Biophysical characterization of the DNA interaction with the biogenic polyamine putrescine: A single molecule study

Publio, Bruno C.; Moura, Tiago; Lima, Carlos Henrique Moreira; Rocha, M. S.

doi:10.1016/j.ijbiomac.2018.01.142

Cited by 14 publications

(8 citation statements)

References 20 publications

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“…Polyamines have been implicated in cellular functions such as nucleic acid and chromatin structure maintenance and protein synthesis [22,23]. Experimental and modeling data demonstrate that natural polyamines can affect DNA conformation and aggregation [24]. us, DiAcSpm may play a potential role in cancer-related gene regulation.…”

Section: Discussionmentioning

confidence: 99%

N1, N12-Diacetylspermine Is Elevated in Colorectal Cancer and Promotes Proliferation through the miR-559/CBS Axis in Cancer Cell Lines

Chu²,

Li³

et al. 2021

Journal of Oncology

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N1, N12-Diacetylspermine (DiAcSpm) has been reported to be upregulated in the urine of cancer patients. Mass spectrometry has shown elevated DiAcSpm expressions in colorectal cancer (CRC) tissues. However, the diagnostic application of DiAcSpm is not available due to a lack of diagnostic grade antibodies. Also, its biological roles in CRC cells remain unexplored. In the present study, we developed an antibody that directly detected DiAcSpm expression in paraffin-embedded tissues. We also characterized its biological characteristics and underlying mechanisms. Polyclonal antibodies were generated by immunizing animals with a synthetic product of DiAcSpm. Antibody DAS AB016 showed strong sensitivity against DiAcSpm in CRC tissues. Immunohistochemistry results showed that DiAcSpm expression was significantly elevated in CRC tissues. High levels of DiAcSpm correlated with the clinical stage and Ki67 index. DiAcSpm treatment increased levels of proliferation, cell cycle progression, and cyclin D1 and cyclin E proteins in CRC cell lines, SW480 and Caco-2. DiAcSpm also upregulated ATP production in these two cell lines. RNA-sequencing showed that DiAcSpm downregulated miR-559, which was confirmed using RT-qPCR. The luciferase reporter assay, western blotting, and RT-qPCR showed that cystathionine β-synthase (CBS) was the target of miR-559. miR-559 inhibited, while CBS accelerated, CRC proliferation. In addition, CBS siRNA knockdown blocked the biological effects of DiAcSpm on CRC cells. In conclusion, DiAcSpm was found to be increased in CRC tissues using a newly developed antibody. DiAcSpm accelerated CRC proliferation by regulating the miR-559/CBS axis.

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Section: Discussionmentioning

confidence: 99%

N1, N12-Diacetylspermine Is Elevated in Colorectal Cancer and Promotes Proliferation through the miR-559/CBS Axis in Cancer Cell Lines

Chu²,

Li³

et al. 2021

Journal of Oncology

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“…First, guanidine (guanidinium chloride, or guanidine hydrochloride, GuHCl) were tested as it is a commonly used chaotropic agent at high concentrations to denature double-stranded DNA [67,68]. Second, salts of putrescine and spermidine were chosen for testing our DNA bows because they have been reported previously to interact with DNA and shorten the persistence length of DNA [21,69,70]. Third, we tested EtBr and SYBR safe, which are commonly used DNA intercalators and DNA staining dyes in gel electrophoresis [71][72][73].…”

Section: Detection Of Small Organic Molecules Using Bent Dna Bowsmentioning

confidence: 99%

Bent DNA Bows as Sensing Amplifiers for Detecting DNA-Interacting Salts and Molecules

Freeland

Zhang

Wang

et al. 2020

Sensors

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Due to the central role of DNA, its interactions with inorganic salts and small organic molecules are important. For example, such interactions play important roles in various fundamental cellular processes in living systems and are involved in many DNA-damage related diseases. Strategies to improve the sensitivity of existing techniques for studying DNA interactions with other molecules would be appreciated in situations where the interactions are too weak. Here we report our development and demonstration of bent DNA bows for amplifying, sensing, and detecting the interactions of 14 inorganic salts and small organic molecules with DNA. With the bent DNA bows, these interactions were easily visualized and quantified in gel electrophoresis, which were difficult to measure without bending. In addition, the strength of the interactions of DNA with the various salts/molecules were quantified using the modified Hill equation. This work highlights the amplification effects of the bending elastic energy stored in the DNA bows and the potential use of the DNA bows for quantitatively measuring DNA interactions with small molecules as simple economic methods; it may also pave the way for exploiting the bent DNA bows for other applications such as screening DNA-interacting molecules and drugs.

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“…Glu is also essential for tetrahydrofolate polyglutamylation 11 . Ptr is important for bacterial growth and for efficient DNA replication, transcription, and translation 12 , 13 and plays an important role in maintaining compact conformations of negatively charged nucleic acids 14 . Ptr is also involved in multiple antibiotic resistance mechanisms under stress conditions 15 .…”

Section: Introductionmentioning

confidence: 99%

A systems approach discovers the role and characteristics of seven LysR type transcription factors in Escherichia coli

Rodionova

Gao

Monk

et al. 2022

Sci Rep

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Although Escherichia coli K-12 strains represent perhaps the best known model bacteria, we do not know the identity or functions of all of their transcription factors (TFs). It is now possible to systematically discover the physiological function of TFs in E. coli BW25113 using a set of synergistic methods; including ChIP-exo, growth phenotyping, conserved gene clustering, and transcriptome analysis. Among 47 LysR-type TFs (LTFs) found on the E. coli K-12 genome, many regulate nitrogen source utilization or amino acid metabolism. However, 19 LTFs remain unknown. In this study, we elucidated the regulation of seven of these 19 LTFs: YbdO, YbeF, YcaN, YbhD, YgfI, YiaU, YneJ. We show that: (1) YbdO (tentatively re-named CitR) regulation has an effect on bacterial growth at low pH with citrate supplementation. CitR is a repressor of the ybdNM operon and is implicated in the regulation of citrate lyase genes (citCDEFG); (2) YgfI (tentatively re-named DhfA) activates the dhaKLM operon that encodes the phosphotransferase system, DhfA is involved in formate, glycerol and dihydroxyacetone utilization; (3) YiaU (tentatively re-named LpsR) regulates the yiaT gene encoding an outer membrane protein, and waaPSBOJYZU operon is also important in determining cell density at the stationary phase and resistance to oxacillin microaerobically; (4) YneJ, re-named here as PtrR, directly regulates the expression of the succinate-semialdehyde dehydrogenase, Sad (also known as YneI), and is a predicted regulator of fnrS (a small RNA molecule). PtrR is important for bacterial growth in the presence of l-glutamate and putrescine as nitrogen/energy sources; and (5) YbhD and YcaN regulate adjacent y-genes on the genome. We have thus established the functions for four LTFs and identified the target genes for three LTFs.

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Biophysical characterization of the DNA interaction with the biogenic polyamine putrescine: A single molecule study

Cited by 14 publications

References 20 publications

N1, N12-Diacetylspermine Is Elevated in Colorectal Cancer and Promotes Proliferation through the miR-559/CBS Axis in Cancer Cell Lines

N1, N12-Diacetylspermine Is Elevated in Colorectal Cancer and Promotes Proliferation through the miR-559/CBS Axis in Cancer Cell Lines

Bent DNA Bows as Sensing Amplifiers for Detecting DNA-Interacting Salts and Molecules

A systems approach discovers the role and characteristics of seven LysR type transcription factors in Escherichia coli

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