Article
Genetics & Heredity
Gustavo Carvalho, Alberto Diaz-Talavera, Patricia A. Calvo, Luis Blanco, Maria I. Martinez-Jimenez
Summary: PrimPol, a crucial enzyme for DNA replication, shows a strong preference for incorporating dNTPs over ddNTPs to prevent premature termination of primers, as demonstrated by its crystal structure and interactions with specific residues such as Arg(291).
Article
Multidisciplinary Sciences
Xiang Feng, Michelle M. Spiering, Ruda de Luna Almeida Santos, Stephen J. Benkovic, Huilin Li
Summary: The authors demonstrate the assembly process of the T4 primosome, consisting of gp41 helicase and gp61 primase, using cryo-EM structures. They show that gp41 undergoes a conformational change upon ssDNA binding, leading to ring closure and helicase activation. The activated helicase recruits the gp61 primase through a bipartite binding mode, resulting in the assembly of the primosome on the helicase hexamer.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Zuanning Yuan, Roxana Georgescu, Huilin Li, Michael E. E. O'Donnell
Summary: DNA polymerase α has separate RNA and DNA polymerase subunits to form a unique-length RNA-DNA primer. Cryo-EM structures of each stage in primer synthesis reveal large conformational changes among the four subunits and explain how primer length is limited.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Arthur W. H. Li, Katerina Zabrady, Lewis J. Bainbridge, Matej Zabrady, Sehr Naseem-Khan, Madison B. Berger, Peter Kolesar, G. Andres Cisneros, Aidan J. Doherty
Summary: This study reveals the molecular mechanism of how primases initiate primer synthesis, which is conserved in replicative primases and CRISPR-associated primase-polymerases. The study also shows that the catalytic domain of primases is sufficient for primer formation.
Review
Biochemistry & Molecular Biology
Katerina Zabrady, Arthur W. H. Li, Aidan J. Doherty
Summary: Members of the Prim-Pol superfamily are widely present in various species and play important roles in maintaining genome stability. This review focuses on Prim-Pol members with experimentally established structural models, discussing the mechanisms of DNA primer synthesis initiation and the involvement of ancillary domains/subunits. A general model for primer initiation is also proposed, considering the stimulatory effects of these domains/subunits.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Victor Juarez-Quintero, Antolin Peralta-Castro, Claudia G. Benitez Cardoza, Tom Ellenberger, Luis G. Brieba
Summary: The crystal structure of full-length T7 DNA polymerase reveals two novel structural motifs and highlights the importance of insertion1 in the exonuclease domain.
BIOCHEMICAL JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Daryl M. Gohl, Benjamin Auch, Amanda Certano, Brice LeFrancois, Anne Bouevitch, Evgueni Doukhanine, Christina Fragel, Jean Macklaim, Emily Hollister, John Garbe, Kenneth B. Beckman
Summary: Proofreading polymerases have the ability to correct errors during DNA replication and edit PCR primers to match template sequences. The editing activity can be measured and compared using synthetic DNA standards, revealing editing extent and effects of different polymerases and cycling conditions. Additionally, primer editing can be tuned by incorporating phosphorothioate linkages and has the potential to rescue mismatches in 16S rRNA gene-targeting primers in microbiome analysis.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Chemistry, Multidisciplinary
Diego Nunez-Villanueva, Christopher A. Hunter
Summary: The template-directed synthesis of nucleic acids in the polymerase chain reaction was achieved by attaching a high affinity primer to a mixed sequence template. The study demonstrated a substantial template effect through H-bonding interactions between the phenols on the template and phosphine oxides on the azide. The use of a compound with multiple H-bonding capability resulted in the highest rate acceleration.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Multidisciplinary Sciences
Aniko Mentes, Krisztian Papp, David Visontai, Jozsef Steger, Istvan Csabai, Anna Medgyes-Horvath, Orsolya Anna Pipek
Summary: Due to the increasing mutations in the SARS-CoV-2 genome, we propose an analysis pipeline to identify genomic variations in PCR target regions. We provide a publicly available list of these mutations based on a large dataset. Our approach distinguishes between mutations that may impact PCR efficiency and those that are likely neutral. Samples are categorized based on the estimated effect of mutations, indicating the likelihood of misclassification. Constant monitoring of variations in primer target regions is recommended as different variant strains may change the efficiency of PCR primer sets over time.
