Review
Polymer Science
Incherah Bekkouche, Alexander Y. Y. Shishonin, Alexandre A. A. Vetcher
Summary: The structure of triple-stranded DNA, consisting of three oligonucleotide chains, is explored. Hoogsteen base pairing is described as a mechanism for forming triple-stranded DNA. The involvement of these structures in various diseases is discussed. The focus of the review is on the development of biomedical oligonucleotides with triple-stranded DNA.
Article
Chemistry, Multidisciplinary
Eike-Christian Wamho, Anna Romanov, Hellen Huang, Benjamin J. Read, Eric Ginsburg, Grant A. Knappe, Hyun Min Kim, Nicholas P. Farrell, Darrell J. Irvine, Mark Bathe
Summary: Viruslike particles (VLPs) fabricated using wireframe DNA origami are programmable platforms for vaccines and gene therapy. Researchers have found that inhibiting endonucleases with minor groove binders (MGBs) can increase the stability of these VLPs, making them more effective for therapeutic and vaccine applications.
Review
Biochemical Research Methods
Liam Adair, Elizabeth J. New
Summary: Small-molecule fluorophores are versatile tools for studying cellular architecture and biological processes. However, their application in vivo faces challenges such as biocompatibility, chemostability, photostability, and light penetration. Recent advances in designing fluorophores with improved properties and functionalization with targeting and sensing groups have allowed the development of in vivo fluorogenic, ratiometric, and reversible sensors.
CURRENT OPINION IN BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Marina C. Perieteanu, Leah M. C. McGee, Craig D. Shaw, Donna S. MacMillan, Abedawn Khalaf, Kirsten Gillingwater, Rebecca Beveridge, Katharine C. Carter, Colin J. Suckling, Fraser J. Scott
Summary: The study found that Strathclyde minor groove binders (S-MGBs) have potent activity against Leishmania parasites, and modification of the tertiary amine tail with an N-oxide derivative can lead to selective anti-leishmanial activity. The findings suggest that S-MGBs can be further studied as novel therapeutics for the treatment of leishmaniasis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Pharmacology & Pharmacy
Chun Li, Zunzhen Zhou, Chao Ren, Yi Deng, Feng Peng, Qiongfen Wang, Hong Zhang, Yuan Jiang
Summary: Triplex-forming oligonucleotides (TFOs) can specifically and strongly bind to double-stranded DNA, inhibiting gene expression. Their potential use in antigene therapy has led to their prominence, particularly in anti-cancer research. Despite a recent decline in their application, TFOs still have the potential to down-regulate target gene expression and function as carriers of active substances.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Kotaro Nishiyama, Keita Mori, Yusuke Takezawa, Mitsuhiko Shionoya
Summary: Metal-responsive triplex-forming oligonucleotides incorporating 5-hydroxyuracil nucleobases were synthesized, showing reversible regulation of binding to target natural DNA duplexes by the addition and removal of Gd-III ions under isothermal conditions.
CHEMICAL COMMUNICATIONS
(2021)
Article
Infectious Diseases
Hasan Y. Alniss, Naveed A. Khan, Anania Boghossian, Noor Akbar, Hadeel M. Al-Jubeh, Yousef A. Msallam, Balsam Q. Saeed, Ruqaiyyah Siddiqui
Summary: In this study, twelve DNA minor groove binders (MGBs) were synthesized and tested for their antiamoebic activity. The compounds showed significant effects on amoeba viability, cyst formation, cyst development, and amoeba-mediated host-cell death.
Review
Biochemistry & Molecular Biology
Sachin B. Wagh, Vladimir A. Maslivetc, James J. La Clair, Alexander Kornienko
Summary: Fluorescent probes are widely used in various fields, and the development of new experimental designs has facilitated innovation in probe discovery methods.
Article
Chemistry, Analytical
Dian Li, Ying Liu, Shengrong Yu, Dailiang Zhang, Xiao Wang, Hongmei Zhong, Kangdi He, Ying Wang, Yong-Xiang Wu
Summary: A novel nanoprobe platform with two-photon dye-doped silica nanoparticles was developed for FRET-based ratiometric biosensing and bioimaging targeting endogenous ATP. The nanoprobe showed satisfactory ratiometric fluorescence responses for ATP detection with high sensitivity and selectivity in vivo, indicating its potential as a valuable molecular imaging tool for biomedical applications.
Article
Chemistry, Multidisciplinary
Raquel Eustaquio, Joao P. Prates Ramalho, Ana T. Caldeira, Antonio Pereira
Summary: A series of novel 2-piperidinium-4-styrylcoumarin derivatives with large Stokes shifts and high fluorescence quantum yields were synthesized using an efficient and low-cost synthetic strategy as potential fluorescent labels for biomolecules. Density functional theory and time-dependent density functional theory calculations were performed to rationalize the observed photophysical properties.
