 1 – 3 was tested against the lung cancer cell line (A549) and complex 2 with -NCS moiety shows maximum activity in the micromolar range. A rationale for the observed activity is proposed in light of the other properties of these molecules. A novel benzothiazole derived tridentate ligand is utilized for the synthesis of copper(II) complexes with a motive to develop new Cu complexes for therapeutic purposes. Studies on DNA binding, protein binding, nuclease activity, antioxidant activity, and cytotoxicity on lung cancer (A549) cell line are described. Unlabelled Image • Development of benzothiazole based Cu(II) complexes for therapeutic purposes • Detailed characterization by various methods including single-crystal X-ray diffraction • DNA binding and nuclease activity showing hydrolytic and oxidative cleavage of DNA • Bovine Serum Albumin (BSA) binding and antioxidant properties have been evaluated • Cytotoxicity study on lung cancer (A549) cell line showing antiproliferative activity [ABSTRACT FROM AUTHOR]

Background: Detection of human hepatitis B virus (HBV) DNA in the urine of patients with chronic hepatitis B infection (CHB) has been reported previously, suggesting urine could provide a potential route of horizontal HBV transmission. However, it is not clear whether the HBV DNA detected in urine is indeed full-length, infectious viral DNA. The aim of this study is to assess the potential infectivity of urine from patients with CHB and to correlate HBV DNA detection in urine with clinical parameters, such as serum viral load and HBeAg status.Methods: Urine from 60 CHB patients with serum viral loads ranging from undetectable to 108 IU/mL were analyzed for HBV DNA and serum immune markers. HBV DNA was detected from total urine DNA and size-fractionated urine DNA (separated into ≤1 kb and > 1 kb fractions) by PCR analysis of six regions of the HBV genome.Results: Twenty-seven of 59 (45.7%) patients with HBV serum viral load (≥20 IU/mL) contained at least 20 copies per mL of fragmented HBV DNA in urine detected in at least 1 of the 6 PCR assay regions. Only one patient contained HBV DNA detected by all six regions, and was found to have evidence of blood in the urine. Sixteen of 25 urine samples with high viral load (> 105 IU/mL) and 11 of 34 urine samples with low viral load (< 105 IU/mL) contained detectable HBV DNA. Twelve of 27 (44.44%) patients with detectable HBV DNA in urine were HBeAg positive, and only 5 of these HBeAg positive patients were in the group of 33 (15.15%) patients with no detectable HBV DNA in urine. By Fishers' exact test, HBV DNA in urine is significantly associated with high serum viral load (P = 0.0197) and HBeAg (P = 0.0203).Conclusions: We conclude that urine from CHB patients with healthy kidney function should not contain full-length HBV DNA, and therefore should not be infectious. [ABSTRACT FROM AUTHOR]