Article
Virology
Elizabeth T. Ogunbunmi, Samuel D. Love, Katherine A. Rhodes, Adriana Morales, Margaret H. Wilch, Jeremy Jonas, Bentley A. Fane
Summary: The production of enzymes, transcription factors, and viral receptors directly influences the niches viruses can inhabit. Some prokaryotic hosts can thrive in widely differing environments, including considerations of temperature and physical parameters. These variables may directly alter host physiology, preventing viral replication. Alternatively, they could negatively inhibit infection processes in a host-independent manner. The members of three sister Microviridae genera (canonical species oX174, G4 and alpha 3) infect the same host, but alpha 3-like viruses are naturally cold sensitive, which could effectively exclude them from low-temperature environments (<28 degrees C). Exclusion appeared to be independent of host cell physiology. Instead, it could be largely attributed to low-temperature packaging defects. The results presented here demonstrate how physical parameters, such as temperature, can directly influence viral diversification and niche determination in a host-independent manner.
JOURNAL OF VIROLOGY
(2022)
Article
Virology
Elizabeth T. Ogunbunmi, Aaron P. Roznowski, Bentley A. Fane
Summary: Most icosahedral viruses condense their genomes into volume-constrained capsids, but ssDNA viruses have specific genome biosynthesis and packaging mechanisms. The packaging of ssDNA genomes combines elements from both dsDNA and ssRNA systems, potentially affecting both packaging and postpackaging phenomena.
JOURNAL OF VIROLOGY
(2021)
Article
Chemistry, Multidisciplinary
Itaru Yanagi, Rena Akahori, Ken-ichi Takeda
Summary: The study investigated the ionic current blockades when poly-(dT)(60) or dNTPs passed through SiN nanopores in an aqueous solution containing (NH4)(2)SO4. The dwell time of poly-(dT)(60) and dCTP in the nanopores was significantly longer in the aqueous solution containing (NH4)(2)SO4 compared to the solution without it. The prolonged dwell time effect was also observed when the nanopores were fabricated via dielectric breakdown in the aqueous solution containing (NH4)(2)SO4 and remained even after replacing the solution with one without (NH4)(2)SO4. Furthermore, the four types of dNTPs could be statistically identified based on their current blockade values when passed through the same nanopore.
Article
Multidisciplinary Sciences
Jae Young Lee, Heeyuen Koh, Do-Nyun Kim
Summary: This study presents a computational framework for analyzing the equilibrium and non-equilibrium dynamics of structured DNA assemblies. The framework successfully simulates the dynamic reconfiguration of DNA structures in response to changes in ion concentration. This research offers a rational method for designing responsive and reconfigurable DNA machines.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Yoav Shamir, Amir Goldbourt
Summary: F-specific filamentous phages undergo an intermediate step where gVp homodimers bind to newly synthesized DNA strands, preparing the circular genome for assembly. We report the atomic-resolution structure of the gVp monomer bound to ssDNA of fd phage, which shows significant conformational changes and facilitates the binding mechanism. This study provides insights into the assembly process of the gVp-ssDNA complex.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Yoav Shamir, Amir Goldbourt
Summary: The atomic-resolution structure of the gVp monomer bound to ssDNA of fd phage in the nucleoprotein complex has been elucidated via magic-angle spinning solid-state NMR. The study reveals significant conformational changes of gVp monomer upon ssDNA binding, which may facilitate the binding mechanism.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Multidisciplinary
