Article
Biochemistry & Molecular Biology
Chang Lu, Anand Lopez, Jinkai Zheng, Juewen Liu
Summary: This study examined the possibility of using DNA intrinsic fluorescence to study aptamer binding. The results showed that DNA hybridization led to a decrease in fluorescence, while specific aptamers induced fluorescence increases. The length of the terminal stem had an impact on the fluorescence change for certain aptamers, while others failed to produce a fluorescence change.
Article
Biochemistry & Molecular Biology
Md. Saddam Husain Ansari, Naveen Kumar, Sriyans Jain, N. Yogesh Balakarthick, Ranjan Sen
Summary: We screened a clone from a genomic library of mycobacteriophages and found it to have mycobactericidal properties. This clone codes for a protein called Gp49, which is highly conserved among mycobacteriophages and likely plays a role in phage DNA replication. Gp49 is a high-affinity heparin-binding protein that can bind to both linear dsDNA and ssDNA/cooperatively, inhibiting transcription and displacing DNA-binding proteins. Its heparin-binding ability could have therapeutic/diagnostic applications in bacterial sepsis treatment.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Biochemistry & Molecular Biology
Shravya Rao Madku, Bijaya Ketan Sahoo, K. Lavanya, Ragaiahgari Srinivas Reddy, Anna Tanuja Safala Bodapati
Summary: The binding nature of posaconazole, a triazole antifungal drug, with calf-thymus DNA was investigated using spectroscopic techniques and molecular docking studies. A binding constant of the order of 103 M-1 was observed, indicating a strong interaction between posaconazole and calf-thymus DNA. The experimental results suggested that posaconazole binds within the minor groove of calf-thymus DNA, which was further confirmed by molecular docking studies.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Chemistry, Inorganic & Nuclear
Mingchang Zhu, Xiaoxi Ji, Songling Wang, Yi Zhou, Huahong Bao, Shuhan Li, Enjun Gao, Shuangyan Wu, Jing Wang, Qing Chen, Jin Xu, Xiaopeng Zhu
Summary: A novel Zn(II) complex based on 2(1,2,4)triazol-1-yl-isonicotinic acid was successfully designed and synthesized under hydrothermal conditions. Various experiments were conducted to analyze its binding mode with DNA and apoptotic effect on cells, showing promising biological activity.
INORGANIC CHEMISTRY COMMUNICATIONS
(2021)
Article
Chemistry, Analytical
Xun Gong, Soo-Yeon Cho, Sydney Kuo, Babatunde Ogunlade, Kathryn Tso, Daniel P. Salem, Michael S. Strano
Summary: Colloidal single-walled carbon nanotubes offer a promising platform for molecular recognition at the nanoscale. By modifying the noncovalent corona phases of the nanotubes, optical sensors can be designed through a phenomenon known as corona phase molecular recognition. In this study, the interactions between dilute divalent metal cations and DNA corona phases were explored, leading to improved experimental conditions for sensing metal ions and the detection of nanomolar levels of mercury ions in fish tissue extract.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Analytical
Shizheng Wang, Xiaochen Ma, Zifu Yang, Xiangchun Zhang, Xiaolei Chen, Yuqing Xia, Xueyun Gao, Xiaojun Ren
Summary: Differential expression of RNA splice variants among individual cells contributes to cell heterogeneity in gene expression, but current techniques face challenges in single-cell analysis. In this study, we developed DNA-templated dual-functional nanocluster probes for in situ imaging and accurate quantification of RNA splice variants at the single-cell level.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Ivana Mikulin, Ivana Ljubic, Ivo Piantanida, Aleksey Vasilev, Mihail Mondeshki, Meglena Kandinska, Lidija Uzelac, Irena Martin-Kleiner, Marijeta Kralj, Lidija-Marija Tumir
Summary: The new analogs of commercial cyanine dyes exhibited strong affinities to various nucleic acids, especially towards GC-DNA base pairs. They showed intercalation properties at low dye-DNA/RNA ratios and potent antiproliferative activity against cancer cell lines, making them promising theranostic agents.
