Article
Biochemical Research Methods
Adam Golcs, Korinna Kovacs, Panna Vezse, Peter Huszthy, Tunde Toth
Summary: A new fluorescent bis(acridino)-macrocycle with two allyl groups was synthesized and studied for metal ion recognition and selectivity effects, determining important thermodynamic constants. The sensor molecule is recommended for Zn2+ -selective optochemical analyzers based on covalently immobilized ionophores due to its unique pH-independent metal ion recognition ability unaffected by anions and other potentially occurring metal ions in biological samples.
JOURNAL OF FLUORESCENCE
(2022)
Article
Chemistry, Multidisciplinary
Weier Liu, Linghui Kong, Mao Quan, Huan Yao, Liupan Yang, Ho Yu Au-Yeung, Wei Jiang
Summary: In this study, an endo-functionalized naphthobox was reported to exhibit highly selective binding towards methyl viologen over other analogues. X-ray single crystal structure and Density Functional Theory (DFT) calculations revealed that the endo-functionalized groups in the cavity of the naphthobox played a crucial role in achieving the high binding selectivity through multiple C-H···N, C-H···π, and π···π interactions with methyl viologen.
CHINESE CHEMICAL LETTERS
(2022)
Review
Biochemistry & Molecular Biology
Mohamed A. Sobhy, Muhammad Tehseen, Masateru Takahashi, Amer Bralic, Alfredo De Biasio, Samir M. Hamdan
Summary: FEN1 is a key component in the molecular machinery of DNA replication and repair. The study reviewed in this article focuses on using single-molecule fluorescence to study important mechanistic details of FEN1 enzymatic reaction, providing a guide for studying other biomolecular enzymatic reactions. The research shows that FEN1 actively bends the substrate to control active site assembly, preventing off-target cleavage.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Materials Science, Biomaterials
Chuan Gu, Fangjian Shan, Lifang Zheng, Yue Zhou, Jun Hu, Gaojian Chen
Summary: Surface-enhanced Raman scattering (SERS) is a widely used technique in the biological field, which allows non-destructive detection and molecular-level detection of biomolecules. In this study, a glycopolymer-based composite surface was fabricated using a specific interaction between a carbohydrate and protein, enabling specific SERS detection of proteins.
JOURNAL OF MATERIALS CHEMISTRY B
(2022)
Article
Biochemistry & Molecular Biology
Caroline P. P. Shepard, Raymond G. G. Emehiser, Saswata Karmakar, Patrick J. J. Hrdlicka
Summary: The development of chemically modified oligonucleotides that can recognize complementary chromosomal DNA regions without sequence restrictions has long been a goal for scientists. In this study, Invader probes modified with intercalator-functionalized nucleotides were found to efficiently recognize chromosomal DNA targets with excellent binding specificity. The insights gained from this study will facilitate the design of efficient Invader probes for applications in the life sciences.
Article
Chemistry, Analytical
Yan Zhang, Jinping Hu, Xiao-Yun Yang, Chun-yang Zhang
Summary: This method utilizes single-molecule detection and bidirectional strand displacement amplification to simultaneously detect UDG and hAAG with high sensitivity and good selectivity, enabling quantification of multiple DNA glycosylases at the single-cell level.
Article
Biochemistry & Molecular Biology
Li Xue, Dehao Yu, Lingling Wang, Jing Sun, Ying Song, Yuanyuan Jia, Ang Wu, Beibei Zhang, Wenyi Mi, Heli Fan, Huabing Sun
Summary: This study developed a drug that selectively kills cancer cells by taking advantage of the difference in glutathione (GSH) concentration. The drug captures and blocks the repair of AP sites in DNA, leading to cell death. Additionally, the drug exhibits selective antitumor activity and photocytotoxicity.
ACS CHEMICAL BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Yoshiki Hashimoto, Yoshiki Imagawa, Kaho Nagano, Ryuichi Maeda, Naho Nagahama, Takeru Torii, Natsuki Kinoshita, Nagisa Takamiya, Keiko Kawauchi, Hisae Tatesishi-Karimata, Naoki Sugimoto, Daisuke Miyoshi
Summary: In this study, new structure-selective G-quadruplex ligands were developed using a simple and fast screening system. The affinity, selectivity, enzymatic inhibitory activity and cytotoxicity of these ligands were demonstrated, along with a relationship between their structural selectivity and cytotoxicity.
