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Journal articles on the topic 'RNA G-Quadruplexes'

Author: Grafiati

Published: 30 November 2024

Last updated: 31 July 2025

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1

Agarwal, Tani, Gopal Jayaraj, Satya Prakash Pandey, Prachi Agarwala, and Souvik Maiti. "RNA G-Quadruplexes: G-quadruplexes with “U” Turns." Current Pharmaceutical Design 18, no. 14 (2012): 2102–11. http://dx.doi.org/10.2174/138161212799958468.

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Zhang, Rongxin, Yajun Liu, Xingxing Zhang, et al. "Detecting and Profiling Endogenous RNA G-Quadruplexes in the Human Transcriptome." International Journal of Molecular Sciences 22, no. 15 (2021): 8012. http://dx.doi.org/10.3390/ijms22158012.

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G-quadruplexes are the non-canonical nucleic acid structures that are preferentially formed in G-rich regions. This structure has been shown to be associated with many biological functions. Regardless of the broad efforts on DNA G-quadruplexes, we still have limited knowledge on RNA G-quadruplexes, especially in a transcriptome-wide manner. Herein, by integrating the DMS-seq and the bioinformatics pipeline, we profiled and depicted the RNA G-quadruplexes in the human transcriptome. The genes that contain RNA G-quadruplexes in their specific regions are significantly related to immune pathways

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Li, Wei, Weiwu Zeng, Yi Chen, et al. "Biotinylation and isolation of an RNA G-quadruplex based on its peroxidase-mimicking activity." Analyst 144, no. 15 (2019): 4472–76. http://dx.doi.org/10.1039/c9an00353c.

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Millevoi, Stefania, Hervé Moine, and Stéphan Vagner. "G-quadruplexes in RNA biology." Wiley Interdisciplinary Reviews: RNA 3, no. 4 (2012): 495–507. http://dx.doi.org/10.1002/wrna.1113.

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Koralewska, Natalia, Agnieszka Szczepanska, Kinga Ciechanowska, et al. "RNA and DNA G-quadruplexes bind to human dicer and inhibit its activity." Cellular and Molecular Life Sciences 78, no. 7 (2021): 3709–24. http://dx.doi.org/10.1007/s00018-021-03795-w.

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AbstractGuanine (G)-rich single-stranded nucleic acids can adopt G-quadruplex structures. Accumulating evidence indicates that G-quadruplexes serve important regulatory roles in fundamental biological processes such as DNA replication, transcription, and translation, while aberrant G-quadruplex formation is linked to genome instability and cancer. Understanding the biological functions played by G-quadruplexes requires detailed knowledge of their protein interactome. Here, we report that both RNA and DNA G-quadruplexes are bound by human Dicer in vitro. Using in vitro binding assays, mutation

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Mestre-Fos, Santi, Petar I. Penev, Suttipong Suttapitugsakul, et al. "G-Quadruplexes in Human Ribosomal RNA." Journal of Molecular Biology 431, no. 10 (2019): 1940–55. http://dx.doi.org/10.1016/j.jmb.2019.03.010.

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Criscuolo, Andrea, Ettore Napolitano, Claudia Riccardi, Domenica Musumeci, Chiara Platella, and Daniela Montesarchio. "Insights into the Small Molecule Targeting of Biologically Relevant G-Quadruplexes: An Overview of NMR and Crystal Structures." Pharmaceutics 14, no. 11 (2022): 2361. http://dx.doi.org/10.3390/pharmaceutics14112361.

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G-quadruplexes turned out to be important targets for the development of novel targeted anticancer/antiviral therapies. More than 3000 G-quadruplex small-molecule ligands have been described, with most of them exerting anticancer/antiviral activity by inducing telomeric damage and/or altering oncogene or viral gene expression in cancer cells and viruses, respectively. For some ligands, in-depth NMR and/or crystallographic studies were performed, providing detailed knowledge on their interactions with diverse G-quadruplex targets. Here, the PDB-deposited NMR and crystal structures of the comple

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Dumetz, Franck, Eugene Yui-Ching Chow, Lynne M. Harris, et al. "G-quadruplex RNA motifs influence gene expression in the malaria parasite Plasmodium falciparum." Nucleic Acids Research 49, no. 21 (2021): 12486–501. http://dx.doi.org/10.1093/nar/gkab1095.