Article
Chemistry, Physical
Aleyamma Alexander, Archana Sumohan Pillai, Govindaraj Sri Varalakshmi, Nallamuthu Ananthi, Haridas Pal, Israel V. M. V. Enoch, Mhejabheen Sayed
Summary: Non-canonical nucleic acid forms, such as G-quadruplexes, play a significant role in biological processes and have been targeted for cancer therapy. This article presents the synthesis and characterization of benzimidazole derivatives and their binding interactions with G-quadruplex and double-stranded DNAs.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Chemistry, Analytical
Anna S. Efimova, Mariya A. Ustimova, Nelly S. Chmelyuk, Maxim A. Abakumov, Yury V. Fedorov, Olga A. Fedorova
Summary: This study synthesized new styryl dyes with N-methylpyridine or N-methylquinoline scaffolds and examined their binding affinity for DNA in cell-free solution. The substitution of heterocyclic residue from pyridine to quinoline and variation in the phenyl part greatly influenced their binding modes, binding affinities, and spectroscopic responses. Biological experiments demonstrated the low toxicity of the synthesized dyes and their ability to selectively stain mitochondria in living cells.
Article
Chemistry, Applied
Ryan J. Sapia, Colin Campbell, Adam J. Reed, Vladimir B. Tsvetkov, Yulia Gerasimova
Summary: GelRed is a widely used nucleic acid-binding dye that preferentially binds to thymine-rich sequences in DNA. The interactions between GelRed and oligothymidylate are likely stabilized by electrostatic interactions and hydrogen bonding. The molecular dynamic simulations propose a possible structure of the GelRed-oligothymidilate complex.
Article
Biochemical Research Methods
G. Mahalakshmi, B. Selvakumar, K. N. Vennila, P. Lakshmana Rao, S. Madhuri, M. Seenivasaperumal, Kuppanagounder P. Elango
Summary: Four new naphthyridine derivatives with amino acid or boronic acid moieties were synthesized and characterized, and their binding mechanism with DNA was investigated through various spectral and thermodynamic techniques. The results indicate that these probes interact with DNA through different modes, and they show effective fluorescent staining in DNA gel electrophoresis experiments.
JOURNAL OF FLUORESCENCE
(2021)
Article
Chemistry, Physical
Shunmugasundaram Gurusamy, Kumar Krishnaveni, Murugesan Sankarganesh, Veerasamy Sathish, Pounraj Thanasekaran, Alagarsamy Mathavan
Summary: A novel naphthalene-based Schiff-base ligand (NNP) was synthesized and characterized, showing selective colorimetric response towards Co2+ and Cu2+ cations, high antioxidant effect, and strong binding affinity with DNA and BSA. The results suggest NNP's potential for biological and environmental monitoring studies as well as the design of new multiple target detection and binding sensors.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Chemistry, Analytical
Junhao Wang, Yuanyuan Liu, Tingting Zhao, Jiaheng Shi, Jing Chen, Dan Li, Yanyun Cui, Shenghao Xu, Xiliang Luo
Summary: Strategies for tumor-specific molecular imaging based on signal amplification have potential in evaluating tumor metastasis and progression. However, traditional amplification strategies are limited by off-tumor signal leakage. In this study, an enzyme-activated autonomous-motion DNAzyme signal amplification strategy (E-DNAzyme) was designed for improved spatial specificity in tumor-specific molecular imaging, which can be specifically activated by overexpressed APE1 in tumor cells. The proposed E-DNAzyme showed a lower detection limit and a higher discrimination ratio compared to traditional amplification strategies.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Jacquelyn Niederschulte, Yang Song, Andrew H. Park, James K. Bashkin, Cynthia M. Dupureur
Summary: Polyamides are powerful DNA ligands that can bind DNA with high affinity and specificity. Studies on the binding kinetics of a large anti-HPV hairpin polyamide to DNA revealed two distinct binding phases, indicating high mismatch tolerance and binding site stoichiometry. This suggests the potential efficacy of polyamide as an antiviral agent.
