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Single-Molecule Methods for Characterizing Different DNA Higher-Order Structures Review

Yonglin Liu, Tianyuan Bian, Yan Liu, Zhimin Li, Yufeng Pei, Jie Song

Engineering 2023, Volume 24, Issue 5,   Pages 277-292 doi: 10.1016/j.eng.2022.10.009

Abstract:

DNA is considered to be not only a carrier of the genetic information of life but also a highly programmableDifferent DNA structures are related to their biological and chemical functions.However, the bulk assay ignores the heterogeneity of DNA structures in solution.(ss/dsDNA), DNA higher-order structures, and DNA nanostructures.methods to understand the biophysical properties of DNA and other bio-matter and soft matter.

Keywords: Single-molecule methods     DNA structure     Mechanical properties     Conformational transitions    

Developing a Transformation-Independent and Unbiased qPCR Assay to Rapidly Evaluate the Determinants of DNA Article

Xiaoyan Ma, Xinxin Liang, Yi-Xin Huo

Engineering 2019, Volume 5, Issue 4,   Pages 803-810 doi: 10.1016/j.eng.2019.06.002

Abstract: Conventional evaluation of the DNA assembly efficiency (AE) requires transformation, and the whole processused restriction ligation, Golden Gate assembly, and Gibson assembly for the assembly of two or more DNAThe method was then employed to investigate the effects of terminal secondary structures on DNA assemblyThe qPCR-based approach presented here should facilitate the development of DNA assembly techniques and

Keywords: Assembly efficiency     DNA assembly     qPCR     Secondary structure     Transformation    

Engineering DNA Materials for Sustainable Data Storage Using a DNA Movable-Type System Article

Zi-Yi Gong, Li-Fu Song, Guang-Sheng Pei, Yu-Fei Dong, Bing-Zhi Li, Ying-Jin Yuan

Engineering 2023, Volume 29, Issue 10,   Pages 130-136 doi: 10.1016/j.eng.2022.05.023

Abstract:

DNA molecules are green materials with great potential for high-density and long-term data storageHowever, the current data-writing process of DNA data storage via DNA synthesis suffers from high costsHere, we developed a DNA movable-type storage system that can utilize DNA fragments pre-produced by cellIn this system, these pre-generated DNA fragments, referred to herein as "DNA movable types,"the costly and environmentally hazardous process of de novo DNA synthesis.

Keywords: 合成生物学     DNA信息存储     DNA活字存储系统     经济性DNA数据存储    

The role of PARP1 in the DNA damage response and its application in tumor therapy

Zhifeng Wang, Fengli Wang, Tieshan Tang, Caixia Guo

Frontiers of Medicine 2012, Volume 6, Issue 2,   Pages 156-164 doi: 10.1007/s11684-012-0197-3

Abstract: ADP-ribosyl)ation of many key proteins in vivo and thus plays important roles in multiple DNAThe present review will focus on recent progress on the role of PARP1 in the DNA damage response andresistance of BRCA-deficient tumors to PARP inhibitors is also briefly discussed from the perspective of DNA

Keywords: PARP1     synthetic lethality     PARP inhibitor     DNA repair     cancer     NHEJ    

Functional role of ATM in the cellular response to DNA damage

Ming LIU, Wenxiang HU

Frontiers of Chemical Science and Engineering 2011, Volume 5, Issue 2,   Pages 179-187 doi: 10.1007/s11705-009-0268-4

Abstract: our understanding of the mechanism of activation of ATM and its signaling pathways, explore whether DNA

Keywords: ataxia-telangiectasia mutated (ATM)     cell cycle checkpoint     DNA damage     signalling transduction    

Generation and repair of AID-initiated DNA lesions in B lymphocytes

Zhangguo Chen,Jing H. Wang

Frontiers of Medicine 2014, Volume 8, Issue 2,   Pages 201-216 doi: 10.1007/s11684-014-0324-4

Abstract: AID induces U:G mismatch lesions in DNA that are subsequently converted into point mutations or DNA doubleThus, AID poses a threat to the genome of B cells if AID-initiated DNA lesions cannot be properly repairedregulate the specificity of AID targeting and the repair pathways responsible for processing AID-initiated DNA

Keywords: class switch recombination     somatic hypermutation     activation-induced deaminase     DNA repair     genomic instability    

Epigenetic silencing of BEND4, a novel DNA damage repair gene, is a synthetic lethal marker for ATM inhibitor