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Abstract G-quadruplexes are non-helical secondary structures that can fold in vivo in both DNA and RNA. In human cells, they can influence replication, transcription and telomere maintenance in DNA, or translation, transcript processing and stability of RNA. We have previously showed that G-quadruplexes are detectable in the DNA of the malaria parasite Plasmodium falciparum, despite a very highly A/T-biased genome with unusually few guanine-rich sequences. Here, we show that RNA G-quadruplexes can also form in P. falciparum RNA, using rG4-seq for transcriptome-wide structure-specific RNA probi

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Sanchez-Martin, Victoria, Miguel Soriano, and Jose Antonio Garcia-Salcedo. "Quadruplex Ligands in Cancer Therapy." Cancers 13, no. 13 (2021): 3156. http://dx.doi.org/10.3390/cancers13133156.

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Nucleic acids can adopt alternative secondary conformations including four-stranded structures known as quadruplexes. To date, quadruplexes have been demonstrated to exist both in human chromatin DNA and RNA. In particular, quadruplexes are found in guanine-rich sequences constituting G-quadruplexes, and in cytosine-rich sequences forming i-Motifs as a counterpart. Quadruplexes are associated with key biological processes ranging from transcription and translation of several oncogenes and tumor suppressors to telomeres maintenance and genome instability. In this context, quadruplexes have prom

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10

Rouleau, Samuel, Jean-Pierre Sehi Glouzon, Andrea Brumwell, Martin Bisaillon, and Jean-Pierre Perreault. "3′ UTR G-quadruplexes regulate miRNA binding." RNA 23, no. 8 (2017): 1172–79. http://dx.doi.org/10.1261/rna.060962.117.

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11

Teng, Ye, Hisae Tateishi-Karimata, and Naoki Sugimoto. "RNA G-Quadruplexes Facilitate RNA Accumulation in G-Rich Repeat Expansions." Biochemistry 59, no. 21 (2020): 1972–80. http://dx.doi.org/10.1021/acs.biochem.0c00130.

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12

Illodo, Sara, Cibrán Pérez-González, Ramiro Barcia, Flor Rodríguez-Prieto, Wajih Al-Soufi, and Mercedes Novo. "Spectroscopic Characterization of Mitochondrial G-Quadruplexes." International Journal of Molecular Sciences 23, no. 2 (2022): 925. http://dx.doi.org/10.3390/ijms23020925.

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Guanine quadruplexes (G4s) are highly polymorphic four-stranded structures formed within guanine-rich DNA and RNA sequences that play a crucial role in biological processes. The recent discovery of the first G4 structures within mitochondrial DNA has led to a small revolution in the field. In particular, the G-rich conserved sequence block II (CSB II) can form different types of G4s that are thought to play a crucial role in replication. In this study, we decipher the most relevant G4 structures that can be formed within CSB II: RNA G4 at the RNA transcript, DNA G4 within the non-transcribed s

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Reina, Chiara, and Vincenzo Cavalieri. "Epigenetic Modulation of Chromatin States and Gene Expression by G-Quadruplex Structures." International Journal of Molecular Sciences 21, no. 11 (2020): 4172. http://dx.doi.org/10.3390/ijms21114172.

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G-quadruplexes are four-stranded helical nucleic acid structures formed by guanine-rich sequences. A considerable number of studies have revealed that these noncanonical structural motifs are widespread throughout the genome and transcriptome of numerous organisms, including humans. In particular, G-quadruplexes occupy strategic locations in genomic DNA and both coding and noncoding RNA molecules, being involved in many essential cellular and organismal functions. In this review, we first outline the fundamental structural features of G-quadruplexes and then focus on the concept that these DNA

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14

Sanchez-Martin, Victoria, Carmen Lopez-Pujante, Miguel Soriano-Rodriguez, and Jose A. Garcia-Salcedo. "An Updated Focus on Quadruplex Structures as Potential Therapeutic Targets in Cancer." International Journal of Molecular Sciences 21, no. 23 (2020): 8900. http://dx.doi.org/10.3390/ijms21238900.