Article
Chemistry, Physical
Ashraf A. El-Bindary, Zeinab M. Anwar, Taissir El-Shafaie
Summary: In this study, fluorescence spectra and UV-Vis absorption were utilized to investigate the binding of quercetin and rutin flavonoids with DNA. The results suggest that the binding of amino acids with DNA has a significant effect on the binding constant of flavonoids with DNA, transforming the type of interaction from electrostatic to van der Waals force or hydrogen bond.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Meeting Abstract
Biophysics
Gregory M. K. Poon, Shuo Wang, Gaofei He, Ana Tolic, Miles H. Linde, James K. Bashkin, W. David Wilson
BIOPHYSICAL JOURNAL
(2015)
Editorial Material
Chemistry, Medicinal
Gaofei He, James K. Bashkin
FUTURE MEDICINAL CHEMISTRY
(2015)
Meeting Abstract
Biochemistry & Molecular Biology
Elena Vasilieva, Yang Song, Kevin J. Koeller, G. Davis Harris, James K. Bashkin, Cynthia M. Dupureur
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2015)
Article
Biochemistry & Molecular Biology
Gaofei He, Ana Tolic, James K. Bashkin, Gregory M. K. Poon
NUCLEIC ACIDS RESEARCH
(2015)
Article
Biochemistry & Molecular Biology
Elena Vasilieva, Jacquelyn Niederschulte, Yang Song, George Davis Harris, Kevin J. Koeller, Puhong Liao, James K. Bashkin, Cynthia M. Dupureur
Article
Biochemistry & Molecular Biology
C. H. Castaneda, M. J. Scuderi, T. G. Edwards, G. D. Harris, C. M. Dupureur, K. J. Koeller, C. Fisher, J. K. Bashkin
Article
Chemistry, Organic
Beibei Liu, Shuo Wang, Karl Aston, Kevin J. Koeller, Shahrzad Fanny Hakami Kermani, Carlos H. Castaneda, M. Jose Scuderi, Rensheng Luo, James K. Bashkin, W. David Wilson
ORGANIC & BIOMOLECULAR CHEMISTRY
(2017)
Article
Virology
Ryan H. Gumpper, Weike Li, Carlos H. Castaneda, M. Jose Scuderi, James K. Bashkin, Ming Luo
JOURNAL OF VIROLOGY
(2018)
Article
Biochemistry & Molecular Biology
Yang Song, Jacquelyn Niederschulte, Kristin N. Bales, James K. Bashkin, Cynthia M. Dupureur
Article
Biochemistry & Molecular Biology
Yang Song, Jacquelyn Niederschulte, Kristin N. Bales, Andrew H. Park, James K. Bashkin, Cynthia M. Dupureur
Article
Biochemistry & Molecular Biology
Beibei Liu, James K. Bashkin, Gregory M. K. Poon, Shuo Wang, Siming Wang, W. David Wilson
Article
Biochemistry & Molecular Biology
Jacquelyn Niederschulte, Yang Song, Andrew H. Park, James K. Bashkin, Cynthia M. Dupureur
Summary: Polyamides are powerful DNA ligands that can bind DNA with high affinity and specificity. Studies on the binding kinetics of a large anti-HPV hairpin polyamide to DNA revealed two distinct binding phases, indicating high mismatch tolerance and binding site stoichiometry. This suggests the potential efficacy of polyamide as an antiviral agent.
Article
Biochemistry & Molecular Biology
Jacquelyn Niederschulte, Yang Song, James K. Bashkin, Cynthia M. Dupureur
Summary: This study presents a comparative kinetic analysis of the binding behavior of hairpin polyamides (PAs) with different sizes to DNA. The results reveal complex and distinct association kinetics for PAs of different sizes. The smaller PA6 shows biphasic association kinetics, while the larger PA20 exhibits simpler kinetics. Moreover, as the size of PAs increases, the residence time also increases, which is important for certain biological activities.
Article
Biochemistry & Molecular Biology
William C. Putnam, James K. Bashkin
Summary: Artificial ribonucleases, known as synthetic ribozymes, were synthesized by linking the RNA transesterification catalyst copper (II) terpyridine to an abasic threoninol backbone residue. The study found that oligonucleotides with a (2S,3S)-threoninol backbone were more efficient at RNA transesterification than their (2R,3R)-isomer counterpart.
