Article
Chemistry, Multidisciplinary
Siddhant Seth, Kanako Ishino, Kai Takeda, Shigetaka Nakamura, Kenzo Fujimoto
Summary: This study investigated the effects of base-pair mismatch on the deamination of cytosine cross-linked with 3-cyanovinyl-carbazole. The complementary base of the target cytosine was changed to adenine, thymine, cytosine, 5-methylcytosine, and uracil. It was found that the fastest deamination of cytosine to uracil occurs when C-C mismatching occurs.
Article
Biochemical Research Methods
Ho Joung Lee, Hyun Ju Kim, Young-Jun Park, Sang Jun Lee
Summary: Mismatch tolerance is a major obstacle for accurate genome editing with the CRISPR/Cas system. In this study, the authors found that oligonucleotide-directed single-base substitutions were rarely introduced in the microbial genome using CRISPR/Cpf1-mediated negative selection. They observed that the cleavage efficiency of the DNA targets could be maximally improved when five nucleotides were truncated at the 3'-end of the crRNA. However, the efficiency decreased when a single mismatch was introduced at the 3'-end of the truncated crRNA. Based on these findings, the authors proposed that the maximally truncated crRNA-Cpf1 complex could distinguish between single-base-edited and unedited targets in vivo. The system showed high efficiency in single-base substitutions and nucleotide editing, making it a simple and efficient tool for microbial genome editing.
ACS SYNTHETIC BIOLOGY
(2022)
Review
Genetics & Heredity
Akhtar Ali, Wei Xiao, Masroor Ellahi Babar, Yanzhen Bi
Summary: This review provides insights into the action mode of NHEJ and HR, and proposes future directions for genome editing, emphasizing the need to switch repair pathways for higher editing accuracy and efficiency.
Article
Cell Biology
Despoina Sakellariou, Sara Thornby Bak, Esin Isik, Sonia Barroso, Antonio Porro, Andres Aguilera, Jiri Bartek, Pavel Janscak, Javier Pena-Diaz
Summary: The study reveals that the mismatch repair protein MutS beta is enriched at telomeres in ALT cancer cells, preventing the accumulation of G-quadruplex (G4) structures and R-loops, thus maintaining telomere integrity during alternative lengthening of telomeres.
Article
Chemistry, Analytical
Tzu-Yu Pan, Hwang-Shang Kou, Shou-Mei Wu, Chun-Chi Wang
Summary: In this study, a method combining single base-pair mismatch polymerase chain reaction (SM-PCR) and streptavidin magnetic microbeads (MB) was established for genotyping of codons 12 and 13 of K-RAS gene. The method involved the use of three primers and two restriction enzymes to distinguish single nucleotide polymorphisms. The wild type of codons 12 and 13 was digested, while the mutant type was not, and magnetic microbeads were used for purification. The method showed good consistency with direct sequencing results, indicating its feasibility and efficiency for genotyping in populations.
SENSORS AND ACTUATORS B-CHEMICAL
(2023)
Article
Chemistry, Physical
Cornelia Baeckmann, Constantin Eisen, Hanspeter Kahlig, Patrick Guggenberger, Freddy Kleitz
Summary: Hollow mesoporous silica particles (HMSPs) are promising nanocatalysts for greener chemical processes, with improved synthesis methods resulting in precise control over size and pore structure. Additionally, selective functionalization with amine groups has been achieved through optimized extraction protocols.