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Non-canonical, four-stranded nucleic acids secondary structures are present within regulatory regions in the human genome and transcriptome. To date, these quadruplex structures include both DNA and RNA G-quadruplexes, formed in guanine-rich sequences, and i-Motifs, found in cytosine-rich sequences, as their counterparts. Quadruplexes have been extensively associated with cancer, playing an important role in telomere maintenance and control of genetic expression of several oncogenes and tumor suppressors. Therefore, quadruplex structures are considered attractive molecular targets for cancer t

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15

Beaudoin, Jean-Denis, Rachel Jodoin, and Jean-Pierre Perreault. "In-line probing of RNA G-quadruplexes." Methods 64, no. 1 (2013): 79–87. http://dx.doi.org/10.1016/j.ymeth.2013.02.017.

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Tassinari, Martina, Sara N. Richter, and Paolo Gandellini. "Biological relevance and therapeutic potential of G-quadruplex structures in the human noncoding transcriptome." Nucleic Acids Research 49, no. 7 (2021): 3617–33. http://dx.doi.org/10.1093/nar/gkab127.

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Abstract Noncoding RNAs are functional transcripts that are not translated into proteins. They represent the largest portion of the human transcriptome and have been shown to regulate gene expression networks in both physiological and pathological cell conditions. Research in this field has made remarkable progress in the comprehension of how aberrations in noncoding RNA drive relevant disease-associated phenotypes; however, the biological role and mechanism of action of several noncoding RNAs still need full understanding. Besides fulfilling its function through sequence-based mechanisms, RNA

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17

Roxo, Carolina, and Anna Pasternak. "Changes in physicochemical and anticancer properties modulated by chemically modified sugar moieties within sequence-related G-quadruplex structures." PLOS ONE 17, no. 8 (2022): e0273528. http://dx.doi.org/10.1371/journal.pone.0273528.

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We systematically investigated the influence of locked nucleic acid (LNA), unlock nucleic acid (UNA), and 2’-O-methyl-RNA (2’-O-Me-RNA) residues on the thermal stability, structure folding topology, biological activity and enzymatic resistance of three sequence-related DNA G-quadruplexes. In order to better understand the mechanism of action of the studied modifications, a single-position substitution in the loops or G-tetrads was performed and their influence was analyzed for a total of twenty-seven modified G-quadruplex variants. The studies show that the influence of each modification on th

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18

Xu, Yan, and Makoto Komiyama. "G-Quadruplexes in Human Telomere: Structures, Properties, and Applications." Molecules 29, no. 1 (2023): 174. http://dx.doi.org/10.3390/molecules29010174.

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G-quadruplexes, intricate four-stranded structures composed of G-tetrads formed by four guanine bases, are prevalent in both DNA and RNA. Notably, these structures play pivotal roles in human telomeres, contributing to essential cellular functions. Additionally, the existence of DNA:RNA hybrid G-quadruplexes adds a layer of complexity to their structural diversity. This review provides a comprehensive overview of recent advancements in unraveling the intricacies of DNA and RNA G-quadruplexes within human telomeres. Detailed insights into their structural features are presented, encompassing th

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Liu, Xiao, and Yan Xu. "HnRNPA1 Specifically Recognizes the Base of Nucleotide at the Loop of RNA G-Quadruplex." Molecules 23, no. 1 (2018): 237. http://dx.doi.org/10.3390/molecules23010237.

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Human telomere RNA performs various cellular functions, such as telomere length regulation, heterochromatin formation, and end protection. We recently demonstrated that the loops in the RNA G-quadruplex are important in the interaction of telomere RNA with heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1). Here, we report on a detailed analysis of hnRNPA1 binding to telomere RNA G-quadruplexes with a group of loop variants using an electrophoretic mobility shift assay (EMSA) and circular dichroism (CD) spectroscopy. We found that the hnRNPA1 binds to RNA G-quadruplexes with the 2’-O-methyl

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Brázda, Václav, Yu Luo, Martin Bartas, et al. "G-Quadruplexes in the Archaea Domain." Biomolecules 10, no. 9 (2020): 1349. http://dx.doi.org/10.3390/biom10091349.

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The importance of unusual DNA structures in the regulation of basic cellular processes is an emerging field of research. Amongst local non-B DNA structures, G-quadruplexes (G4s) have gained in popularity during the last decade, and their presence and functional relevance at the DNA and RNA level has been demonstrated in a number of viral, bacterial, and eukaryotic genomes, including humans. Here, we performed the first systematic search of G4-forming sequences in all archaeal genomes available in the NCBI database. In this article, we investigate the presence and locations of G-quadruplex form

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Lyu, Kaixin, Eugene Yui-Ching Chow, Xi Mou, Ting-Fung Chan, and Chun Kit Kwok. "RNA G-quadruplexes (rG4s): genomics and biological functions." Nucleic Acids Research 49, no. 10 (2021): 5426–50. http://dx.doi.org/10.1093/nar/gkab187.