Victoria E. Paluzzi, Cuizheng Zhang, Chengde Mao
Summary: Small ssDNA circles are difficult to prepare, as they often form concatemers instead of monomeric circles. This study presents a simple method to overcome this problem by designing complementary linker molecules. The method allows for the enzymatic ligation of ssDNA as short as 16 nts into monomeric circles at high concentration and high yield.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
Lei Tian, Keli Zhu, Yuanyuan Chen, Xiaowei Zheng, Heng Zhang, Zhi Geng, Wenqian Li, Niannian Ding, Jingyu Chen, Yuhui Dong, Peng Cao, Yong Gong, Zhenfeng Zhang
Summary: The KTSC domain containing proteins are widely distributed in different organisms, but their function is still uncertain. This study characterizes Mvu8s protein from Methanolobus vulcani and shows its specific binding to single-stranded DNA. The crystal structure of Mvu8s reveals its homo-tetramer arrangement and the mechanism of single-stranded DNA wrapping.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Biochemical Research Methods
Kilian Vogele, Elisabeth Falgenhauer, Sophie von Schonberg, Friedrich C. Simmel, Tobias Pirzer
Summary: Cell-free systems allow interference with gene expression processes using small DNA molecules complementary to the mRNA, achieving significant reduction in gene expression. This technique was successfully applied to modulate gene expression from the native T7 phage genome, leading to improved gene replication and amplification in droplet-based experiments.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Yoshiya Kikukawa, Ryoji Kawazoe, Ryo Miyahara, Takato Sakurada, Yusuke Nagata, Shigeki Sasaki, Yosuke Taniguchi
Summary: In this study, a method for detecting the presence of 8-oxo-2'-deoxyguanosine in DNA was developed, and the signal was successfully amplified. This has important implications for elucidating the pathogenesis of various diseases.
CHEMICAL COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Simone Altmann, Eva Rico, Sandra Carvalho, Melanie Ridgway, Anna Trenaman, Hannah Donnelly, Michele Tinti, Susan Wyllie, David Horn
Summary: This study reports a simple method for rapid and precise editing of priority drug targets in trypanosomatids. By targeting and editing drug targets, combined with sequencing technology, potential impacts on drug efficacy can be assessed quickly.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Yanhong Liu, Linsheng Zhang, Maochao Guo, Liu Chen, Baixing Wu, Hongda Huang
Summary: The study reveals that phages have evolved Aca1 and Aca2 proteins to inhibit host CRISPR-Cas systems by binding to acr-aca promoters. The structural basis for the repression roles of Aca proteins is elucidated, shedding light on the repression roles of other Aca family proteins and the autoregulation roles of acr-aca operons.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Review
Biochemistry & Molecular Biology
Jun-Tao Guo, Fareeha Malik
Summary: Single-stranded DNA binding proteins (SSBs) play critical roles in maintaining genome stability and transcriptional regulation, and machine learning-based approaches have been developed for predicting SSBs from double-stranded DNA binding proteins (DSBs).
Article
Chemistry, Physical
Xun Gong, Nicholas Renegar, Retsef Levi, Michael S. Strano
Summary: Nanoparticle corona phase design allows for molecular recognition for sensing applications. In this study, the largest DNA-SWCNT PL response library was generated and machine learning techniques were utilized to understand the dependence of molecular recognition and DNA sequence.