Article
Multidisciplinary Sciences
Hela Benaissa, Karim Ounoughi, Isabelle Aujard, Evelyne Fischer, Rosette Goiame, Julie Nguyen, Alison G. Tebo, Chenge Li, Thomas Le Saux, Giulia Bertolin, Marc Tramier, Lydia Danglot, Nicolas Pietrancosta, Xavier Morin, Ludovic Jullien, Arnaud Gautier
Summary: Fluorescent reporters covering the visible spectrum are essential for imaging living cells and organisms. The authors have developed a collection of fluorogenic chromophores spanning from blue to red using a single engineered protein tag. This tool allows for tuning fluorescence color and properties, providing versatility for imaging proteins in live cells and optimizing FRET biosensors.
NATURE COMMUNICATIONS
(2021)
Review
Biochemical Research Methods
Lulu Winer, Leila Motiei, David Margulies
Summary: The development of fluorescent labels, sensors, and analytical techniques for detecting and imaging proteins in the life sciences has been driven by the crucial role of fluorescence detection. Many research groups have utilized oligodeoxynucleotides (ODNs) to develop simple-to-produce, modular, and versatile fluorescent tools for studying proteins. The important properties of DNA probes include tight control over protein binders and fluorescent dyes, as well as the ability to predict molecular architectures through self-assembly, inherent solubility, and stability.
BIOCONJUGATE CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
David A. Rusling
Summary: The introduction of the nucleobase 6-amino-5-nitropyridin-2-one (Z) enables stable and selective triplex formation of synthetic TFOs at neutral pH and above, overcoming the limitation of cytosine protonation at low pH. Furthermore, a universal strategy for enzymatic assembly of Z-containing TFOs using commercially available deoxyribonucleotide triphosphate has been demonstrated, aiming to improve the recognition properties of TFOs and reduce the cost and expertise associated with their chemical syntheses.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Karen P. Fong, Ismail A. Ahmed, Marco Mravic, Hyunil Jo, Oleg Kim, Rustem Litvinov, John W. Weisel, William F. DeGrado, Feng Gai, Joel S. Bennett
Summary: The study demonstrates the utility of 4-cyanotryptophan as a two-photon fluorescence reporter for imaging integrins, showcasing its ability to monitor protein behavior and interactions in cellular environments with minimal disruption to protein structure and function.
Article
Chemistry, Physical
Luiza de Carvalho Bertozo, Marco Tutone, Bruna Pastrello, Luiz Carlos da Silva-Filho, Giulia Culletta, Anna Maria Almerico, Valdecir Farias Ximenes
Summary: An aminoquinoline probe AQ4 has been developed as a new and efficient DNA minor groove fluorescent probe, demonstrating specificity for the minor groove compared to other established probes. AQ4 showed similar properties to Hoechst stain, but different from acridine orange and ethidium bromide. It had a higher fluorescent signal-to-noise ratio compared to Hoechst stain.
JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY A-CHEMISTRY
(2023)
Article
Pharmacology & Pharmacy
Olga A. Krasheninina, Evgeny K. Apartsin, Elena Fuentes, Aleksandra Szulc, Maksim Ionov, Alya G. Venyaminova, Dzmitry Shcharbin, F. Javier de la Mata, Maria Bryszewska, Rafael Gomez
Article
Biochemical Research Methods
Anna Davydova, Mariya Vorobyeva, Eugenia Bashmakova, Pavel Vorobjev, Olga Krasheninina, Alexey Tupikin, Marsel Kabilov, Vasilisa Krasitskaya, Ludmila Frank, Alya Venyaminova
ANALYTICAL BIOCHEMISTRY
(2019)
Article
Biochemistry & Molecular Biology
Mariya I. Meschaninova, Darya S. Novopashina, Olga A. Semikolenova, Vladimir N. Silnikov, Alya G. Venyaminova
Article
Chemistry, Multidisciplinary
Marianna Teplova, Christoph Falschlunger, Olga Krasheninina, Michaela Egger, Aiming Ren, Dinshaw J. Patel, Ronald Micura
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2020)
Article
Biochemistry & Molecular Biology
A. S. Davydova, O. A. Krasheninina, A. E. Tupikin, M. R. Kabilov, A. G. Venyaminova, M. A. Vorobyeva
RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY
(2019)
Article
Biochemistry & Molecular Biology
Olga A. Krasheninina, Veniamin S. Fishman, Alexander A. Lomzov, Alexey Ustinov, Alya G. Venyaminova
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2020)
Article
Chemistry, Multidisciplinary
Olga A. Krasheninina, Julia Thaler, Matthias D. Erlacher, Ronald Micura
Summary: This study introduces a new method for metal-free diazotransfer on native RNA, which can be used for tagging and developing other RNA tools. The azido-RNA obtained by this method can be further processed through well-established bioorthogonal reactions, expanding its applications.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biochemistry & Molecular Biology
Darya S. Novopashina, Mariya A. Vorobyeva, Alexander A. Lomzov, Vladimir N. Silnikov, Alya G. Venyaminova