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Abstract G-quadruplexes (G4s) are non-classical DNA or RNA secondary structures that have been first observed decades ago. Over the years, these four-stranded structural motifs have been demonstrated to have significant regulatory roles in diverse biological processes, but challenges remain in detecting them globally and reliably. Compared to DNA G4s (dG4s), the study of RNA G4s (rG4s) has received less attention until recently. In this review, we will summarize the innovative high-throughput methods recently developed to detect rG4s on a transcriptome-wide scale, highlight the many novel and

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22

Kwok, Chun Kit, Giovanni Marsico, and Shankar Balasubramanian. "Detecting RNA G-Quadruplexes (rG4s) in the Transcriptome." Cold Spring Harbor Perspectives in Biology 10, no. 7 (2018): a032284. http://dx.doi.org/10.1101/cshperspect.a032284.

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23

Balak, O. K., and O. Yu Lymanska. "Identification of conserved G-quadruplex motifs in the genome of bovine immunodeficiency virus." Veterinary Medicine: inter-departmental subject scientific collection, no. 110 (October 23, 2024): 71–77. https://doi.org/10.36016/vm-2024-110-10.

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Guanine rich DNA and RNA fragments tend to form stable noncanonical secondary structures ― G quadruplexes (G4) ― which can be of different topologies (monomolecular, interstranded bimolecular, interstranded tetramolecular). Canonical G4s contain 2 4 G tetrads, which are stabilized by stacking interactions, Hoogsteen hydrogen bonds and connected by a loop of 1 12 nucleotides. Based on the analysis of the nucleotide sequence, conservative G quadruplexes that can be formed in genomic RNA and proviral DNA of the bovine immunodeficiency virus (BIV) were determined. In addition to the known potentia

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Asamitsu, Sefan, Masayuki Takeuchi, Susumu Ikenoshita, Yoshiki Imai, Hirohito Kashiwagi, and Norifumi Shioda. "Perspectives for Applying G-Quadruplex Structures in Neurobiology and Neuropharmacology." International Journal of Molecular Sciences 20, no. 12 (2019): 2884. http://dx.doi.org/10.3390/ijms20122884.

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The most common form of DNA is a right-handed helix or the B-form DNA. DNA can also adopt a variety of alternative conformations, non-B-form DNA secondary structures, including the DNA G-quadruplex (DNA-G4). Furthermore, besides stem-loops that yield A-form double-stranded RNA, non-canonical RNA G-quadruplex (RNA-G4) secondary structures are also observed. Recent bioinformatics analysis of the whole-genome and transcriptome obtained using G-quadruplex–specific antibodies and ligands, revealed genomic positions of G-quadruplexes. In addition, accumulating evidence pointed to the existence of th

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Puig Lombardi, Emilia, and Arturo Londoño-Vallejo. "A guide to computational methods for G-quadruplex prediction." Nucleic Acids Research 48, no. 1 (2019): 1–15. http://dx.doi.org/10.1093/nar/gkz1097.

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Abstract Guanine-rich nucleic acids can fold into the non-B DNA or RNA structures called G-quadruplexes (G4). Recent methodological developments have allowed the characterization of specific G-quadruplex structures in vitro as well as in vivo, and at a much higher throughput, in silico, which has greatly expanded our understanding of G4-associated functions. Typically, the consensus motif G3+N1–7G3+N1–7G3+N1–7G3+ has been used to identify potential G-quadruplexes from primary sequence. Since, various algorithms have been developed to predict the potential formation of quadruplexes directly fro

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Jayaraj, Gopal Gunanathan, Satyaprakash Pandey, Vinod Scaria, and Souvik Maiti. "Potential G-quadruplexes in the human long non-coding transcriptome." RNA Biology 9, no. 1 (2012): 81–89. http://dx.doi.org/10.4161/rna.9.1.18047.

