Remodeling Chromatin Induces Z-DNA Conformation Detected through Fourier Transform Infrared Spectroscopy

Li, Yalin; Huang, Qing; Yao, Guidong; Wang, Xiaoyi; Zhang, Fengqiu; Wang, Tao; Shao, Changsheng; Zheng, Xinxin; Jing, Xumiao; Zhou, Huiyue

doi:10.1021/acs.analchem.0c02432

Cited by 9 publications

(6 citation statements)

References 55 publications

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“…As shown in Figure e, the SERS peak intensity of aldehyde samples was markedly enhanced and higher than that of non-aldehydes. The SERS spectra of different aldehyde gases are very similar (Figure f), but they can still be distinguished based on PCA, which is a multivariate analysis method often applied to find the essential difference in a large number of spectral data. , Hence, we performed PCA to reduce the dimensionality of spectral data of five kinds of aldehydes, as shown in Figure h; the colors of the ovals in the PCA plots clearly show the difference among the five species of aldehydes, indicating different spectral properties of even similar aldehyde molecules.…”

Section: Results and Discussionmentioning

confidence: 99%

SERS Approach to Probe the Adsorption Process of Trace Volatile Benzaldehyde on Layered Double Hydroxide Material

Muhammad

Chu

et al. 2021

Anal. Chem.

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The study of the physicochemical process of volatile organic compound (VOC) adsorption on porous materials is significant for design and screening of adsorbent materials and treatment of VOCs. Traditional measurement methods for studying the adsorption process require lots of adsorbates and adsorbents and are time-consuming. We proposed a facile strategy to study the adsorption process of trace gaseous aldehydes on layered double hydroxide (LDH) using surface-enhanced Raman spectroscopy (SERS). We prepared a composite of Ag nanocubes@hollow Co–Ni LDH (AgNCs@Co–Ni LDH) with a strong adsorption capability and high SERS sensitivity. The adsorption properties of LDH for benzaldehyde in terms of general kinetics and isotherms were investigated. The kinetic adsorption process could be fitted better by the pseudo-first-order kinetics with a higher correlation coefficient than by the pseudo-second-order model, and the adsorption rate of 0.0308 min–1 was obtained from the fitting curve. The isotherm adsorption fits the Langmuir isotherm model, and its adsorption constant is 6.25 × 106 L/mol. Taking advantage of the excellent adsorptive performance and SERS activity, the AgNCs@Co–Ni LDH composite can be used as an effective SERS probe to detect gaseous aldehydes, and it shows a linear dynamic range (5–100 ppb) with a limit of detection reaching 1.83 ppb for benzaldehyde, better than that achieved by previous studies. Therefore, this work has not only established a new measurement method for probing the adsorption process with extremely low consumption of both adsorbates and adsorbents, but also may lay the groundwork for the construction of rapid and ultra-sensitive SERS sensors for probing VOCs in the future.

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Section: Results and Discussionmentioning

confidence: 99%

SERS Approach to Probe the Adsorption Process of Trace Volatile Benzaldehyde on Layered Double Hydroxide Material

Muhammad

Chu

et al. 2021

Anal. Chem.

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“…So, what function does ZBP1 perform in PCs that other anti-viral sensors may not? We note that ZNA-forming sequences are able to modulate gene expression in some experimental models, with effects correlated with Z-DNA formation [ 80 , 81 , 82 ]. The most common way to induce the flip from right to left-handed DNA is through the action of an RNA polymerase, which powers the formation of Z-DNA as it separates the DNA strands to make RNA.…”

Section: Zbp1 and The Silencing Of Ebvmentioning

confidence: 99%

“…Engagement of different classes of E-box binding proteins at sites of Z-formation could also produce other outcomes [ 107 ]. For example, engagement of the EBV encoded BZLF1 protein would induce EBV lytic replication rather than latency [ 108 ], while binding of the BRG1 subunit the SWI/SNF (encoded by SMARCA4) to sites of Z-DNA formation would promote chromatin remodeling [ 81 , 82 , 109 , 110 ], impacting the transcription of viral genes. Outcomes then reflect the regulation and the relative affinity of the different CMC competing with each other at locations where Z-DNA forms and are modulated by the factors already engaged at those sites.…”