Article
Microbiology
Almaz Nigatu Tesfahun, Marina Alexeeva, Migle Tomkuviene, Aysha Arshad, Prashanna Guragain, Arne Klungland, Saulius Klimasauskas, Peter Ruoff, Svein Bjelland
Summary: Mis-insertion by DNA polymerase III can lead to all possible non-cognate base pairs in DNA, resulting in base substitutions if not corrected by exonuclease or mismatch repair. In vitro evidence suggests that the C.C mismatch can be processed by base excision repair initiated by E. coli formamidopyrimidine-DNA glycosylase (Fpg). Fpg may play a role in resolving C.C and other pyrimidine.pyrimidine mismatches, increasing survival at the expense of some mutagenesis.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Chemistry, Physical
Alex Marti, Gala Ogalla, Antonio M. Echavarren
Summary: The enantioselective reaction of 1,6-enynes with O-, N-, and C-nucleophiles has been achieved through matched ion pair gold(I) catalysis. The chiral gold(I) cation and anion are H-bonded through a urea group, leading to very high levels of enantiocontrol (>99:1 er) for a wide range of substrates. DFT studies highlight the importance of the H-bond donor group in anchoring the matched chiral cation- and anion-favoring additional noncovalent interactions.
Article
Automation & Control Systems
Vivek Singh Baghel, Syed Sadaf Ali, Surya Prakash
Summary: The unalterable nature of fingerprint biometrics leads to permanent identity loss if an original fingerprint template is compromised. Reconstructing a fingerprint image from the original template is feasible. To protect the template, a noninvertible and alignment-free technique is proposed, which generates a secure fingerprint template in the form of binary vectors using the pair-polar minutiae structures. The results show the effectiveness of the proposed technique compared to existing state-of-the-art methods.
IEEE TRANSACTIONS ON INDUSTRIAL INFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Yuan Zhuang, Jiangle Liu, Hao Wu, Qingguo Zhu, Yongchang Yan, Haowei Meng, Peng R. Chen, Chengqi Yi
Summary: The HOPE method utilizes paired pegRNAs encoding the same edits to achieve high editing efficiency in human embryonic kidney and colorectal carcinoma cells, showing improved product purity compared to the original PE3 system. This enhanced tool has the potential to broaden both fundamental research and therapeutic applications of prime editing.
NATURE CHEMICAL BIOLOGY
(2022)
Article
Chemistry, Analytical
Rodtichoti Wannapob, Surachada Chuaychob, Masahiro Fujita, Mizuo Maeda
Summary: Electrochemical impedance spectroscopy (EIS) was utilized to detect non-Watson-Crick base pairs of DNA, where a significant increase in charge-transfer resistance (Rct) was observed for terminal base mismatches but not internal base mismatches. Moreover, unpaired and overhang DNA at the terminal were found to hinder charge transfer to the electrode surface through EIS measurements. Additionally, the steric properties of DNA strands were successfully detected using EIS.
ANALYTICAL SCIENCES
(2021)
Article
Chemistry, Organic
Min-Xuan Zhang, Hung-Te Cheng, Sheng-Hsien Chiu
Summary: Malonate diesters can thread into a di(ethylene glycol)-containing macrocycle with the templating effect of a Na+ ion, and rotaxanes can be synthesized efficiently by applying several stoppering reactions. A molecular switch was constructed using this recognition system, in which the interlocked macrocycle can be moved between two rarely used stations (malonate and TAA) by acid/base addition and the presence/absence of Na+ ions.
Article
Cell Biology
Jonathan Barroso-Gonzalez, Laura Garcia-Exposito, Pablo Galaviz, Michelle Lee Lynskey, Joshua A. M. Allen, SongMy Hoang, Simon C. Watkins, Hilda A. Pickett, Roderick J. O'Sullivan
Summary: Alternative lengthening of telomeres (ALT) is a telomere-elongation mechanism observed in 15% of cancer subtypes. Disruption of the MutSa DNA mismatch repair complex leads to striking telomere hyperextension in ALT cells. MutSa is specifically recruited to telomeres in ALT cells by associating with the PCNA subunit of the replisome, counteracting the role of BLM helicase in stabilizing hyper-extended telomeres and maintaining the survival of MutSa-deficient ALT cancer cells.