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27

Volná, Adriana, Martin Bartas, Václav Karlický, et al. "G-Quadruplex in Gene Encoding Large Subunit of Plant RNA Polymerase II: A Billion-Year-Old Story." International Journal of Molecular Sciences 22, no. 14 (2021): 7381. http://dx.doi.org/10.3390/ijms22147381.

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G-quadruplexes have long been perceived as rare and physiologically unimportant nucleic acid structures. However, several studies have revealed their importance in molecular processes, suggesting their possible role in replication and gene expression regulation. Pathways involving G-quadruplexes are intensively studied, especially in the context of human diseases, while their involvement in gene expression regulation in plants remains largely unexplored. Here, we conducted a bioinformatic study and performed a complex circular dichroism measurement to identify a stable G-quadruplex in the gene

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28

Hagihara, Masaki. "Inhibition of protein synthesis through RNA-based tandem G-quadruplex formation." Chemical Communications 57, no. 65 (2021): 8063–66. http://dx.doi.org/10.1039/d1cc02995a.

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29

Bugaut, A., and S. Balasubramanian. "5'-UTR RNA G-quadruplexes: translation regulation and targeting." Nucleic Acids Research 40, no. 11 (2012): 4727–41. http://dx.doi.org/10.1093/nar/gks068.

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Shrestha, Prakash, Shan Xiao, Soma Dhakal, Zheng Tan, and Hanbin Mao. "Nascent RNA transcripts facilitate the formation of G-quadruplexes." Nucleic Acids Research 42, no. 11 (2014): 7236–46. http://dx.doi.org/10.1093/nar/gku416.

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Berlyoung, April S., and Bruce A. Armitage. "Assembly and Characterization of RNA/DNA Hetero-G-Quadruplexes." Biochemistry 59, no. 42 (2020): 4072–80. http://dx.doi.org/10.1021/acs.biochem.0c00657.

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32

Fay, Marta M., Shawn M. Lyons, and Pavel Ivanov. "RNA G-Quadruplexes in Biology: Principles and Molecular Mechanisms." Journal of Molecular Biology 429, no. 14 (2017): 2127–47. http://dx.doi.org/10.1016/j.jmb.2017.05.017.

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33

Umar, Mubarak I., and Chun Kit Kwok. "Specific suppression of D-RNA G-quadruplex–protein interaction with an L-RNA aptamer." Nucleic Acids Research 48, no. 18 (2020): 10125–41. http://dx.doi.org/10.1093/nar/gkaa759.

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Abstract G-quadruplexes (G4s) are nucleic acid structure motifs that are of significance in chemistry and biology. The function of G4s is often governed by their interaction with G4-binding proteins. Few categories of G4-specific tools have been developed to inhibit G4–protein interactions; however, until now there is no aptamer tool being developed to do so. Herein, we present a novel L-RNA aptamer that can generally bind to D-RNA G-quadruplex (rG4) structure, and interfere with rG4–protein interaction. Using hTERC rG4 as the target for in vitro selection, we report the shortest L-aptamer bei

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Pavlova, Iuliia, Mikhail Iudin, Anastasiya Surdina, Vjacheslav Severov, and Anna Varizhuk. "G-Quadruplexes in Nuclear Biomolecular Condensates." Genes 14, no. 5 (2023): 1076. http://dx.doi.org/10.3390/genes14051076.

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G-quadruplexes (G4s) have long been implicated in the regulation of chromatin packaging and gene expression. These processes require or are accelerated by the separation of related proteins into liquid condensates on DNA/RNA matrices. While cytoplasmic G4s are acknowledged scaffolds of potentially pathogenic condensates, the possible contribution of G4s to phase transitions in the nucleus has only recently come to light. In this review, we summarize the growing evidence for the G4-dependent assembly of biomolecular condensates at telomeres and transcription initiation sites, as well as nucleol

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He, Lei, Zhenyu Meng, Qianqian Guo, et al. "Fluorogenic Pt complexes distinguish the quantity and folding behavior of RNA G-quadruplexes between live cancerous and healthy cells." Chemical Communications 56, no. 92 (2020): 14459–62. http://dx.doi.org/10.1039/d0cc05622g.

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Teng, Ye, Ming Zhu, and Zhidong Qiu. "G-quadruplexes in Repeat Expansion Disorders." International Journal of Molecular Sciences 24, no. 3 (2023): 2375. http://dx.doi.org/10.3390/ijms24032375.