SCIENTIFIC REPORTS
(2022)
Review
Biochemistry & Molecular Biology
Lewis J. Bainbridge, Katerina Zabrady, Aidan J. Doherty
Summary: To pass on genetic information to the next generation, cells need to accurately replicate their genomes. This process is aided by enzymes called DNA polymerases, which replicate nucleic acid polymers. However, most polymerases require specialized replicases called primases to initiate DNA synthesis by creating short polynucleotide primers. Replicative primases belong to a diverse enzyme superfamily known as Primase-Polymerases (Prim-Pols), which play important roles in DNA metabolism. This review examines the catalytic mechanisms utilized by Prim-Pols to initiate primer synthesis.
BIOSCIENCE REPORTS
(2023)
Article
Biochemistry & Molecular Biology
Christina N. Giramma, McKenna B. DeFoer, Jue D. Wang
Summary: Primase plays a crucial role in DNA replication by synthesizing RNA primers, and its activity in bacteria can be regulated by (p)ppGpp. The presence of (p)ppGpp in Bacillus subtilis inhibits DNA replication, particularly primer extension, to ensure genome stability under environmental stress. High levels of (p)ppGpp, combined with low GTP concentration, effectively suppress primase activity in B. subtilis.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Computer Science, Software Engineering
Madhavi Latha Yadav Bangaru, Ravi Kumar Medabalimi, Sobhan Babu, Nidhanapati K. Raghavendra
Summary: Silent mutations allowing for restriction site modification can aid in screening successful mutants during site-directed mutagenesis. However, introducing a new restriction site requires the analysis of degenerate sequences within mutant primers, which becomes increasingly laborious, time-consuming, and prone to errors as the number of degenerate codons increases. A software named 'REMP' was developed to instantly generate degenerate sequences with restriction sites that are 6-8 base pairs in length, allowing users to edit the list of restriction sites without the need for writing computer code or knowing a program language.
Article
Biochemistry & Molecular Biology
Yi-Chen Tsai, Wen-Yih Chen, Chi-cheng Chiu
Summary: Polymerase chain reaction (PCR) is a powerful molecular biology assay for gene detection and quantification. Oligonucleotides containing methyl phosphotriester (MPTE-DNA) have been developed with enhanced DNA hybridization and improved gene detection sensitivity. However, the site-specific methylation of DNA primers affects PCR amplification efficiencies, and the detailed mechanism is still unknown.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Linhong Ning, Yuanhong Li, Zhimei Zhang, Yuan Zhou, Li Yang, Qinghai Yu, Feng Yu, Zehui Tong
Summary: MicroRNAs (MiRNAs) are key regulators of gene expression and important biomarkers for disease diagnosis. This study developed a label-free and sensitive miRNA detection method using primer exchange reaction (PER) and DNA-templated silver nanoclusters (AgNCs). The method achieved low detection limit and wide dynamic range, and demonstrated promising clinical application by detecting miRNA-31 expression in pancreatitis patients.
APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY
(2023)
Article
Biophysics
Xudan Shen, Mingcheng Xu, Hechen Wang, Hua Wang, Minzhe Shen, Jadera Talap, Haihong Hu, Su Zeng, Shunxiang Gao, Sheng Cai
Summary: Researchers have developed a novel PS-LAMP assay for detecting DNA methylation levels in samples from renal cell carcinoma patients. The assay outperforms traditional methods and offers a noninvasive way to detect methylation in various biological samples.