JOURNAL OF INORGANIC BIOCHEMISTRY
(2022)
Meeting Abstract
Chemistry, Multidisciplinary
Shuo Wang, Karl Aston, Kevin J. Koeller, James K. Bashkin, W. David Wilson
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY
(2014)
Article
Biochemical Research Methods
Saranya Krishnan, Shina Sasi, Preshobha Kodakkattumannil, Salima Al Senaani, Geetha Lekshmi, Martin Kottackal, Khaled M. A. Amiri
Summary: This study aimed to develop an efficient DNA extraction protocol suitable for diverse plant species and tissues. A reliable and consistent protocol was described for the extraction of high-quality DNA from difficult-to-extract plant species. The optimized protocol was successful in extracting high-quality DNA from various plant species and tissues, making it useful for genomic studies of recalcitrant plants.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Eisaku Hokazono, Saori Fukumoto, Takeshi Uchiumi, Susumu Osawa
Summary: This study proposes a method for detecting nucleic acid amplification using pyrophosphate, which requires only two reagents and an automated analyzer. The technique has high sensitivity and reproducibility, and can detect pyrophosphate within 10 minutes. Therefore, this method has the potential to be a new, rapid, and simple detection technique for amplified nucleic acids.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Drew S. Sowersby, L. Kevin Lewis
Summary: SURE electrophoresis is a new method for concentrating samples in gels, which allows efficient detection of highly dilute DNA samples. This approach generates single bands with enhanced signal intensities and minimal band broadening.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Hongyi Liang, Guoliang Yin, Guangxi Shi, Zhiyong Liu, Xiaofei Liu, Jingwei Li
Summary: The mechanism of Echinacoside (ECH) in treating breast cancer (BC) was explored through network pharmacology and experimental validation. It was found that ECH plays an important role in anti-BC by regulating the PI3K/AKT/HIF-1 alpha/VEGF signaling pathway, and it exhibits multi-target and multi-pathway effects.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Daniel S. Kantner, Emily Megill, Anna Bostwick, Vicky Yang, Carmen Bekeova, Alexandria Van Scoyk, Erin L. Seifert, Michael W. Deininger, Nathaniel W. Snyder
Summary: This study compared the results of different methods for measuring the amount of acetyl-Coenzyme A. The colorimetric ELISA kit did not produce interpretable results, while the fluorometric enzymatic kit showed comparable results to the LC-MS-based methods depending on the matrix and extraction conditions. LC-MS/MS and LC-HRMS methods produced well-aligned results, especially when using stable isotope-labeled internal standards.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Jingyan Xu, Hanying Tan, Xionghui Ma, Linjing Su, Zhi Zhang, Yuhao Xiong
Summary: This study investigates the co-catalytic capabilities of MoO3 nanosheets in enhancing the enzyme-like catalytic activity of a two-dimensional ultrathin Fe(III)-modified covalent triazine framework (Fe-CTF) under neutral pH conditions. The Fe-CTF/MoO3 co-catalytic system exhibits enzyme-mimicking activity and enables the development of a colorimetric method for glucose detection. Furthermore, a straightforward one-pot colorimetric method is established for screening XOD inhibitors.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Lichao Zhang, Kang Xiao, Xueting Wang, Liang Kong
Summary: A novel fusion technology was designed to identify FAD-binding sites, achieving the best results on two independent test datasets and outperforming existing methods significantly. The high performance and certainty of the method were demonstrated through statistical tests and cross-entropy loss analysis.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Abdulkadir Kilic, Mehmet Aslan, Abdulkadir Levent
Summary: This study developed a simple, rapid, sensitive, and selective voltammetric technique for the electrochemical characterization and detection of the highly risky drug Edoxaban. The optimized voltammetric method showed good analytical working range and was successfully applied to urine and tablet samples.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Su Hyun Kim, Nara Shin, Jong-Min Jeon, Jeong-Jun Yoon, Jeong Chan Joo, Hee Taek Kim, Shashi Kant Bhatia, Yung-Hun Yang
Summary: To address environmental issues caused by traditional plastics, bioplastics have gained attention as alternatives. Although bioplastics have better degradability, their degradation still takes longer than anticipated. This study proposes a novel screening method to identify bioplastic degraders faster, saving time and providing more quantitative data.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Irem Okman Kocoglu, Pinar Esra Erden, Esma Kilic
Summary: In this study, an electrochemical biosensor based on carbon nanofibers and ionic liquid modification was constructed for tyramine detection. The biosensor showed linear response, low detection limit, high sensitivity, and exhibited good reproducibility, stability, and anti-interference ability.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Liana U. Akhmetzianova, Timur M. Davletkulov, Assol R. Sakhabutdinova, Alexey Chemeris, Irek M. Gubaydullin, Ravil R. Garafutdinov
Summary: A new program called LAMPrimers iQ has been developed for high-quality LAMP primer design, and its advantages in providing higher specificity and reliable detection of viral RNA were validated using SARS-CoV-2 coronavirus RNA as a model target.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Tommaso Pileri, Alberto Sinibaldi, Agostino Occhicone, Norbert Danz, Elena Giordani, Matteo Allegretti, Frank Sonntag, Peter Munzert, Patrizio Giacomini, Francesco Michelotti
Summary: This study developed a biosensing device based on one-dimensional photonic crystal to detect HER2 in breast cancer. The device combines label-free and fluorescence operation modes, allowing for real-time and accurate detection in less than 20 minutes. It offers a promising technique for combined label-free and fluorescence detection in disease diagnosis and therapeutic monitoring.
ANALYTICAL BIOCHEMISTRY
(2024)