CHEMICAL COMMUNICATIONS
(2023)
Article
Chemistry, Analytical
Gaihua Cao, Keyi Long, Yue Qiu, Lan Peng, Haiyan Han, Yongzhong Wang, Danqun Huo, Changjun Hou
Summary: In this study, a DNA: RNA hybrid G-quadruplet (HQ) detection platform was developed using strand displacement amplification (SDA) and Baby Spinach RNA aptamer for the detection of single nucleotide variant (SNV) of circulating tumor DNA (ctDNA) and miRNA-21. The HQ-based biosensor showed stronger fluorescence activation of DFHBI-1T compared to Baby Spinach RNA alone. Through the use of the platform and the highly specific FspI enzyme, the biosensor achieved ultra-sensitive detection of SNV of ctDNA (PIK3CA H1047R gene) and miRNA-21, with high anti-interference ability in complex actual samples. This label-free biosensor provides a sensitive and accurate method for early diagnosis of breast cancer and opens up a new application model for RNA aptamers.
Article
Chemistry, Analytical
Juan C. Stockert, Alfonso Blazquez-Castro
Summary: Many fluorophores, including acridine orange, exhibit orthochromatic vs. metachromatic behavior depending on their concentration and binding mode to cellular substrates. This article revisits the differential acridine orange fluorescence in selected biological examples, which can be used to identify single-stranded or double-stranded nucleic acids. The authors propose a potential molecular mechanism involving the degree of overlap of excited state orbitals.
Article
Chemistry, Multidisciplinary
Yan Xiong, Stanislav Tsitkov, Henry Hess, Oleg Gang, Yifei Zhang
Summary: This study establishes a cascade system using reversible DNA-directed colocalization of enzymes on microspheres to directly evaluate the colocalization effect. In a regime of highly dilute microspheres of particular sizes, the colocalized cascade shows enhanced activity compared to the freely diffusing cascade. The findings provide theoretical support for the rational design of highly efficient multienzyme catalysts.
Article
Multidisciplinary Sciences
Maya Sen, Dylan Mooijman, Alex Chialastri, Jean-Charles Boisset, Mina Popovic, Bjorn Heindryckx, Susana M. Chuva de Sousa Lopes, Siddharth S. Dey, Alexander van Oudenaarden
Summary: Erasure of DNA methylation from the parental genomes is crucial for resetting the methylome of differentiated gametes to pluripotent cells in the blastocyst. Researchers present a high-throughput single-cell method enabling strand-specific quantification of DNA methylation and identify distinct modes of DNA demethylation dynamics during early mammalian development.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Kyle B. Vrtis, James M. Dewar, Gheorghe Chistol, R. Alex Wu, Thomas G. W. Graham, Johannes C. Walter
Summary: Research has shown that collisions between the replicative CMG helicase and nicks in DNA templates can lead to different forms of double-strand breaks, causing replisome disassembly.
Article
Chemistry, Analytical
Da-Qian Feng, Guoliang Liu
Summary: A new multicolor silver nanoclusters/graphene oxide hybrid material has been demonstrated to achieve emission shift and enhancement through entropy-driven enzyme-free toehold-mediated strand displacement reaction. By designing two different synthesis routes, the material successfully constructs a biosensor for influenza A virus subtype genes, resulting in significant fluorescence enhancement and emission shift. This novel approach shows promising application prospect in accurate diagnosis and treatment with remarkable emission recovery rates and multichannel signal.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Jinwoo Kim, Dabin Ahn, Chin-Ju Park
Summary: The TAD and FHD of FOXO4 form an intramolecular complex primarily governed by hydrophobic interactions, sharing the same surface for DNA binding; The FHD-TAD complex exhibits different exchange rates with target and non-target DNA, affecting the kinetic function of FHD; TAD modulates the recognition of target promoter DNA sequences by FOXO4, providing a new kinetic perspective on target sequence selection by transcription factors.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Chemistry, Physical
Paramjyothi C. Nandajan, Hyeong-Ju Kim, Santiago Casado, Soo Young Park, Johannes Gierschner
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2018)
Article
Chemistry, Organic
Prakash P. Neelakandan, Paramjyothi C. Nandajan, Baby Subymol, Danaboyina Ramaiah
ORGANIC & BIOMOLECULAR CHEMISTRY
(2011)
Article
Chemistry, Multidisciplinary
Paramjyothi C. Nandajan, Prakash P. Neelakandan, Danaboyina Ramaiah
Article
Chemistry, Multidisciplinary
Mambattakkara Viji, Akhil K. Nair, Paramjyothi C. Nandajan, Danaboyina Ramaiah
Article
Chemistry, Physical
Hyun-Jun Lee, Jaekwan Kim, Abasi Abudulimu, Juan Cabanillas-Gonzalez, Paramjyothi C. Nandajan, Johannes Gierschner, Larry Lueer, Soo Young Park
JOURNAL OF PHYSICAL CHEMISTRY C
(2020)
Article
Chemistry, Multidisciplinary
Hyeong-Ju Kim, Paramjyothi C. Nandajan, Johannes Gierschner, Soo Young Park
ADVANCED FUNCTIONAL MATERIALS
(2018)