Frontiers of Medicine doi: 10.1007/s11684-023-1053-3

Abstract: Mechanistically, BEND4 involves non-homologous end joining signaling by interacting with Ku80 and promotes DNA

Keywords: BEND4     DNA methylation     synthetic lethality     NHEJ pathway    

Environmental pollution and DNA methylation: carcinogenesis, clinical significance, and practical applications

Yi Cao

Frontiers of Medicine 2015, Volume 9, Issue 3,   Pages 261-274 doi: 10.1007/s11684-015-0406-y

Abstract: Studies on DNA methylation are among the earliest and most conducted epigenetic research linked to cancerIn this review, the roles of DNA methylation in carcinogenesis and their significance in clinical medicinewere summarized, and the effects of environmental pollutants, particularly air pollutants, on DNA methylationFurthermore, prospective applications of DNA methylation to environmental pollution detection and cancer

Keywords: environmental pollution     DNA methylation     cancer     biomarker     diagnosis     therapy     prevention    

Molecular simulation of the interaction mechanism between CodY protein and DNA in

Linchen Yuan, Hao Wu, Yue Zhao, Xiaoyu Qin, Yanni Li

Frontiers of Chemical Science and Engineering 2019, Volume 13, Issue 1,   Pages 133-139 doi: 10.1007/s11705-018-1737-4

Abstract: In , the global transcriptional regulatory factor CodY can interact with the promoter DNA to regulateIn order to study the mechanism of interaction between CodY and its target DNA, molecular docking andARG218, SER219, ASN223, LYS242 and GLY243, among which SER186, ARG218 and LYS242 play a vital role in DNA

Keywords: CodY     DNA     molecular docking     molecular dynamics    

Effects of DNA damage on oocyte meiotic maturation and early embryonic development

Shen YIN,Junyu MA,Wei SHEN

Frontiers of Agricultural Science and Engineering 2014, Volume 1, Issue 3,   Pages 185-190 doi: 10.15302/J-FASE-2014035

Abstract: DNA damage is one of the most common threats to meiotic cells.Here, we reviewed exogenous factors which could induce DNA damage.Specially, we addressed the different effects of DNA damage on mouse oocytes and embryonic developmentComplex DNA damage, double-strand breaks, represents a more difficult repair process and involves variousUnderstanding the mechanisms involved in DNA damage responses may improve therapeutic strategies for

Keywords: DNA damage     double-strand breaks (DSBs)     oocyte     embryo    

A DNA Computing Model for the Graph Vertex Coloring Problem Based on a Probe Graph Article

Jin Xu, Xiaoli Qiang, Kai Zhang, Cheng Zhang, Jing Yang

Engineering 2018, Volume 4, Issue 1,   Pages 61-77 doi: 10.1016/j.eng.2018.02.011

Abstract:

The biggest bottleneck in DNA computing is exponential explosion, in which the DNA molecules usedTo overcome this bottleneck and improve the processing speed, we propose a DNA computing model to solveIn this article, a 3-colorable graph with 61 vertices is used to illustrate the capability of the DNAAll these tiny strands are operated by DNA self-assembly and parallel PCR.the largest among both the electronic and non-electronic computers that have been developed since the DNA

Keywords: DNA computing     Graph vertex coloring problem     Polymerase chain reaction    

hydrophobic environment triggering reactive fluorescence probe to real-time monitor mitochondrial DNA

Frontiers of Chemical Science and Engineering 2022, Volume 16, Issue 1,   Pages 92-102 doi: 10.1007/s11705-021-2063-9

Abstract: Mitochondrial DNA has a special structure that is prone to damage resulting in many serious diseases,Therefore, the rapid and specific monitoring of mitochondrial DNA damage is urgently needed for biologicalIn this design, MBI-CN conjugates to mitochondrial DNA without causing additional damages.significative fluorescence signal changes at 437 and 553 nm within 25 s for the damaged mitochondria DNA, it is a potentially effective detection tool for the real-time monitoring of mitochondrial DNA damage

Keywords: hydrolysis reaction     mitochondrial DNA damage     in situ hydrophobic environment trigger     fluorescence    

Bacterial inactivation, DNA damage, and faster ATP degradation induced by ultraviolet disinfection

Chao Yang, Wenjun Sun, Xiuwei Ao

Frontiers of Environmental Science & Engineering 2020, Volume 14, Issue 1, doi: 10.1007/s11783-019-1192-6

Abstract: • Long amplicon is more effective to test DNA damage induced by UV. • ATP in bacteria does not degradeWe used quantitative polymerase chain reaction (qPCR) to investigate DNA damage and evaluated adenosineThe results of qPCR effectively showed the DNA damage induced by UV when using longer gene amplicons,in that sufficiently long amplicons of both 16S and gadA indicated that the UV induced DNA damages.