BIOSENSORS & BIOELECTRONICS
(2023)
Article
Genetics & Heredity
Maxwell R. Mumbach, Ansuman T. Satpathy, Evan A. Boyle, Chao Dai, Benjamin G. Gowen, Seung Woo Cho, Michelle L. Nguyen, Adam J. Rubin, Jeffrey M. Granja, Katelynn R. Kazane, Yuning Wei, Trieu Nguyen, Peyton G. Greenside, M. Ryan Corces, Josh Tycko, Dimitre R. Simeonov, Nabeela Suliman, Rui Li, Jin Xu, Ryan A. Flynn, Anshul Kundaje, Paul A. Khavari, Alexander Marson, Jacob E. Corn, Thomas Quertermous, William J. Greenleaf, Howard Y. Chang
Article
Biology
Kunwoo Lee, Vanessa A. Mackley, Anirudh Rao, Anthony T. Chong, Mark A. Dewitt, Jacob E. Corn, Niren Murthy
Article
Genetics & Heredity
Chris D. Richardson, Katelynn R. Kazane, Sharon J. Feng, Elena Zelin, Nicholas L. Bray, Axel J. Schafer, Stephen N. Floor, Jacob E. Corn
Article
Multidisciplinary Sciences
Mikaela D. Stewart, Elena Zelin, Abhinav Dhall, Tom Walsh, Esha Upadhyay, Jacob E. Corn, Champak Chatterjee, Mary-Claire King, Rachel E. Klevit
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2018)
Article
Biochemistry & Molecular Biology
Jin-Soo Kim, Jacob E. Corn
Article
Biochemistry & Molecular Biology
Beeke Wienert, Jiyung Shin, Elena Zelin, Kathleen Pestal, Jacob E. Corn
Article
Cell Biology
Jin Rui Liang, Emily Lingeman, Saba Ahmed, Jacob E. Corn
JOURNAL OF CELL BIOLOGY
(2018)
Review
Cell Biology
Charles D. Yeh, Christopher D. Richardson, Jacob E. Corn
NATURE CELL BIOLOGY
(2019)
Article
Biochemistry & Molecular Biology
Jin Rui Liang, Emily Lingeman, Thao Luong, Saba Ahmed, Matthias Muhar, Truc Nguyen, James A. Olzmann, Jacob E. Corn
Article
Biochemical Research Methods
Beeke Wienert, Stacia K. Wyman, Charles D. Yeh, Bruce R. Conklin, Jacob E. Corn
Article
Multidisciplinary Sciences
John C. Rose, Nicholas A. Popp, Christopher D. Richardson, Jason J. Stephany, Julie Mathieu, Cindy T. Wei, Jacob E. Corn, Dustin J. Maly, Douglas M. Fowler
NATURE COMMUNICATIONS
(2020)
Article
Biochemical Research Methods
Sebastian M. Siegner, Mehmet E. Karasu, Markus S. Schroder, Zacharias Kontarakis, Jacob E. Corn
Summary: PnB Designer is a web-based application that simplifies the design of pegRNAs for PEs and guide RNAs for BEs, allowing for easy design of targeting guide RNAs for single or multiple targets on variant or reference genomes. It can also be used to design guide RNAs to install or revert SNVs, scanning the genome with different ABE PAM variants and returning the best BE to use.
BMC BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
Lukas Moeller, Eric J. Aird, Markus S. Schroeder, Lena Kobel, Lucas Kissling, Lilly van de Venn, Jacob E. Corn
Summary: This study presents a HDR improvement strategy called Recursive Editing, which selectively retargets undesired indel outcomes to create more opportunities for HDR. The authors introduce a software tool called REtarget for the design of Recursive Editing experiments. By using REtarget-designed guide RNAs, Recursive Editing can simultaneously enhance HDR efficiency and reduce undesired indels. This approach proves to be easy to use and has little experimental burden.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Sebastian M. Siegner, Laura Ugalde, Alexandra Clemens, Laura Garcia-Garcia, Juan A. Bueren, Paula Rio, Mehmet E. Karasu, Jacob E. Corn
Summary: This article presents a gene editing strategy using base editors to correct pathogenic gene mutations in Fanconi Anemia patients' stem cells. The experimental results demonstrate that optimized base editing can restore gene expression and function, indicating the therapeutic potential for Fanconi Anemia.
NATURE COMMUNICATIONS
(2022)
Article
Biology
Mandy Y. Boontanrart, Elia Machler, Simone Ponta, Jan C. Nelis, Viviana G. Preiano, Jacob E. Corn
Summary: The ss-hemoglobinopathies, such as sickle cell disease and ss-thalassemia, can be treated by increasing the expression of delta-globin through gene editing techniques. This offers a new therapeutic approach for these genetic diseases.