Article
Biochemistry & Molecular Biology
Hui Yang, Elena Eremeeva, Mikhail Abramov, Maarten Jacquemyn, Elisabetta Groaz, Dirk Daelemans, Piet Herdewijn
Summary: An enzymatic method was developed to generate partially base-modified RNA constructs, as well as fully modified RNA constructs featuring multiple modified bases. The efficiency of the fully modified RNA constructs was enhanced by using different T7 RNA polymerase variants. The study also demonstrated the successful incorporation of modified bases into PCR products and the effectiveness of the modified RNA constructs in CRISPR-Cas9 cleavage assays.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Dillon B. Nye, Nathan A. Tanner
Summary: Recent advances in next generation sequencing technologies have made it possible to read DNA molecules hundreds of kilobases in length. This has motivated the development of DNA amplification methods capable of producing long amplicons. In this study, the researchers investigated strand-displacement amplification reactions using the T7 replisome, a multiprotein complex involved in DNA replication. They utilized Oxford Nanopore long-read sequencing technology to gain insight into the reaction mechanism. The results revealed chimeric DNA reads and a connection between template switching and polymerase exonuclease activity.
Article
Biochemistry & Molecular Biology
Stefan Schuetz, Christian Bergsdorf, Benedikt Goretzki, Andreas Lingel, Martin Renatus, Alvar D. Gossert, Wolfgang Jahnke
Summary: This study utilizes Nuclear Magnetic Resonance (NMR) spectroscopy and Surface Plasmon Resonance (SPR) to investigate the interactions between the proteins MYC and MAX, and their roles in regulating cellular processes.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Immunology
Sandra Eltschkner, Samantha Mellinger, Soren Buus, Morten Nielsen, Kajsa M. M. Paulsson, Karin Lindkvist-Petersson, Helena Westerdahl
Summary: Long-distance migratory animals such as birds and bats have evolved a unique adaptive immunity with highly duplicated Major Histocompatibility Complex (MHC) genes to withstand diverse pathogens. A study on the MHC class I protein, Acar3, from the great reed warbler reveals a peculiar peptide-binding mode that potentially facilitates interactions with innate immune receptors. The investigation highlights the importance of studying the immune system of wild animals to uncover unique immune mechanisms absent in humans and model organisms.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Xuezheng Wang, Yuantao Tang, Jiawei Xu, He Leng, Guojun Shi, Zaifeng Hu, Jiale Wu, Yuwen Xiu, Jianxun Feng, Qing Li
Summary: This study uncovers a new mechanism for parental histone recycling, revealing the important role of histone chaperone FACT and its N-terminus of the Spt16 subunit in budding yeast. The Spt16-N domain interacts with the replicative helicase MCM2-7, facilitating the formation of a critical ternary complex for efficient parental histone recycling and transfer to the lagging strand.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Analytical
Pinky Chowdhury, Byung Seok Cha, Seokjoon Kim, Eun Sung Lee, Taehwi Yoon, Jisu Woo, Ki Soo Park
Summary: In this study, a simple electrochemical biosensor was developed for the specific detection of KRAS gene mutation using the differential pulse voltammetry technique. The biosensor utilizes the mismatch-specific cleavage activity of T7E1 enzyme coupled with horseradish peroxidase to catalyze the oxidation reaction, enabling the detection of mutant genes. The use of a nanocomposite further enhances the electrochemical signal. The biosensor shows potential for the detection of mutations in early disease diagnosis.
Article
Biochemistry & Molecular Biology
Liudmila A. Abrosimova, Nikita A. Kuznetsov, Natalia A. Astafurova, Anastasiia R. Samsonova, Andrey S. Karpov, Tatiana A. Perevyazova, Tatiana S. Oretskaya, Olga S. Fedorova, Elena A. Kubareva
Summary: The interaction between Nt.BspD6I and DNA was studied using fast kinetics techniques for the first time, revealing the important role of divalent metal cations in complex formation at all steps. Specific binding of Nt.BspD6I to DNA was confirmed to be more efficient at its recognition site compared to random DNA, with DNA bending observed during substrate binding. The optimal size of Nt.BspD6I's binding site in DNA determined in this study should be considered in the detection methods of nucleic acid sequences and base modifications using NEs.