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The repeat expansions are the main genetic cause of various neurodegeneration diseases. More than ten kinds of repeat sequences with different lengths, locations, and structures have been confirmed in the past two decades. G-rich repeat sequences, such as CGG and GGGGCC, are reported to form functional G-quadruplexes, participating in many important bioprocesses. In this review, we conducted an overview concerning the contribution of G-quadruplex in repeat expansion disorders and summarized related mechanisms in current pathological studies, including the increasing genetic instabilities in re

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Falabella, Micol, Rafael J. Fernandez, F. Brad Johnson, and Brett A. Kaufman. "Potential Roles for G-Quadruplexes in Mitochondria." Current Medicinal Chemistry 26, no. 16 (2019): 2918–32. http://dx.doi.org/10.2174/0929867325666180228165527.

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Some DNA or RNA sequences rich in guanine (G) nucleotides can adopt noncanonical conformations known as G-quadruplexes (G4). In the nuclear genome, G4 motifs have been associated with genome instability and gene expression defects, but they are increasingly recognized to be regulatory structures. Recent studies have revealed that G4 structures can form in the mitochondrial genome (mtDNA) and potential G4 forming sequences are associated with the origin of mtDNA deletions. However, little is known about the regulatory role of G4 structures in mitochondria. In this short review, we will explore

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Dell’Oca, Maria Chiara, Roberto Quadri, Giulia Maria Bernini, et al. "Spotlight on G-Quadruplexes: From Structure and Modulation to Physiological and Pathological Roles." International Journal of Molecular Sciences 25, no. 6 (2024): 3162. http://dx.doi.org/10.3390/ijms25063162.

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G-quadruplexes or G4s are non-canonical secondary structures of nucleic acids characterized by guanines arranged in stacked tetraplex arrays. Decades of research into these peculiar assemblies of DNA and RNA, fueled by the development and optimization of a vast array of techniques and assays, has resulted in a large amount of information regarding their structure, stability, localization, and biological significance in native systems. A plethora of articles have reported the roles of G-quadruplexes in multiple pathways across several species, ranging from gene expression regulation to RNA biog

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Heddi, Brahim, Vee Vee Cheong, Herry Martadinata, and Anh Tuân Phan. "Insights into G-quadruplex specific recognition by the DEAH-box helicase RHAU: Solution structure of a peptide–quadruplex complex." Proceedings of the National Academy of Sciences 112, no. 31 (2015): 9608–13. http://dx.doi.org/10.1073/pnas.1422605112.

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Four-stranded nucleic acid structures called G-quadruplexes have been associated with important cellular processes, which should require G-quadruplex–protein interaction. However, the structural basis for specific G-quadruplex recognition by proteins has not been understood. The DEAH (Asp-Glu-Ala-His) box RNA helicase associated with AU-rich element (RHAU) (also named DHX36 or G4R1) specifically binds to and resolves parallel-stranded G-quadruplexes. Here we identified an 18-amino acid G-quadruplex-binding domain of RHAU and determined the structure of this peptide bound to a parallel DNA G-qu

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Ida, Jeunice, Soo Chan, Jörn Glökler, Yee Lim, Yee Choong, and Theam Lim. "G-Quadruplexes as An Alternative Recognition Element in Disease-Related Target Sensing." Molecules 24, no. 6 (2019): 1079. http://dx.doi.org/10.3390/molecules24061079.

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G-quadruplexes are made up of guanine-rich RNA and DNA sequences capable of forming noncanonical nucleic acid secondary structures. The base-specific sterical configuration of G-quadruplexes allows the stacked G-tetrads to bind certain planar molecules like hemin (iron (III)-protoporphyrin IX) to regulate enzymatic-like functions such as peroxidase-mimicking activity, hence the use of the term DNAzyme/RNAzyme. This ability has been widely touted as a suitable substitute to conventional enzymatic reporter systems in diagnostics. This review will provide a brief overview of the G-quadruplex arch

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Raguseo, Federica, Souroprobho Chowdhury, Aisling Minard, and Marco Di Antonio. "Chemical-biology approaches to probe DNA and RNA G-quadruplex structures in the genome." Chemical Communications 56, no. 9 (2020): 1317–24. http://dx.doi.org/10.1039/c9cc09107f.