Keywords: UV disinfection     DNA damage     qPCR     ATP    

Degradation of extracellular genomic, plasmid DNA and specific antibiotic resistance genes by chlorination

Menglu Zhang, Sheng Chen, Xin Yu, Peter Vikesland, Amy Pruden

Frontiers of Environmental Science & Engineering 2019, Volume 13, Issue 3, doi: 10.1007/s11783-019-1124-5

Abstract:

Extracellular DNA structure damaged by chlorination was characterizedlistitem>

Typical chlorine doses will likely effectively diminish extracellular DNA

Plasmid DNA/ARGs were less readily broken downthan genomic DNA.listitem>

The Bioanalyzer methodology effectively documented damage incurred to DNA

Keywords: Antibiotic resistance     Antibiotic resistance genes (ARGs)     Extracellular DNA/ARGs     Chlorination    

Detection of oxidative stress and DNA damage in freshwater snail

Daoud Ali, Huma Ali, Saud Alifiri, Saad Alkahtani, Abdullah A Alkahtane, Shaik Althaf Huasain

Frontiers of Environmental Science & Engineering 2018, Volume 12, Issue 5, doi: 10.1007/s11783-018-1039-6

Abstract:

Freshwater snail (Lymnea luteola L.) is good bio indicator of water pollution.

Profenofos is tested for its molluscicidal activity against Lymnea luteola L. snail.

Deleterious effects on some oxidative stress were detected.

Profenofos has a genotoxic effect on Lymnea luteola L. snails.

Keywords: Acute toxicity     Profenofos     ROS     oxidative stress     DNA damage     Lymnea luteola    

Title Author Date Type Operation

Single-Molecule Methods for Characterizing Different DNA Higher-Order Structures

Yonglin Liu, Tianyuan Bian, Yan Liu, Zhimin Li, Yufeng Pei, Jie Song

Journal Article

Developing a Transformation-Independent and Unbiased qPCR Assay to Rapidly Evaluate the Determinants of DNA

Xiaoyan Ma, Xinxin Liang, Yi-Xin Huo

Journal Article

Engineering DNA Materials for Sustainable Data Storage Using a DNA Movable-Type System

Zi-Yi Gong, Li-Fu Song, Guang-Sheng Pei, Yu-Fei Dong, Bing-Zhi Li, Ying-Jin Yuan

Journal Article

The role of PARP1 in the DNA damage response and its application in tumor therapy

Zhifeng Wang, Fengli Wang, Tieshan Tang, Caixia Guo

Journal Article

Functional role of ATM in the cellular response to DNA damage

Ming LIU, Wenxiang HU

Journal Article

Generation and repair of AID-initiated DNA lesions in B lymphocytes

Zhangguo Chen,Jing H. Wang

Journal Article

Epigenetic silencing of BEND4, a novel DNA damage repair gene, is a synthetic lethal marker for ATM inhibitor

Journal Article

Environmental pollution and DNA methylation: carcinogenesis, clinical significance, and practical applications

Yi Cao

Journal Article

Molecular simulation of the interaction mechanism between CodY protein and DNA in

Linchen Yuan, Hao Wu, Yue Zhao, Xiaoyu Qin, Yanni Li

Journal Article

Effects of DNA damage on oocyte meiotic maturation and early embryonic development

Shen YIN,Junyu MA,Wei SHEN

Journal Article

A DNA Computing Model for the Graph Vertex Coloring Problem Based on a Probe Graph

Jin Xu, Xiaoli Qiang, Kai Zhang, Cheng Zhang, Jing Yang

Journal Article

hydrophobic environment triggering reactive fluorescence probe to real-time monitor mitochondrial DNA

Journal Article

Bacterial inactivation, DNA damage, and faster ATP degradation induced by ultraviolet disinfection

Chao Yang, Wenjun Sun, Xiuwei Ao

Journal Article

Degradation of extracellular genomic, plasmid DNA and specific antibiotic resistance genes by chlorination

Menglu Zhang, Sheng Chen, Xin Yu, Peter Vikesland, Amy Pruden

Journal Article

Detection of oxidative stress and DNA damage in freshwater snail

Daoud Ali, Huma Ali, Saud Alifiri, Saad Alkahtani, Abdullah A Alkahtane, Shaik Althaf Huasain

Journal Article