Article
Chemistry, Multidisciplinary
Hermann Neitz, Irene Bessi, Valentin Kachler, Manuela Michel, Claudia Hoebartner
Summary: This study demonstrates the use of tolane-perfluorotolane interaction as a base pair replacement in DNA by modifying the DNA backbone. Thermodynamic analyses show that only THH/TFF heteropairs connected to the BuNA backbone significantly stabilize the DNA duplex, while no such effect is observed with the shorter GNA linker. NMR studies confirm the preference of the BuNA backbone for enhanced polar pi-stacking. This work defines the principles of tailoring orthogonal supramolecular interactions by small structural changes in the DNA backbone and inspires future studies of arene-fluoroarene-programmed assembly of DNA.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Arya Arun, Andrew Docker, Hui Min Tay, Paul D. Beer
Summary: A series of squaramide-based heteroditopic [2]rotaxanes have been synthesized using a template-directed stoppering method, highlighting the coordination of the Lewis basic squaramide carbonyls with sodium cation templates. The [2]rotaxanes exhibit enhanced binding strengths for bromide and iodide ions due to the ambidentate nature of the squaramide axle motif. The length and nature of the polyether cation binding unit of the macrocycle component significantly affect the ion-pair binding affinities of the [2]rotaxanes.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Xuemin Chen, Yanxiang Cui, Robert B. Best, Huaibin Wang, Z. Hong Zhou, Wei Yang, Martin Gellert
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2020)
Review
Biochemistry & Molecular Biology
Yang Gao, Wei Yang
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2020)
Article
Multidisciplinary Sciences
Woo Suk Choi, Peng He, Arti Pothukuchy, Jimmy Gollihar, Andrew D. Ellington, Wei Yang
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Biochemistry & Molecular Biology
Xuemin Chen, Xiang Xu, Yun Chen, Joyce C. Cheung, Huaibin Wang, Jiansen Jiang, Natalia de Val, Tara Fox, Martin Gellert, Wei Yang
Summary: This study reports cryo-EM structures of DNA-PK in both inactive and activated forms bound to DNA end or complexed with Ku70/80 and DNA, revealing the sequential transition of DNA-PK from inactive to activated forms. Activation of the kinase involves unprecedented stretching and twisting within individual solenoid segments, indicating a general regulatory mechanism of HEAT-repeat proteins.
Article
Biochemistry & Molecular Biology
Woo Suk Choi, Bochao Liu, Zhiyuan Shen, Wei Yang
Summary: BCCIP was isolated based on its interactions with tumor suppressors BRCA2 and p21, and deficiency of BCCIP resulted in embryonic lethality in mice with impaired cell proliferation and chromosome instability. Structurally, BCCIP is similar to GCN5-related acetyltransferases (GNATs) but with different sequence motifs, and it may have potential binding sites for partner proteins and enzymatic activity.
Article
Cell Biology
Janice Ortega, Grace Sanghee Lee, Liya Gu, Wei Yang, Guo-Min Li
Summary: The study reveals that the sliding of MutS alpha is necessary for mismatch removal in MMR, MutS alpha recruits MutL alpha to form a mismatch-bound complex and initiates MMR by nicking the daughter strand 5' to the mismatch, Exo1 conducts excision, solving the mechanism of MMR initiation and mispair removal.
Article
Biochemistry & Molecular Biology
Alexandra Vaisman, Krystian Lazowski, Martin A. M. Reijns, Erin Walsh, John P. McDonald, Kristiniana C. Moreno, Dominic R. Quiros, Marlen Schmidt, Harald Kranz, Wei Yang, Karolina Makiela-Dzbenska, Roger Woodgate
Summary: The Escherichia coli dnaE gene encodes the alpha-catalytic subunit of DNA polymerase III, with the study focusing on the role of residues H760 and S759 in maintaining genome stability. Out of 38 mutants created, only nine were successfully sub-cloned, with three having substitutions at H760 and six having substitutions at S759. Further characterization revealed altered phenotypes in terms of deoxyribonucleotide base selectivity and ribonucleotide discrimination for certain alleles.
