Article
Chemistry, Multidisciplinary
Ya-Ling Tan, A-Qian Huang, Li-Juan Tang, Jian-Hui Jiang
Summary: The development of multiplexed droplet loop-mediated isothermal amplification (multiplexed dLAMP) technique, which allows simultaneous quantification of multiple targets, provides a highly sensitive digital nucleic acid method for rapid and effective detection of viruses and other pathogens. The technology not only has been successfully demonstrated in the laboratory, but also holds promise for digital detection of HCV and HIV RNA in clinical applications. With high precision and low detection limits, it offers a new approach for the prevention and control of infectious diseases.
Article
Multidisciplinary Sciences
Paolo Rissone, Cristiano Bizarro, Felix Ritort
Summary: Accurate understanding of RNA hybridization is crucial for comprehending the structure and function of RNA. In this study, we mechanically unzipped and rezipped a 2-kbp RNA hairpin using optical tweezers, and successfully derived the free energies of the 10 nearest-neighbor base pairs (NNBP) in sodium and magnesium ions with a precision of 0.1 kcal/mol. The force-distance curves (FDCs) exhibited strong irreversible effects, hysteresis, and several intermediates, which made it challenging to extract the NNBP energies using existing methods. However, by combining suitable RNA synthesis with a tailored pulling protocol, we were able to obtain fully reversible FDCs, which were necessary to derive the NNBP energies. Our findings also revealed that base stacking and base pairing played a crucial role in stabilizing the intermediate states observed in the FDCs. Formation of stem-loop structures appeared to be a general mechanism explaining various behaviors observed in RNA folding.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Multidisciplinary
Yifei Zhou, Kuan Lu, Qiang Li, Chaochao Fan, Chuanzheng Zhou
Summary: Fluoro-substitution on the ribose moiety is a common way to modulate the structure and function of nucleic acids, and in this study, the 4'-F-deoxythymidine (T4'-F) was found to maintain the North conformation tendency in duplexes, causing local structural perturbations. Overall, the 4'-F-deoxyribonucleotide structurally resembles the 2'-F-deoxyribonucleotide but imparts less structural perturbation to the duplexes.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Review
Chemistry, Physical
Qian Ma, Chao Zhang, Mingzhi Zhang, Da Han, Weihong Tan
Summary: The demands for faster information processing speed and denser data storage are driving the development of new computation modes. DNA, as an important biomolecule, has shown great potential in information processing and storage, while also playing key biological roles. By combining these capabilities, DNA computing has opened up new fields in biology and biomedicine, with a focus on intelligent diagnostics for biomedical applications.
Article
Multidisciplinary Sciences
Shuntaro Takahashi, Saki Matsumoto, Pallavi Chilka, Saptarshi Ghosh, Hiromichi Okura, Naoki Sugimoto
Summary: In biological systems, the synthesis of nucleic acids is catalyzed by enzymes in aqueous solutions. This study investigates the effects of polyethylene glycol on the fidelity of RNA synthesis and finds that it can promote the polymerization of non-complementary ribonucleotides. These findings suggest that changes in solution properties can alter the substrate specificity of RNA polymerase and increase genetic diversity.
SCIENTIFIC REPORTS
(2022)
Article
Chemistry, Multidisciplinary
Baoting Dou, Hui Zhou, Yajun Hong, Liming Zhao, Po Wang
Summary: A newly developed electrochemical sensing system allows for the selective detection of microRNA 122 with high sensitivity, low cost, and easy manipulation, which is significant for disease diagnosis and molecular biology research.
CHEMICAL COMMUNICATIONS
(2021)
Article
Biophysics
Saranya Thiruvottriyur Shanmugam, Stanislav Trashin, Karolien De Wael
Summary: The study developed a photoelectrochemical method for DNA detection, evaluating different photosensitizers under specific laser wavelengths and successfully achieving photocurrent detection of DNA under certain conditions. By using magnetic beads and DNA probes labeled with specific photosensitizers, sensitive and robust detection of complementary DNA targets was achieved.
