Article
Spectroscopy
David A. Price, Poornima Wedamulla, Tayler D. Hill, Taylor M. Loth, Sean D. Moran
Summary: Guanine-rich nucleic acid sequences can form G-quadruplex structures with different characteristics. By comparing the polarization dependences of cross-peaks in two-dimensional infrared (2D IR) spectra, parallel-stranded and antiparallel-stranded G-quadruplexes can be distinguished. This study reveals key features of a Bcl-2 proximal promoter and demonstrates the convenience of using 2D IR spectroscopy for analyzing G-quadruplex structures.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2022)
Article
Chemistry, Multidisciplinary
Anirban Ghosh, Marko Trajkovski, Marie-Paule Teulade-Fichou, Valerie Gabelica, Janez Plavec
Summary: Human telomeric G-quadruplex DNA structures are attractive targets for anticancer drugs. However, the polymorphism of the target complicates drug design. This study reports the discovery of a G-quadruplex ligand that can completely change the fold of the DNA structure, providing valuable insights into the coordination structure of G-quadruplexes.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Multidisciplinary
Chao Gao, Jixin Chen, Naureen Anwar, Jieya Deng, Zhangqian Wang, Muhammad Umer, Yi He
Summary: This study compared the stability and compactness of insect monomeric and multimeric G-quadruplex structures in K+ and Na+ solutions. It was found that insect telomeric G-quadruplexes are more stable and compact in Na+ solutions. The interaction between BMPQ-1 and insect multimeric G-quadruplexes was investigated, and BMPQ-1 was found to have a significant inhibitory effect on the proliferation of pest cells.
Article
Biochemistry & Molecular Biology
Julia Svetlova, Makar Sardushkin, Natalia Kolganova, Edward Timofeev
Summary: Recent advances in G-quadruplex studies have shown their important role in key biological processes, with highly specific interactions between GQ structures and cellular proteins. It is now accepted that GQ loop elements play a major role in protein recognition, but the extent to which the GQ core contributes to maintaining the recognition interface remains unclear. Core guanines not only support a particular type of GQ architecture, but also set structural parameters that make GQ protein recognition sensitive to quadruplex topology.
Article
Biochemistry & Molecular Biology
Vera A. Spiridonova, Yulia O. Naumova, Polina A. Nikolaeva, Tatiana M. Novikova, Galina Ya. Kolomijtseva
Summary: The unfolding process of G-quadruplex structure in the RE31 DNA-aptamer and its complex with thrombin, under the influence of fluorescently labeled complementary oligonucleotides of varying lengths that form double-helix structures, has been investigated. It is proposed that G-quadruplex unfolding involves the formation of an intermediate complex with an oligonucleotide. Thermodynamic parameters and kinetics differ between the free aptamer and its complex with thrombin. Extending the oligonucleotide sequence complementary to G-quadruplex by two nucleotides to cover the hinge region has little effect on the conformational transition of the free aptamer, but it significantly affects the aptamer-protein complex, possibly due to thrombin-induced conformational transition involving the hinge region.
BIOCHEMISTRY-MOSCOW
(2022)
Article
Chemistry, Physical
Pallavi Agrawal, Maya S. Nair
Summary: This study evaluated the binding of andrographolide with CREB1 G-quadruplex and Thrombin Binding Aptamer (TBA) using molecular docking, dynamics, and simulation. The data showed that andrographolide can stabilize G-quadruplexes. It binds to the CREB1 G-quadruplex by forming hydrogen bonds and has the potential to target G-quadruplex forming DNA sequences in various oncogenes.
MOLECULAR SIMULATION
(2023)
Article
Multidisciplinary Sciences
Ahyun Son, Veronica Huizar Cabral, Zijue Huang, Theodore J. Litberg, Scott Horowitz
Summary: Recent research has found that G-quadruplex (G4) nucleic acids are effective in preventing protein aggregation and improving protein folding in Escherichia coli. Through in vitro protein folding experiments, it was discovered that G4s can accelerate protein folding by rescuing kinetically trapped intermediates. Time-course folding experiments in E. coli further showed that G4s primarily enhance protein folding quality instead of preventing protein aggregation. This study suggests that nucleic acids and ATP-independent chaperones may play important roles in determining the folding fate of proteins.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Sara Illodo, Cibran Perez-Gonzalez, Ramiro Barcia, Flor Rodriguez-Prieto, Wajih Al-Soufi, Mercedes Novo
Summary: Guanine quadruplexes (G4s) are four-stranded structures formed within guanine-rich DNA and RNA sequences that play a crucial role in biological processes. The recent discovery of G4 structures within mitochondrial DNA has brought significant advancements to the field. This study investigates the relevant G4 structures formed within CSB II and reveals the stability differences among different sequences.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Poulomi Das, Khac Huy Ngo, Fernaldo Richtia Winnerdy, Arijit Maity, Blaz Bakalar, Yves Mechulam, Emmanuelle Schmitt, Anh Tuan Phan
Summary: This study investigates the adaptability of left-handed G4 structures towards the presence of bulges, presenting the structural characteristics of left-handed G4s accommodating varying numbers of bulges. Bulges in left-handed G4s exhibit distinct features compared to those in right-handed G4s, and elucidation of the intricate structural details may enhance understanding of the potential roles and limitations of these unique structures.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Fika Ayu Safitri, Anh Thi Tram Tu, Kazuaki Hoshi, Miwako Shobo, Dandan Zhao, Arief Budi Witarto, Sony Heru Sumarsono, Ernawati Arifin Giri-Rachman, Kaori Tsukakoshi, Kazunori Ikebukuro, Tomohiko Yamazaki
Summary: The development of monomeric antiparallel G4 CpG ODNs with different CpG motifs has shown high immunostimulatory potency. The flanking sequence and CpG motif sequence play a role in influencing the immunostimulatory effects.