Summary: This study synthesized novel oligonucleotide conjugates with closo-dodecaborate attached to different terminal positions of DNA, RNA, 2'-O-Me RNA, and 2'-F-Py RNA oligomers. The incorporation of boron clusters influenced the stability and double helix structure of the oligomers, with different effects observed for DNA and RNA sequences.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Mariya A. Vorobyeva, Maya A. Dymova, Darya S. Novopashina, Elena Kuligina, Valentina V. Timoshenko, Iaroslav A. Kolesnikov, Sergey Yu Taskaev, Vladimir A. Richter, Alya G. Venyaminova
Summary: The study successfully demonstrated the use of a 2'-F-RNA aptamer specific to human glioblastoma cells as a boron delivery agent for BNCT, resulting in effective reduction of cell viability. This proof of principle highlights the potential of aptamers for targeted delivery of boron-10 isotopes in BNCT, paving the way for the engineering of novel BNCT agents with high specificity and low toxicity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Vera Ulyanova, Alsu Nadyrova, Elena Dudkina, Aleksandra Kuznetsova, Albina Ahmetgalieva, Dzhigangir Faizullin, Yulia Surchenko, Darya Novopashina, Yuriy Zuev, Nikita Kuznetsov, Olga Ilinskaya
Summary: Small cationic guanyl-preferring ribonucleases produced by Bacillus species have similar protein tertiary structure but differ in dimer conformation and stability. This study reveals distinctions in their structures and catalytic activity towards different RNA substrates. The differences in activity and sensitivity to the inhibitor protein barstar are related to structural features of the proteins. Minor changes in structure can significantly affect the stability and functional activities of these enzymes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Olga Semikolenova, Lubov Sakovina, Elizaveta Akhmetova, Daria Kim, Ivan Vokhtantsev, Victor Golyshev, Mariya Vorobyeva, Sergey Novopashin, Darya Novopashina
Summary: A new approach utilizing a photoactivatable CRISPR/Cas9 gene-editing system was proposed, where the system involves the use of auxiliary photocleavable oligodeoxyribonucleotides (PC-DNAs) to release crRNA after UV irradiation, restoring Cas9 activity. The study found that the nanoCRISPR/Cas9 system incorporating carbon-encapsulated iron nanoparticles showed the most promising results, with potential applications in magnetic field-controlled delivery of CRISPR system and spatiotemporal gene editing.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Anastasiia T. Davletgildeeva, Alexandra A. Kuznetsova, Darya S. Novopashina, Alexander A. Ishchenko, Murat Saparbaev, Olga S. Fedorova, Nikita A. Kuznetsov
Summary: AP-endonucleases are multifunctional enzymes that are required for cell viability. In this study, the effect of metal ions on the exo- and endonuclease activities of four homologous APE1-like endonucleases was analyzed. It was found that these enzymes showed similar dependence patterns on metal ions' concentrations in terms of AP-endonuclease activity. The efficiency of the 3'-5' exonuclease activity was highest in hAPE1, while the endoribonuclease activity varied among the enzymes. These findings indicate that substrate specificity and cleavage efficiency are controlled by factors external to the catalytic site.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Darya S. S. Novopashina, Maya A. A. Dymova, Anna S. S. Davydova, Mariya I. I. Meschaninova, Daria O. O. Malysheva, Elena V. V. Kuligina, Vladimir A. A. Richter, Iaroslav A. A. Kolesnikov, Sergey Yu. Taskaev, Mariya A. A. Vorobyeva
Summary: Boron neutron capture therapy (BNCT) is a unique anti-cancer treatment strategy that improves treatment accuracy by precisely positioning a neutron beam and delivering boron compounds. This study demonstrates the feasibility of using cell-specific RNA aptamers for targeted delivery of boron clusters in BNCT. The results show that the amount of boron-loaded aptamer inside the cell exceeds 1 x 10^9 atoms/cell, and the efficacy of boron-loaded RNA conjugates is comparable to that of B-10-boronophenylalanine.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Anatoly A. Bulygin, Victoria N. Syryamina, Aleksandra A. Kuznetsova, Darya S. Novopashina, Sergei A. Dzuba, Nikita A. Kuznetsov
Summary: This study investigated the molecular events in the process of damage recognition by Apurinic/apyrimidinic endonuclease 1 (APE1) through DEER spectroscopy and kinetic analysis. The results showed that specific mutants of APE1 had higher activity in recognizing and repairing damaged DNA, revealing the factors that affect its substrate specificity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Hao Chen, Michaela Egger, Xiaochen Xu, Laurin Flemmich, Olga Krasheninina, Aiai Sun, Ronald Micura, Aiming Ren
NUCLEIC ACIDS RESEARCH
(2020)