Article
Biophysics
Jiehan Chong, Dario De Vecchis, Adam J. Hyman, Oleksandr Povstyan, Melanie J. Ludlow, Jian Shi, David J. Beech, Antreas C. Kalli
Summary: Using computational methods, the three-dimensional structure of full-length Piezo1 was predicted, revealing a trilobed dome that extends beyond the radius of the protein in the membrane and preferential interactions with cholesterol and PIP2 molecules. These findings suggest the importance of N-terminal regions for Piezo1 function and interactions with the lipid bilayer.
BIOPHYSICAL JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Emma-Lucille Blayney, Milna Chennath, Charles G. Cranfield, Ronald J. Clarke
Summary: The Na+, K+-ATPase is an integral membrane protein that uses ATP hydrolysis to transport Na+ and K+ ions across the plasma membrane. It has essential roles in various physiological processes and is regulated through phosphorylation by protein kinase C (PKC) and Src kinase families. The study used the mirror tree method to analyze the coevolution between these kinases and Na+, K+-ATPase. The results suggested that the theta and eta isoforms of PKC and Src kinase are the most likely to interact with Na+, K+-ATPase. These findings will guide future experimental studies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Genetics & Heredity
Seibun Li, Mika Toya, Masamitsu Sato
Summary: The study introduced new vectors and selection markers, simplifying the genome editing process using CRISPR/Cas9 in fission yeast. By optimizing culture conditions and streamlining transformation procedures, the efficiency and convenience of genome editing were improved.
Article
Biochemistry & Molecular Biology
Artemiy S. Bakman, Stanislav S. Boichenko, Aleksandra A. Kuznetsova, Alexander A. Ishchenko, Murat Saparbaev, Nikita A. Kuznetsov
Summary: Base excision repair (BER) is an important system for maintaining genome stability by repairing DNA lesions. It involves multiple enzymes, including DNA glycosylases, endonucleases, DNA polymerase beta, and DNA ligase. Protein-protein interactions play a crucial role in coordinating BER, but their mechanisms and roles are poorly understood.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Ryan P. McGlinchey, Xiaodan Ni, Jared A. Shadish, Jiansen Jiang, Jennifer C. Lee
Summary: The study demonstrates that C-terminal truncations can accelerate the aggregation of alpha-synuclein, while the role of N-terminal truncations remains unclear. The research found that N-terminal truncations modulated the aggregation kinetics and fibril morphologies of alpha-synuclein.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Diana Romero-Zamora, Makoto T. Hayashi
Summary: In this study, it was found that WRN, a member of the RECQ helicase family, can suppress mitotic telomere deprotection independently of its exonuclease and helicase activities. The N-terminal amino acids 168-333 of WRN were identified as the region responsible for this suppressive effect. The suppressive activity of WRN is dependent on TRF2 and regulated by phosphorylation during mitotic arrest.
SCIENTIFIC REPORTS
(2023)
Article
Medicine, Research & Experimental
Lukas Villiger, Lukas Schmidheini, Nicolas Mathis, Tanja Rothgangl, Kim Marquart, Gerald Schwank
Summary: Base editors are RNA-guided deaminases that enable specific nucleotide transitions at target sites. By omitting the Cas9-HNH nuclease domain, researchers expanded the editing window and engineered adenine base editor variants with PAM-proximally shifted editing windows. This work not only broadens the targeting scope of base editors but also suggests potential future directions in Cas9 protein engineering by replacing the HNH domain with other enzymes acting on ssDNA.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2021)
Article
Multidisciplinary Sciences
Valentina Bonetto, Valeria Magnelli, Maurizio Sabbatini, Flavia Capri, Jack J. W. A. van Loon, Sara Tavella, Maria Angela Masini
Summary: In this study, it was found that exposure to hypergravity resulted in altered physiological performance of the testis, including changes in the structure of seminiferous tubules and decreased expression of key receptors. These alterations may lead to a reduction in sperm count and changes in endocrine parameters.