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G-quadruplexes are nucleic-acids secondary structures that can be formed under physiological conditions. In this review, we critically present the most relevant chemical-biology methods to probe the biological functions of G-quadruplex structures.

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Tosoni, Elena, Ilaria Frasson, Matteo Scalabrin, et al. "Nucleolin stabilizes G-quadruplex structures folded by the LTR promoter and silences HIV-1 viral transcription." Nucleic Acids Research 43, no. 18 (2015): 8884–97. http://dx.doi.org/10.1093/nar/gkv897.

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Abstract Folding of the LTR promoter into dynamic G-quadruplex conformations has been shown to suppress its transcriptional activity in HIV-1. Here we sought to identify the proteins that control the folding of this region of proviral genome by inducing/stabilizing G-quadruplex structures. The implementation of electrophorethic mobility shift assay and pull-down experiments coupled with mass spectrometric analysis revealed that the cellular protein nucleolin is able to specifically recognize G-quadruplex structures present in the LTR promoter. Nucleolin recognized with high affinity and specif

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Wolfe, Andrew L., Kamini Singh, Yi Zhong, et al. "RNA G-quadruplexes cause eIF4A-dependent oncogene translation in cancer." Nature 513, no. 7516 (2014): 65–70. http://dx.doi.org/10.1038/nature13485.

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Lorenz, Ronny, Stephan H. Bernhart, Jing Qin, et al. "2D Meets 4G: G-Quadruplexes in RNA Secondary Structure Prediction." IEEE/ACM Transactions on Computational Biology and Bioinformatics 10, no. 4 (2013): 832–44. http://dx.doi.org/10.1109/tcbb.2013.7.

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Song, Jingwen, Jean-Pierre Perreault, Ivan Topisirovic, and Stéphane Richard. "RNA G-quadruplexes and their potential regulatory roles in translation." Translation 4, no. 2 (2016): e1244031. http://dx.doi.org/10.1080/21690731.2016.1244031.

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Hagen, Timo, Anna L. Malinowska, Helen L. Lightfoot, Martina Bigatti, and Jonathan Hall. "Site-Specific Fluorophore Labeling of Guanosines in RNA G-Quadruplexes." ACS Omega 4, no. 5 (2019): 8472–79. http://dx.doi.org/10.1021/acsomega.9b00704.

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Varshney, Dhaval, Jochen Spiegel, Katherine Zyner, David Tannahill, and Shankar Balasubramanian. "The regulation and functions of DNA and RNA G-quadruplexes." Nature Reviews Molecular Cell Biology 21, no. 8 (2020): 459–74. http://dx.doi.org/10.1038/s41580-020-0236-x.

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Yangyuoru, Philip M., Amy Y. Q. Zhang, Zhe Shi, Deepak Koirala, Shankar Balasubramanian, and Hanbin Mao. "Mechanochemical Properties of Individual Human Telomeric RNA (TERRA) G-Quadruplexes." ChemBioChem 14, no. 15 (2013): 1931–35. http://dx.doi.org/10.1002/cbic.201300350.

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Göç, Yavuz Burak, Jakub Poziemski, Weronika Smolińska, Dominik Suwała, Grzegorz Wieczorek, and Dorota Niedzialek. "Tracking Topological and Electronic Effects on the Folding and Stability of Guanine-Deficient RNA G-Quadruplexes, Engineered with a New Computational Tool for De Novo Quadruplex Folding." International Journal of Molecular Sciences 23, no. 19 (2022): 10990. http://dx.doi.org/10.3390/ijms231910990.

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Abstract:

The initial aim of this work was to elucidate the mutual influence of different single-stranded segments (loops and caps) on the thermodynamic stability of RNA G-quadruplexes. To this end, we used a new NAB-GQ-builder software program, to construct dozens of two-tetrad G-quadruplex topologies, based on a designed library of sequences. Then, to probe the sequence–morphology–stability relationships of the designed topologies, we performed molecular dynamics simulations. Their results provide guidance for the design of G-quadruplexes with balanced structures, and in turn programmable physicochemi

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Pandey, Satyaprakash, Prachi Agarwala, and Souvik Maiti. "Effect of Loops and G-Quartets on the Stability of RNA G-Quadruplexes." Journal of Physical Chemistry B 117, no. 23 (2013): 6896–905. http://dx.doi.org/10.1021/jp401739m.

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