Article
Biochemistry & Molecular Biology
Martin Bartas, Kristyna Slychko, Vaclav Brazda, Jiri Cerven, Christopher A. Beaudoin, Tom L. Blundell, Petr Pecinka
Summary: Z-DNA and Z-RNA are important left-handed structures of nucleic acids that play a significant role in various biological processes. Proteins containing the Z alpha domain have been found to interact with Z-DNA/Z-RNA. This study identified new Z-DNA/Z-RNA binding proteins through a search of the PDB structures database and AlphaFold2 protein models.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Mamadou Amadou Diallo, Sebastien Pirotte, Yunlong Hu, Lea Morvan, Krzysztof Rakus, Nicolas M. Suarez, Lee PoTsang, Hisao Saneyoshi, Yan Xu, Andrew J. Davison, Peter Tompa, Joel L. Sussman, Alain Vanderplasschen
Summary: The Z alpha domains exhibit functional diversity in viruses and cells, inducing liquid-liquid phase separation and mediating dsRNA A-to-Z conversion. This study expands our understanding of the mechanisms of action of proteins containing Z alpha domains and provides new hypotheses for further research.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biology
Dmitry Umerenkov, Alan Herbert, Dmitrii Konovalov, Anna Danilova, Nazar Beknazarov, Vladimir Kokh, Aleksandr Fedorov, Maria Poptsova
Summary: Using the DNABERT transformer algorithm trained on experimentally identified Z-DNA forming sequences (Z-flipons), we performed genome-wide interrogation and obtained significant improvements over existing approaches. Z-flipons were found to be enriched in promoters and telomeres, overlapping with genetic loci related to RNA expression, editing, splicing, and disease-associated variants. Our findings also suggest a potential role of Z-RNA in mediating these effects.
LIFE SCIENCE ALLIANCE
(2023)
Article
Biochemistry & Molecular Biology
Youyeon Go, Hye-Bin Ahn, Byeong-Seon Kim, Ae-Ree Lee, Kwang-Im Oh, Joon-Hwa Lee
Summary: Z-DNA binding proteins (ZBPs) play important roles in various biological processes, with studies showing conformational motions during ZBP binding to DNA. A study on the Z alpha domains of human ADAR1 revealed dynamic conformational exchanges during Z-DNA binding, impacting the hydrophobic interactions among helices and hydrogen bonding interactions with the phosphate backbone of Z-DNA.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Review
Genetics & Heredity
Alan Herbert
Summary: Recognition of dsRNA initiates type I interferon responses, with host using MDA5 helicase to distinguish self-transcripts and modulate immune responses. Alu retroelements and helicases like DHX9 and MOV10 also play roles in innate immunity, utilizing nucleic acid structure to define self.
Review
Biochemistry & Molecular Biology
Reetabrita Roy, Pallab Chakraborty, Arindam Chatterjee, Joy Sarkar
Summary: DNA can adopt various conformations, from right-handed B to left-handed Z; Transition between B-Z DNA is influenced by salt concentration and specific proteins; Z-DNA is associated with certain diseases and large-scale deletions in mammalian cells.
FRONTIERS IN BIOSCIENCE-LANDMARK
(2021)
Article
Biochemistry & Molecular Biology
Qin-Xia Song, Chang -Wei Lai, Na-Nv Liu, Xi-Miao Hou, Xu-Guang Xi
Summary: The G4 DNA binding protein Dbp2 has been found to prefer G-rich substrates and plays a dual role in destabilizing and inducing further folding of MycG4 structures. It may also participate in DNA metabolism.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Madhabi M. Bhanjadeo, Partha S. Nial, Chakkarai Sathyaseelan, Ajit K. Singh, Juhi Dutta, Thenmalarchelvi Rathinavelan, Umakanta Subudhi
Summary: The transition from right-handed to left-handed DNA not only plays a controlling role in gene expression switching but also has importance in nanomechanical device design. This study demonstrates that LaCl3 can induce controlled and reversible B-Z transition in short repeat sequences, providing insights into the molecular mechanism of this transition. The binding of LaCl3 to the phosphate backbone of Z-DNA is strong, resulting in the irreversible thermal melting of LaCl3-induced Z-DNA. These findings suggest that LaCl3 can be used as an inducer of left-handed DNA in other short oligonucleotide sequences.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Biochemistry & Molecular Biology
John R. Buzzo, Aishwarya Devaraj, Erin S. Gloag, Joseph A. Jurcisek, Frank Robledo-Avila, Theresa Kesler, Kathryn Wilbanks, Lauren Mashburn-Warren, Sabarathnam Balu, Joseph Wickham, Laura A. Novotny, Paul Stoodley, Lauren O. Bakaletz, Steven D. Goodman
Summary: Biofilms formed by bacteria rely on a rare Z-form DNA structure containing eDNA and DNABII proteins for structural integrity. Stabilization of Z-DNA by DNABII proteins promotes biofilm formation and stability, while disruption of Z-DNA structure can disturb existing biofilms. The universal bacterial DNABII family of proteins is shown to stabilize both bacterial and host eDNA in the Z-form, suggesting a role in biofilm pathogenesis and immune interactions.