MOLECULAR MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Mark T. Gregory, Yang Gao, Qiang Cui, Wei Yang
Summary: Through mutagenesis and structural analysis, researchers delineated the entities surrounding the nucleophile 3'-OH in the reaction catalyzed by DNA polymerase Pol eta, revealing details of the deprotonation process. The study found that the conserved S113 residue stabilizes the primer end by forming a hydrogen bond with the primer 3'-OH in the ground state, and mutation of S113 to alanine reduces catalytic efficiency.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Biochemistry & Molecular Biology
Ayslan Castro Brant, Wei Tian, Vladimir Majerciak, Wei Yang, Zhi-Ming Zheng
Summary: SARS-CoV-2 is a highly contagious respiratory virus causing adult atypical pneumonia COVID-19 with severe acute respiratory syndrome (SARS). This virus enters susceptible cells and directly translates polyproteins to initiate viral genome replication and transcription.
CELL AND BIOSCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Xuemin Chen, Martin Gellert, Wei Yang
Summary: RAG is an RNH-type DNA recombinase evolved to initiate V(D)J gene rearrangement, with crystal structure and biochemical studies shedding light on its evolution from an ordinary transposase to a specialized recombinase.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Lan Liu, Xuemin Chen, Jun Li, Huaibin Wang, Christopher J. Buehl, Noah J. Goff, Katheryn Meek, Wei Yang, Martin Gellert
Summary: DNA-PK plays a dual role in DNA damage repair by protecting and processing broken DNA ends. The type of DNA ends regulates the kinase activity and autophosphorylation of DNA-PK, which in turn coordinate non-homologous end joining (NHEJ) events.
Article
Multidisciplinary Sciences
Woo Suk Choi, Peter J. Weng, Wei Yang
Summary: Telomerase synthesizes telomeres at the ends of linear chromosomes by reverse transcription from a short RNA template. In this study, the potential of the structural cavity of tcTERT to accommodate a looped-out DNA bulge and enable the separation of the RNA/DNA hybrid was investigated. It was found that tcTERT can accommodate and extend a looped-out telomeric repeat in the DNA primer, but retroviral reverse transcriptase cannot. The ternary-complex structure of tcTERT with a downstream RNA/DNA hybrid was also determined, and it was shown to enhance the efficiency of telomere synthesis by tcTERT. Overall, flexible RNA-DNA binding plays a crucial role in telomeric repeat addition.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Xi Yang, Sourav Saha, Wei Yang, Keir C. Neuman, Yves Pommier
Summary: This study elucidates the biochemical mechanisms of human TOP3B, highlighting its differential roles in DNA and RNA catalysis, as well as the impact of regulatory factors on its catalytic performance.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Christopher J. Buehl, Noah J. Goff, Steven W. Hardwick, Martin Gellert, Tom L. Blundell, Wei Yang, Amanda K. Chaplin, Katheryn Meek
Summary: Non- homologous end joining is the main pathway for repairing double-strand breaks in mammals. DNA-PK plays a central role in orchestrating multiple steps in non- homologous end joining. Recent structural studies have revealed two distinct NHEJ complexes that mediate the synapsis of DNA ends. One complex involves a DNA-PK dimer mediated by XLF, while the other complex forms through a domain-swap mechanism involving interaction between the C terminus of Ku80 from one DNA-PK protomer and another DNA-PK protomer. The distance between the synapsed DNA ends in both complexes is the same, suggesting a conserved long-range synaptic complex. A mutational strategy has shown that these two dimers have distinct cellular functions, with one promoting fill-in end processing and the other promoting DNA end resection. The specific DNA-PK dimer formed determines the mechanism by which the ends can be ligated, and this may be influenced by the structure of the DNA ends.
Article
Multidisciplinary Sciences
Jinseok Kim, Chia-Lung Li, Xuemin Chen, Yanxiang Cui, Filip M. Golebiowski, Huaibin Wang, Fumio Hanaoka, Kaoru Sugasawa, Wei Yang
Summary: Nucleotide excision repair is responsible for removing DNA lesions caused by ultraviolet light, cisplatin-like compounds, and bulky adducts. This study reveals the structures of human XPC recognizing DNA lesions and transferring them to the TFIIH core complex for verification and further repair.