Article
Chemistry, Multidisciplinary
Wenxuan Hu, Haitao Jing, Wenqiang Fu, Zengrong Wang, Jiang Zhou, Na Zhang
Summary: In this study, a new type of G-quadruplex structure, parallel homomeric bimolecular G-quadruplex, was demonstrated to undergo strand displacement reaction with short G-rich DNA fragments at room temperature, resulting in the formation of a parallel heteromeric trimolecular G-quadruplex. This provides new insights into the development of complex architectures in G-quadruplex-based DNA nanotechnology.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biotechnology & Applied Microbiology
Vaclav Brazda, Otilia Porubiakova, Alessio Cantara, Natalia Bohalova, Jan Coufal, Martin Bartas, Miroslav Fojta, Jean-Louis Mergny
Summary: The study identified multiple potential G-quadruplex forming sequences in the G4-EA-H1N1 genomes, which could serve as potential therapeutic targets.
Review
Biochemistry & Molecular Biology
Huiling Shu, Rongxin Zhang, Ke Xiao, Jing Yang, Xiao Sun
Summary: G-quadruplexes are non-canonical secondary nucleic acid structures that play important roles in genome regulation. Interactions between G-quadruplexes and proteins have diverse biological functions and potential therapeutic applications.
Article
Biochemical Research Methods
Marco Caterino, Katrin Paeschke
Summary: The nucleic acid structure known as G-quadruplex (G4) plays a significant role in nucleic acid-based mechanisms that impact cellular processes. DNA G4 is well-studied, while RNA G4 is gaining attention for its role in cellular homeostasis. Proper regulation of G4 structures within cells is crucial, and helicases are important in resolving them. However, only a few rG4 unwinding helicases have been identified and characterized so far.
Article
Chemistry, Multidisciplinary
Elaina P. Boyle, Levan Lomidze, Karin Musier-Forsyth, Besik Kankia
Summary: In this study, researchers evaluated the effects of DNA -> RNA substitutions on the stability and topology of nucleic acid quadruplexes. They found that DNA -> RNA substitutions could destabilize or stabilize the quadruplex structure, and that substitutions at certain positions had predictable effects on stability. Furthermore, they were able to design a chimeric DNA/RNA construct with improved stability. These findings have implications for gene expression regulation, medicine, and biotechnology applications.
Article
Biochemistry & Molecular Biology
Shikha Kaushik, Shrikant Kukreti
Summary: Eukaryotic genomes contain pyrimidine-purine rich regions that can form varied DNA conformations, including triple-stranded structures. These structures have therapeutic and nanotechnological applications, emphasizing the importance of understanding their formation. Study on triplex structures in BOLF1 gene of human herpesvirus 4 revealed intramolecular triplexes are more stable than intermolecular ones, contributing to our knowledge about DNA triple helical structures.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Spectroscopy
Mohan Kumar, Mahima Kaushik, Shrikant Kukreti
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2020)
Article
Spectroscopy
Sonia Khurana, Shrikant Kukreti, Mahima Kaushik
Summary: The distance-dependent optical properties of colloidal gold nanoparticles can be used for designing colorimetric sensing modalities for the detection of various analytes. A simple and facile colorimetric detection assay for Sanguinarine (SNG) and Calf Thymus DNA (Ct-DNA) has been developed using citrate-reduced gold nanoparticles (CI-Au NPs). The optimized sensing system allows for the detection and quantification of SNG & Ct-DNA in real samples with satisfactory results and finds application in drug or DNA monitoring.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2021)
Review
Biochemistry & Molecular Biology
Samiksha Kukal, Debleena Guin, Chitra Rawat, Shivangi Bora, Manish Kumar Mishra, Priya Sharma, Priyanka Rani Paul, Neha Kanojia, Gurpreet Kaur Grewal, Shrikant Kukreti, Luciano Saso, Ritushree Kukreti
Summary: ABCG2 is a widely distributed protein in different cell types that plays a crucial role in maintaining cellular homeostasis and protecting tissues against xenobiotic insults, but its expression is influenced by various pathophysiological conditions. Therapeutic interventions should focus on regulating levels of ABCG2 rather than directly inhibiting its function to avoid serious side effects.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Savita Joshi, Anju Singh, Shrikant Kukreti
Summary: This study reports the differential interaction of the positional cationic porphyrin isomers TMPyP3 and TMPyP4 with a parallel G-quadruplex formed in the promoter region of the MRP1 transporter gene. The results suggest that cationic porphyrins can destabilize the G-quadruplex structure. This study is important for understanding the regulation of gene expression by cationic porphyrins.