Article
Biochemical Research Methods
Cathrin Grawe, Miguel Hernandez-Quiles, Pascal W. T. C. Jansen, Annika Brimmers, Michiel Vermeulen
Summary: In recent years, quantitative mass spectrometry-based interaction proteomics technology has been effective in identifying specific DNA-protein interactions. The PASMAN method was developed using a SILAC/TMT-based higher-order multiplexing approach, allowing the determination of specific DNA-protein interactions and their apparent binding affinities. This method was applied to study two CGCG-containing consensus DNA motifs and revealed distinct affinities of two BEN domain-containing proteins, BANP and BEND3, towards these motifs.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Jian Zhang, Sina Ghadermarzi, Akila Katuwawala, Lukasz Kurgan
Summary: Efforts to elucidate protein-DNA interactions at the molecular level rely on accurate predictions of DNA-binding residues in protein sequences. DNAgenie, a new predictor utilizing a custom-designed machine learning architecture, outperforms current methods in predicting residue-level interactions with A-DNA, B-DNA, and single-stranded DNA, reducing cross-predictions and generating promising leads for potential DNA-binding proteins.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Cell Biology
Hui Liu, Yuxuan Liu, Wei Fan, Bing Fan
Summary: This study identified an important role of ZBP1 in regulating F. nucleatum-induced proinflammatory cell death and inflammatory activation.
CELL COMMUNICATION AND SIGNALING
(2022)
Article
Biochemistry & Molecular Biology
Sook Ho Kim, Hae Jun Jung, Il-Buem Lee, Nam-Kyung Lee, Seok-Cheol Hong
Summary: This study investigated the impact of specific DNA sequences on Z-DNA formation, revealing the influence of different repeat sequences on the thermodynamic and kinetic features of Z-DNA formation. TG repeat sequences are advantageous for Z-DNA in terms of torsion and bubble selection, while CG repeat sequences likely act as torsion absorbers.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Chemistry, Physical
Pradeep Pant
Summary: Deoxyribonucleic acid (DNA) is a vital biomacromolecule, and in addition to the traditional B-DNA helical structure, there are other noncanonical conformations. In this study, a locked-sugar-based Z-DNA was found to maintain a stable left-handed conformation even in the absence of counterions, possibly due to the influence of structural rigidity. Through comprehensive analysis of structure and energetics, the stability of the locked model system was investigated, which could be attributed to the widening of the backbone and enhanced electrostatics between complementary strands. The proposed design can help understand Z-DNA conformation even in salt-deprived conditions and can be applied to more advanced DNA modeling techniques.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Biochemistry & Molecular Biology
Kei Segawa, Kazuhiko Igarashi, Kazutaka Murayama
Summary: The function of the transcription factor BACH1 is regulated by heme binding to multiple Cys-Pro (CP) motifs within its intrinsically disordered regions. The individual CP motifs contribute to the regulation of BACH1 activity by accepting heme in different coordination manners and their spatial locations are important for their individual functions. The presence of multiple CP motifs with distinct roles ensures the multifaceted, strict regulation of BACH1 by heme.
Review
Biochemistry & Molecular Biology
Kwang-Im Oh, Jinwoo Kim, Chin-Ju Park, Joon-Hwa Lee
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2020)
Article
Biochemistry & Molecular Biology
Soyoung Cha, Weon Sup Lee, Joonhyeok Choi, Jong Geun Jeong, Ju Ryoung Nam, Jihong Kim, Hak-Nam Kim, Joon-Hwa Lee, Jin-San Yoo, Kyoung-Seok Ryu
JOURNAL OF BIOMOLECULAR NMR
(2020)
Article
Multidisciplinary Sciences
Tsukasa Mashima, Joon-Hwa Lee, Yuji O. Kamatari, Tomohiko Hayashi, Takashi Nagata, Fumiko Nishikawa, Satoshi Nishikawa, Masahiro Kinoshita, Kazuo Kuwata, Masato Katahira
SCIENTIFIC REPORTS
(2020)
Article
Biochemistry & Molecular Biology
Ho-Seong Jin, Na-Hyun Kim, Seo-Ree Choi, Kwang-Im Oh, Joon-Hwa Lee
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2020)
Article
Biochemistry & Molecular Biology
Seo-Ree Choi, Jaewang Lee, Yeo-Jin Seo, Hyun Sun Kong, Minjae Kim, EonSeon Jin, Jung Ryeol Lee, Joon-Hwa Lee