BIOSENSORS & BIOELECTRONICS
(2022)
Article
Endocrinology & Metabolism
Joseph D. D. Racca, Deepak Chatterjee, Yen-Shan Chen, Ratan K. K. Rai, Yanwu Yang, Millie M. M. Georgiadis, Elisha Haas, Michael A. A. Weiss
Summary: The Y-encoded transcription factor SRY plays a crucial role in male differentiation in therian mammals. A high-mobility-group (HMG) box is present in this factor, which allows it to bind to specific DNA sequences and bend the DNA. A study found sex-reversal mutations in the HMG box at position 72, which is invariant among mammalian orthologs. Interestingly, aromatic rings confer higher transcriptional activity compared to other side chains observed at DNA interfaces. Biochemical studies showed that a specific mutation in the aromatic ring accelerates the dissociation of the protein-DNA complex. Molecular dynamics simulations suggest that the mutation disrupts the water-mediated clamp at the tail-DNA interface, resulting in attenuated transcriptional activity. The conservation of this water-mediated clamp suggests its general importance in SRY and metazoan SOX domains.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Article
Biophysics
Benjamin Philipp Fingerhut, Jakob Schauss, Achintya Kundu, Thomas Elsaesser
Summary: The interaction between RNA and its aqueous environment is crucial for defining macromolecular structure and function. Investigating the interaction between a short RNA duplex and magnesium ions, a combined theoretical and experimental study revealed detailed hydration geometries and electrostatic characteristics of phosphate-Mg2+ pairs. The results highlight the importance of local electric field mapping and molecular-level simulations for accurately understanding the electrostatics at the RNA-water interface.
BIOPHYSICAL JOURNAL
(2021)
Article
Chemistry, Analytical
Yan Yu, Ziqing Yu, Xufeng Pan, Lei Xu, Rui Guo, Xiaohua Qian, Feng Shen
Summary: Digital PCR is a method that can accurately and precisely quantify target nucleic acids. The use of digital melting curve analysis (digital MCA) allows for the multiplex quantification of multiple target molecules in a single digital PCR. This method uses a self-partitioning SlipChip microfluidic system, which can generate microdroplets with trackable physical positions. The unique melting temperature (T-m) of amplification products can be used as a fingerprint for further classification.
Article
Chemistry, Multidisciplinary
Zhi Weng, Hongyan Yu, Wang Luo, Yongcan Guo, Qian Liu, Li Zhang, Zhang Zhang, Ting Wang, Ling Dai, Xi Zhou, Xiaole Han, Luojia Wang, Junjie Li, Yujun Yang, Guoming Xie
Summary: In this study, a regulatory tool called cooperative branch migration (CBM) is introduced to flexibly control DNA strand displacement by regulating the complementarity of branch migration domains. CBM exhibits multifunctional regulatory abilities, including rate fine-tuning and continuous dynamic regulation.
Article
Chemistry, Multidisciplinary
Jinqi Deng, Chao Liu, Jiashu Sun
Summary: Extracellular vesicles (EVs) are nanovesicles derived from cells, carrying various molecular cargos and playing important roles in intercellular communication and physiological and pathological processes. DNA-based nanomaterials, with their excellent programmability and modifiability, have emerged as promising tools for detecting molecular cargos carried by EVs. This perspective summarizes recent advancements in EV analysis using different types of DNA-based nanomaterials, including linear DNA probes, DNA nanostructures, and hybrid DNA nanomaterials. The design, construction, advantages, and disadvantages of these DNA nanomaterials, as well as their performance for detecting EVs, are reviewed. The challenges and opportunities in the field of EV analysis by DNA nanomaterials are also discussed.