Article
Cell Biology
Yijin Liu, Alasdair D. J. Freeman, Anne-Cecile Declais, Timothy J. Wilson, Anton Gartner, David M. J. Lilley
Article
Biochemistry & Molecular Biology
Alasdair D. J. Freeman, Michael Stevens, Anne-Cecile Declais, Adam Leahy, Katherine Mackay, Hassane El Mkami, David M. J. Lilley, David G. Norman
Article
Biochemistry & Molecular Biology
Craig MacKay, Anne-Cecile Declais, Cecilia Lundin, Ana Agostinho, Andrew J. Deans, Thomas J. MacArtney, Kay Hofmann, Anton Gartner, Stephen C. West, Thomas Helleday, David M. J. Lilley, John Rouse
Review
Biochemistry & Molecular Biology
Anne-Cecile Declais, David M. J. Lilley
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2008)
Article
Biochemistry & Molecular Biology
Anais Poulet, Remi Buisson, Cendrine Faivre-Moskalenko, Melanie Koelblen, Simon Amiard, Fabien Montel, Santiago Cuesta-Lopez, Olivier Bornet, Francoise Guerlesquin, Thomas Godet, Julien Moukhtar, Francoise Argoul, Anne-Cecile Declais, David M. J. Lilley, Stephen C. Y. Ip, Stephen C. West, Eric Gilson, Marie-Josephe Giraud-Panis
Article
Biochemistry & Molecular Biology
Alasdair D. J. Freeman, Yijin Liu, Anne-Cecile Declais, Anton Gartner, David M. J. Lilley
JOURNAL OF MOLECULAR BIOLOGY
(2014)
Article
Biochemistry & Molecular Biology
Ivan M. Munoz, Karolina Hain, Anne-Cecile Declais, Mary Gardiner, Geraldine W. Toh, Luis Sanchez-Pulido, Johannes M. Heuckmann, Rachel Toth, Thomas Macartney, Berina Eppink, Roland Kanaar, Chris P. Ponting, David M. J. Lilley, John Rouse
Article
Biochemistry & Molecular Biology
Dennis Castor, Nidhi Nair, Anne-Cecile Declais, Christophe Lachaud, Rachel Toth, Thomas J. Macartney, David M. J. Lilley, J. Simon C. Arthur, John Rouse
Article
Biochemistry & Molecular Biology
Yijin Liu, Alasdair D. J. Freeman, Anne-Cecile Declais, David M. J. Lilley
NUCLEIC ACIDS RESEARCH
(2018)
Article
Cell Biology
Simon Pennell, Anne-Cecile Declais, Jiejin Li, Lesley F. Haire, Wioletta Berg, Jose W. Saldanha, Ian A. Taylor, John Rouse, David M. J. Lilley, Stephen J. Smerdon
Article
Genetics & Heredity
Aymeric P. Bailly, Alasdair Freeman, Julie Hall, Anne-Cecile Declais, Arno Alpi, David M. J. Lilley, Shawn Ahmed, Anton Gartner
Article
Biochemistry & Molecular Biology
Ruobo Zhou, Olivia Yang, Anne-Cecile Declais, Hyeonseok Jin, Gwang Hyeon Gwon, Alasdair D. J. Freeman, Yunje Cho, David M. J. Lilley, Taekjip Ha
NATURE CHEMICAL BIOLOGY
(2019)
Article
Multidisciplinary Sciences
Artur P. Kaczmarczyk, Anne-Cecile Declais, Matthew D. Newton, Simon J. Boulton, David M. J. Lilley, David S. Rueda
Summary: This study captures the entire reaction trajectory of a nuclease targeting and resolving a DNA junction at single-molecule level. The results show that the enzyme first binds remotely to dsDNA and undergoes 1D diffusion before cleaving the junction upon encountering it.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Alasdair D. J. Freeman, Anne-Cecile Declais, Timothy J. Wilson, David M. J. Lilley
Summary: ANKLE1 is a GIY-YIG nuclease that processes unresolved junctions in DNA to prevent chromosomal linkages that block cell division. By studying an active domain of human ANKLE1, we found that it unilaterally cleaves cruciform junctions and its activity is impaired when key active residues are mutated. The catalytic mechanism involves pH dependence, divalent cation binding, and temperature dependence, suggesting general acid-base catalysis with involvement of histidine, glutamate, asparagine, and water coordinated to the metal ion.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Ankita Chadda, Alexander G. Kozlov, Binh Nguyen, Timothy M. Lohman, Eric A. Galburt
Summary: In this study, it was found that the DNA damage response in Mycobacterium tuberculosis differs from well-studied model bacteria. The DNA repair helicase UvrD1 in Mtb is activated through a redox-dependent process and is closely associated with the homo-dimeric Ku protein. Additionally, Ku protein is shown to stimulate the helicase activity of UvrD1.
JOURNAL OF MOLECULAR BIOLOGY
(2024)