JOURNAL OF MOLECULAR RECOGNITION
(2022)
Article
Materials Science, Biomaterials
Sonia, Amit Singh, Shivangi, Ritushree Kukreti, Shrikant Kukreti, Mahima Kaushik
Summary: This article introduces a multifunctional nanosystem that combines the photosensitizer Azure B with citrate reduced gold nanoparticles for cancer therapy. The study demonstrates the high heating efficiency and singlet oxygen generation rate of the nanosystem, as well as its interactions with DNA and serum albumin. In addition, the nanosystem exhibits in vitro cytotoxicity in hepatocellular carcinoma cells.
BIOMATERIALS ADVANCES
(2022)
Review
Biochemistry & Molecular Biology
Anju Singh, Ritushree Kukreti, Luciano Saso, Shrikant Kukreti
Summary: Oxidative stress is a metabolic dysfunction caused by the imbalance between reactive oxygen species production and the body's antioxidant defense system. It is closely related to the development of various noncommunicable diseases. Diabetes mellitus, especially type 2 diabetes, is significantly influenced by oxidative stress, which plays a crucial role in insulin signaling pathways.
Review
Biochemistry & Molecular Biology
Manish Kumar Mishra, Samiksha Kukal, Priyanka Rani Paul, Shivangi Bora, Anju Singh, Shrikant Kukreti, Luciano Saso, Karthikeyan Muthusamy, Yasha Hasija, Ritushree Kukreti
Summary: Valproic acid (VPA) is an anticonvulsant drug with therapeutic applications in various disorders. This review discusses the pharmacology, molecular targets of VPA, and modifications and derivatives of VPA, comparing their pharmacological profiles. Challenges for the clinical use of these derivatives are also discussed.
Review
Chemistry, Analytical
Sonia, Komal, Shrikant Kukreti, Mahima Kaushik
Summary: Gold nanoclusters with core size below 2 nm exhibit unique physical and chemical properties, synthesized with the assistance of templates or ligands for stability and high quantum yield, enabling diverse applications across interdisciplinary fields.
Article
Biochemistry & Molecular Biology
Nishu Nain, Anju Singh, Shoaib Khan, Mahima Kaushik, Shrikant Kukreti
Summary: This study investigates the effects of single base substitutions on the structural polymorphism of a gene sequence. The results show that different variants exhibit variations in oligomer concentration and structure, which may have implications for DNA-protein recognition in gene regulation.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Review
Genetics & Heredity
Aparna Bansal, Shikha Kaushik, Shrikant Kukreti
Summary: The discovery of the double-helical structure of DNA has revealed its importance and significance in the development of modern biology and biomedical science. Apart from the predominant B-form, there are various non-canonical DNA structures that play a key role in gene regulation and genetic diseases.
FRONTIERS IN GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Shoaib Khan, Anju Singh, Nishu Nain, Shrikant Kukreti
Summary: This study examines the structural status and cation-dependence of a 17-bp G-rich genomic sequence located in the human TRPA1 gene. The formation and stability of G-quadruplex structures in the presence of alkali metal ions are confirmed, providing insights into DNA-metal ions interactions.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Correction
Chemistry, Multidisciplinary
Aparna Bansal, Priyanka Phogat, Shrikant Kukreti
Article
Chemistry, Multidisciplinary
Aparna Bansal, Priyanka Phogat, Shrikant Kukreti
Summary: This study reveals the formation of an intramolecular non-conventional triplex structure by Chlamydomonas reinhardtii telomere in Na+ solution, which is stabilized by the co-existence of reverse Hoogsteen and Wobble base pairing.
Article
Chemistry, Multidisciplinary
Shoaib Khan, Anju Singh, Nishu Nain, Srishty Gulati, Shrikant Kukreti
Summary: This study compared the ability of Py- and Pu-TFO to form intermolecular triplex with a 27-bp genomic homopurine-homopyrimidine track present in the transcriptional element of the human DACH1 gene. The results showed that only Py-TFO was able to form the triplex, while Pu-TFO exhibited self-association properties that hindered its binding to the target. These findings contribute to our understanding of sequence-specific gene targeting and the design of more specific TFOs based on genomic targets.