ADVANCED MATERIALS
(2023)
Article
Biochemistry & Molecular Biology
Zhikun Zhang, Chunyan Shang, Cuixia Hu, Yumin Liu, Jilong Han
Summary: This article presents a branched DNA-based electrochemical biosensor for sensitive detection of specific nucleic acids. The biosensor utilizes a branched DNA with three sticky ends as a probe for sensitive and specific nucleic acid detection. Additionally, branched DNA-modified gold nanoparticles are employed as signal amplifiers to enhance the sensitivity of the sensor. The hybridization reaction of DNA on the sensor platform enables the detection of nucleic acids without the need for bulky thermal cyclers and enzymes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Multidisciplinary
Yao Yin, Wei Xie, Mengyi Xiong, Yingying Gao, Qin Liu, Da Han, Guoliang Ke, Xiao-Bing Zhang
Summary: Inspired by the naturally confined enzymes on fluid cell membranes, a fluidly confined CRISPR-based DNA reporter (FINDER) was developed on living cell membranes, which was successfully applied for rapid and sensitive cancer cell identification in clinical blood samples. This new phenomenon was then combined with multiple aptamer-based DNA logic gate for cell recognition, thus a FINDER system capable of accurate, rapid and sensitive cancer cell identification was constructed.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Yan Hao, Yanjuan Li, Lei Song, Zhaoxiang Deng
Summary: By using a rapid dehydration method, the synthesis of spherical nucleic acids with record-high DNA density is achieved in seconds, resulting in a 3-time increase in DNA density compared to traditional methods. This ultra-high density DNA grafting facilitates the formation of core-satellite assemblies, making the synthesis of spherical nucleic acids easier and enabling future explorations of the physical, chemical, and biological effects of high-density DNA spherical nucleic acids.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Physics, Multidisciplinary
Alexey K. Mazur, D. L. Shepelyansky
PHYSICAL REVIEW LETTERS
(2015)
Article
Physics, Multidisciplinary
Alexey K. Mazur
PHYSICAL REVIEW LETTERS
(2016)
Article
Biophysics
Alexey K. Mazur, Eugene Gladyshev
BIOPHYSICAL JOURNAL
(2018)
Article
Biochemistry & Molecular Biology
Dmitri Kamashev, Jacques Oberto, Marina Serebryakova, Alexey Gorbachev, Yulia Zhukova, Sergei Levitskii, Alexey K. Mazur, Vadim Govorun
Article
Chemistry, Physical
Alexey K. Mazur
JOURNAL OF PHYSICAL CHEMISTRY B
(2013)
Article
Biochemistry & Molecular Biology
Alexey K. Mazur, Mounir Maaloum
NUCLEIC ACIDS RESEARCH
(2014)
Article
Physics, Fluids & Plasmas
Alexey K. Mazur
Article
Physics, Fluids & Plasmas
Alexey K. Mazur
Article
Physics, Multidisciplinary
Alexey K. Mazur
PHYSICAL REVIEW LETTERS
(2010)
Editorial Material
Physics, Multidisciplinary
Alexey K. Mazur
PHYSICAL REVIEW LETTERS
(2013)
Article
Physics, Multidisciplinary
Alexey K. Mazur, Mounir Maaloum
PHYSICAL REVIEW LETTERS
(2014)
Review
Biochemistry & Molecular Biology
Alexey K. Mazur, Tinh-Suong Nguyen, Eugene Gladyshev
JOURNAL OF MOLECULAR BIOLOGY
(2020)
Article
Biophysics
Florian Carlier, Tinh-Suong Nguyen, Alexey K. Mazur, Eugene Gladyshev
Summary: Repeat-induced point mutation is a genetic process in fungi that creates C-to-T transitions in duplicated genomic sequences, detecting duplications by a recombination-independent mechanism and inducing mutation of adjacent nonrepetitive regions. This process is related to heterochromatin assembly and requires the cytosine methyltransferase DIM-2. The response of mutations is stronger in GC-rich repeats compared to AT-rich repeats, and direct repeats trigger stronger DIM-2-dependent mutation than inverted repeats.
BIOPHYSICAL JOURNAL
(2021)
Article
Multidisciplinary Sciences
Nicholas Rhoades, Tinh-Suong Nguyen, Guillaume Witz, Germano Cecere, Thomas Hammond, Alexey K. Mazur, Eugene Gladyshev
Summary: The pairing of homologous chromosomes during meiosis involves a unique mechanism of DNA homology recognition that allows for the identification and pairing of specific patterns of interspersed homologous sequences. This process, facilitated by REC8, does not rely on meiotic recombination but instead relies on forming quadruplex-based contacts with periodicity values spaced apart at intervals of 2.5 helical turns. The results reconcile genetic and biophysical evidence, identify a role for this process in initiating RNA interference, and suggest a precise mechanism for cross-matching chromosomes using intact dsDNA molecules.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Physics, Fluids & Plasmas
Alexey K. Mazur