NPJ COMPUTATIONAL MATERIALS
(2022)
Article
Biochemistry & Molecular Biology
Amedeo Capobianco, Alessandro Landi, Andrea Peluso
Summary: Molecular dynamics simulations and quantum mechanical/molecular mechanics methods predict that short, single-stranded DNA oligonucleotides adopt conformations similar to crystallographic B-DNA in solution. Single strands rich in adjacent purine nucleobases have more regular arrangements, and poly-thymine single strands also retain helical structure in solution.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Akito Kawai, Shigesada Higuchi, Masaru Tsunoda, Kazuo T. Nakamura, Yuriko Yamagata, Shuichi Miyamoto
Article
Biochemical Research Methods
Kaoru Suzuki, Shi-Yuan Yang, Satoru Shimizu, Ella Czarina Morishita, Jiandong Jiang, Fang Zhang, Md. Mominul Hoque, Yoshiteru Sato, Masaru Tsunoda, Takeshi Sekiguchi, Akio Takenaka
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2011)
Article
Biochemical Research Methods
M. Mominul Hoque, Kaoru Suzuki, Masaru Tsunoda, Jiandong Jiang, Fang Zhang, Atsushi Takahashi, Naomi Ohbayashi, Xiaoxue Zhang, Haruo Tanaka, Satoshi Omura, Akio Takenaka
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
(2012)
Article
Biochemical Research Methods
Kaoru Suzuki, Satoru Shimizu, Ella Czarina Magat Juan, Takahiro Miyamoto, Zhang Fang, Md. Mominul Hoque, Yoshiteru Sato, Masaru Tsunoda, Takeshi Sekiguchi, Akio Takenaka, Shi-Yuan Yang
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS
(2010)
Article
Biochemical Research Methods
Akito Kawai, Shigesada Higuchi, Masaru Tsunoda, Kazuo T. Nakamura, Shuichi Miyamoto
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS
(2012)
Article
Biochemical Research Methods
Kaoru Suzuki, Naomi Ohbayashi, Jiandong Jiang, Xiaoxue Zhang, M. Mominul Hoque, Masaru Tsunoda, Kazutaka Murayama, Haruo Tanaka, Akio Takenaka
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS
(2012)
Article
Biochemistry & Molecular Biology
Fang Zhang, Mominul M. Hoque, Jiandong Jiang, Kaoru Suzuki, Masaru Tsunoda, Yoichi Takeda, Yukishige Ito, Gota Kawai, Haruo Tanaka, Akio Takenaka
Article
Biotechnology & Applied Microbiology
Atsushi Takahashi, Junji Inokoshi, Masaru Tsunoda, Kaoru Suzuki, Akio Takenaka, Takeshi Sekiguchi, Satoshi Omura, Haruo Tanaka
JOURNAL OF ANTIBIOTICS
(2010)
Article
Biochemistry & Molecular Biology
Akito Kawai, Hiroshi Hashimoto, Shigesada Higuchi, Masaru Tsunoda, Mamoru Sato, Kazuo T. Nakamura, Shuichi Miyamoto
JOURNAL OF STRUCTURAL BIOLOGY
(2011)
Article
Biochemistry & Molecular Biology
Ella Czarina Magat Juan, Satoru Shimizu, Xiao Ma, Taizo Kurose, Tsuyoshi Haraguchi, Fang Zhang, Masaru Tsunoda, Akihiro Ohkubo, Mitsuo Sekine, Takayuki Shibata, Christopher L. Millington, David M. Williams, Akio Takenaka
NUCLEIC ACIDS RESEARCH
(2010)
Article
Biochemistry & Molecular Biology
Fang Zhang, Masaru Tsunoda, Kaoru Suzuki, Yuji Kikuchi, Oliver Wilkinson, Christopher L. Millington, Geoffrey P. Margison, David M. Williams, Ella Czarina Morishita, Akio Takenaka
NUCLEIC ACIDS RESEARCH
(2013)
Article
Biochemical Research Methods
Fang Zhang, Masaru Tsunoda, Yuji Kikuchi, Oliver Wilkinson, Christopher L. Millington, Geoffrey P. Margison, David M. Williams, Akio Takenaka
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
(2014)
Article
Biochemical Research Methods
Makiko Kikuchi, Takahiro Yamauchi, Yasuhito Iizuka, Masaru Tsunoda
Summary: This study investigated the function of tyrosine in the MGMT enzyme by comparing crystal structures of mutants and their complexes with substrate analogs. The results suggest that the highly conserved tyrosine may prevent oxidants from entering the active site and play a role in protecting MGMTs from deactivation after repairing alkyl adducts. This provides insights into the molecular mechanisms by which conserved amino acids ensure enzyme integrity and activity.
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Masaru Tsunoda, Takeshi Sakaue, Satoko Naito, Tomoko Sunami, Naoko Abe, Yoshihito Ueno, Akira Matsuda, Akio Takenaka
JOURNAL OF NUCLEIC ACIDS
(2010)