Section: Z-dna E-boxes and H3k9 Methylationmentioning

confidence: 99%

Mono a Mano: ZBP1’s Love–Hate Relationship with the Kissing Virus

Herbert

Федоров

Poptsova

2022

IJMS

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Z-DNA binding protein (ZBP1) very much represents the nuclear option. By initiating inflammatory cell death (ICD), ZBP1 activates host defenses to destroy infectious threats. ZBP1 is also able to induce noninflammatory regulated cell death via apoptosis (RCD). ZBP1 senses the presence of left-handed Z-DNA and Z-RNA (ZNA), including that formed by expression of endogenous retroelements. Viruses such as the Epstein–Barr “kissing virus” inhibit ICD, RCD and other cell death signaling pathways to produce persistent infection. EBV undergoes lytic replication in plasma cells, which maintain detectable levels of basal ZBP1 expression, leading us to suggest a new role for ZBP1 in maintaining EBV latency, one of benefit for both host and virus. We provide an overview of the pathways that are involved in establishing latent infection, including those regulated by MYC and NF-κB. We describe and provide a synthesis of the evidence supporting a role for ZNA in these pathways, highlighting the positive and negative selection of ZNA forming sequences in the EBV genome that underscores the coadaptation of host and virus. Instead of a fight to the death, a state of détente now exists where persistent infection by the virus is tolerated by the host, while disease outcomes such as death, autoimmunity and cancer are minimized. Based on these new insights, we propose actionable therapeutic approaches to unhost EBV.

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“…At present, a variety of biological functions of Z-DNA have been revealed. In general, it is involved in gene regulation [ 7 , 8 ]. For example, it may induce genetic instability and cause a variety of diseases [ 2 , 9 , 10 , 11 ].…”

Section: Introductionmentioning

confidence: 99%

“…Currently, FTIR spectroscopy has already been applied in DNA structure analysis [ 30 , 31 ]. The application of FTIR spectroscopy in the study of DNA conformation has also gained encouraging attention [ 8 , 32 , 33 , 34 , 35 , 36 ]. However, previous research on Z-DNA through FTIR had some limitations, such as the requirement of low hydration to achieve the purpose of Z-DNA detection [ 30 , 37 , 38 ].…”

Section: Introductionmentioning

confidence: 99%

Assessing B-Z DNA Transitions in Solutions via Infrared Spectroscopy

Duan

Zhang

et al. 2023

Biomolecules

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Z-DNA refers to the left-handed double-helix DNA that has attracted much attention because of its association with some specific biological functions. However, because of its low content and unstable conformation, Z-DNA is normally difficult to observe or identify. Up to now, there has been a lack of unified or standard analytical methods among diverse techniques for probing Z-DNA and its transformation conveniently. In this work, NaCl, MgCl2, and ethanol were utilized to induce d(GC)8 from B-DNA to Z-DNA in vitro, and Fourier transform infrared (FTIR) spectroscopy was employed to monitor the transformation of Z-DNA under different induction conditions. The structural changes during the transformation process were carefully examined, and the DNA chirality alterations were validated by the circular dichroism (CD) measurements. The Z-DNA characteristic signals in the 1450 cm−1–900 cm−1 region of the d(GC)8 infrared (IR) spectrum were observed, which include the peaks at 1320 cm−1, 1125 cm−1 and 925 cm−1, respectively. The intensity ratios of A1320/A970, A1125/A970, and A925/A970 increased with Z-DNA content in the transition process. Furthermore, compared with the CD spectra, the IR spectra showed higher sensitivity to Z-DNA, providing more information about the molecular structure change of DNA. Therefore, this study has established a more reliable FTIR analytical approach to assess BZ DNA conformational changes in solutions, which may help the understanding of the Z-DNA transition mechanism and promote the study of Z-DNA functions in biological systems.

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Remodeling Chromatin Induces Z-DNA Conformation Detected through Fourier Transform Infrared Spectroscopy

Cited by 9 publications

References 55 publications

SERS Approach to Probe the Adsorption Process of Trace Volatile Benzaldehyde on Layered Double Hydroxide Material

SERS Approach to Probe the Adsorption Process of Trace Volatile Benzaldehyde on Layered Double Hydroxide Material

Mono a Mano: ZBP1’s Love–Hate Relationship with the Kissing Virus

Assessing B-Z DNA Transitions in Solutions via Infrared Spectroscopy

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