Summary: By studying different isoforms of III antifreeze proteins, it was found that the QAE1 isoform exhibited the highest activity, while mutant constructs of the QAE2 and SP isoforms displayed similar thermal hysteresis and ice recrystallization inhibition activities compared to the QAE1 isoform. In terms of cryopreservation, the QAE1 isoform and active mutants showed better preservation of follicle morphology and more efficient prevention of DNA double-strand breaks. Additionally, active AFPs formed unique hydrogen bonds with the first 310 helix, playing a crucial role in the efficient binding to ice crystals, which was disrupted in inactive isoforms.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Kwang-Im Oh, Ae-Ree Lee, Seo-Ree Choi, Youyeon Go, Kyoung-Seok Ryu, Eun-Hee Kim, Joon-Hwa Lee
Summary: A new global search algorithm was developed to determine the dynamics and mechanism of protein binding, revealing that the α-helical segment plays a key role in the three-state conformational changes of the hZα(ADAR1)-DNA complex, providing information on the global minimum of the conformational transition process.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Juhyun Lee, Si-Eun Sung, Janghyun Lee, Jin Young Kang, Joon-Hwa Lee, Byong-Seok Choi
Summary: The stability of a fluoride riboswitch is influenced by two steps depending on ligands, and the opening dynamics and stabilities of the riboswitch in different ion states are essential for the genetic switching mechanism.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Thananjeyan Balasubramaniyam, Kwnag-Im Oh, Ho-Seong Jin, Hye-Bin Ahn, Byeong-Seon Kim, Joon-Hwa Lee
Summary: This review article summarizes the synthesis methods of chemically modified nucleotides, focusing on the methylation, bromination, and arylation of purines and pyrimidines at specific positions. It also introduces the non-canonical structures of nucleic acids containing these modifications.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Editorial Material
Biochemistry & Molecular Biology
Joon-Hwa Lee, Masato Katahira
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Medicine, Research & Experimental
Shailima Rampogu, Thananjeyan Balasubramaniyam, Joon-Hwa Lee
Summary: Breast cancer is a major cause of female mortality worldwide. Current treatments have side effects, leading to the exploration of natural compounds. Alkaloids, a group of natural compounds, have gained attention for their potential therapeutic use in breast cancer due to their anti-inflammatory, antiviral, and antimicrobial properties. This review discusses 12 alkaloids that have shown promise in inducing apoptosis, inhibiting tumor growth and migration, and inducing autophagy, making them potential components of combination therapy for breast cancer.
BIOMEDICINE & PHARMACOTHERAPY
(2022)
Article
Biochemistry & Molecular Biology
Ho-Seong Jin, Juyeon Son, Yeo-Jin Seo, Seo-Ree Choi, Hye-Bin Ahn, Youyeon Go, Juhee Lim, Kwang-Im Oh, Kyoung-Seok Ryu, Joon-Hwa Lee
Summary: This study reveals that Dlx3-HD selectively recognizes its consensus DNA sequences through the α3 helix and L1 loop regions, exhibiting unique dynamic properties. The dynamic properties of the binding of Dlx3-HD to its consensus DNA sequence can be modulated by varying the salt concentrations.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Thananjeyan Balasubramaniyam, Byeong-Seon Kim, Badvel Pallavi, Ho-Seong Jin, Sung Kuk Kim, Joon-Hwa Lee
Summary: In this study, a simple and eco-friendly method for iodination of pyrimidine derivatives under solvent-free conditions was developed. The advantages of this method include short reaction time, high yields, and environmentally-friendly reaction conditions. This novel approach will contribute to the development of nucleobase-related drug candidates.
Editorial Material
Biochemistry & Molecular Biology
Joon-Hwa Lee
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Physical
Honggyu Seong, Wonbin Nam, Geongil Kim, Joon Ha Moon, Youngho Jin, Seung-Ryong Kwon, Joon-Hwa Lee, Jaewon Choi
Summary: Introducing organic compounds to electrode materials as a replacement for expensive inorganic-based materials is an effective and eco-friendly cost reduction strategy. In this study, amino acid-substituted derivatives of perylene diimide (PDI_AAs) demonstrated redox-active characteristics and were utilized as cathode materials in lithium-ion batteries (LIBs). Among the synthesized PDI_AAs, L-alanine-substituted PDI (PDI_A) exhibited the highest cycling performance, maintaining a capacity of 86 mAhg(-1) with 95% retention after 150 cycles at 50 mAg(-1). Furthermore, PDI_A displayed a long-term cycling performance with a capacity of 47 mAhg(-1) (98% retention) over 5000 cycles at a high current density of 500 mAg(-1). Ex situ attenuated total reflection Fourier-transform infrared spectroscopy (ATR FT-IR) analysis revealed the charge-discharge mechanism of PDI_A electrodes at different charging states.
Review
Biochemistry & Molecular Biology
Men Thi Hoai Duong, Joon-Hwa Lee, Hee-Chul Ahn
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2020)