Destabilization of DNA and RNA G-quadruplex structures formed by GGA repeat due to N6-methyladenine modification

Identification of Endogenous Sequences Interacting with METTL3/METTL14 RNA Methyltransferase

N6-methyladenosine (m6A) is the most abundant RNA modification in mRNA and regulates various biological processes. The RNA-binding properties of m6A writer proteins play an important role in determining RNA modification sites. METTL3 and METTL14 form the core of the m6A writer complex, with METTL3 as the catalytic methyltransferase and METTL14 as the RNA-binding scaffold. Thus far, the comprehensive RNA-binding properties of METTL3/14 remain unknown. Using RNA-capturing microsphere particles (R-CAMPs), immobilizing RNA fragments derived from endogenous RNAs of human lung carcinoma cells, RNA fragments that interacted with the METTL3/14 methyltransferase domain are isolated. Bioinformatics analysis reveals that the pool of isolated sequences contains significantly more regions with the potential to form RNA G-quadruplexes (rG4s) than the randomly extracted RNA sequence pool and that the (GGA) repeat sequences are most enriched. Circular dichroism spectroscopy, gel mobility shift assays, and methylation experiments demonstrate that METTL3/14 binds to RNA sequences containing (GGA) repeats that form rG4 structure much stronger than RNAs that do not form rG4s. This study shows the potential of RNA G-quadruplex structures as a modulator of epitranscriptomic modification of m6As.

Protocol for circular dichroism spectral analysis of the thermal stability of CpG-methylated quadruplex structures

G-quadruplex and intercalated motif are quadruplex structures of which sequences are enriched in promoters. Here, we present a protocol for circular dichroism spectral analysis of the thermal stability of CpG-methylated quadruplex structures. We describe steps for preparing the oligonucleotide sample, measuring the circular dichroism spectrum of methylated quadruplex structures, and calculating thermodynamic parameters using Python 3. For complete details on the use and execution of this protocol, please refer to Kimura et al.1.

Double cross-linked cellulose hydrogel-supported Fe species for efficient wound healing

Traditional dressings often lack adequate skin structure support, which can lead to secondary damage, poor hemostasis, and an increased risk of inflammation due to wound adhesion. In this work, cellulose hydrogels were prepared by physical/chemical double cross-linking via a 'sol-gel' strategy and further loaded with Fe to obtain a three-dimensional (3D) porous cellulose/Fe composite hydrogel (cellulose/Fe gel). The obtained cellulose/Fe gel featured a 3D porous nanofiber structure, excellent water absorption/moisture retention performance, and good mechanical stability. Moreover, it could effectively remove reactive oxygen species (ROS) and inhibit cellular oxidative stress, demonstrating potential anti-inflammatory effects. When applied to wound repair in rats, cellulose/Fe gel, with excellent cell compatibility, effectively stimulated the formation of new blood vessels and significantly reduced the level of inflammatory factors, promoting wound healing. This work provides a new approach for cellulose-based hydrogel wound dressings.

A Compendium of G-Flipon Biological Functions That Have Experimental Validation

As with all new fields of discovery, work on the biological role of G-quadruplexes (GQs) has produced a number of results that at first glance are quite baffling, sometimes because they do not fit well together, but mostly because they are different from commonly held expectations. Like other classes of flipons, those that form G-quadruplexes have a repeat sequence motif that enables the fold. The canonical DNA motif (G3N1-7)3G3, where N is any nucleotide and G is guanine, is a feature that is under active selection in avian and mammalian genomes. The involvement of G-flipons in genome maintenance traces back to the invertebrate Caenorhabditis elegans and to ancient DNA repair pathways. The role of GQs in transcription is supported by the observation that yeast Rap1 protein binds both B-DNA, in a sequence-specific manner, and GQs, in a structure-specific manner, through the same helix. Other sequence-specific transcription factors (TFs) also engage both conformations to actuate cellular transactions. Noncoding RNAs can also modulate GQ formation in a sequence-specific manner and engage the same cellular machinery as localized by TFs, linking the ancient RNA world with the modern protein world. The coevolution of noncoding RNAs and sequence-specific proteins is supported by studies of early embryonic development, where the transient formation of G-quadruplexes coordinates the epigenetic specification of cell fate.

State of art in the chemistry of nucleoside-based Pt(II) complexes

After the fortuitous discovery of the anticancer properties of cisplatin, many Pt(II) complexes have been synthesized, to obtain less toxic leads which could overcome the resistance phenomena. Given the importance of nucleosides and nucleotides as antimetabolites, studying their coordinating properties towards Pt(II) ions is challenging for bioorganic and medicinal chemistry. This review aims to describe the results achieved so far in the aforementioned field, paying particular attention to the synthetic aspects, the chemical-physical characterization, and the biological activities of the nucleoside-based Pt(II) complexes.

Roles of G4-DNA and G4-RNA in Class Switch Recombination and Additional Regulations in B-Lymphocytes

Mature B cells notably diversify immunoglobulin (Ig) production through class switch recombination (CSR), allowing the junction of distant "switch" (S) regions. CSR is initiated by activation-induced deaminase (AID), which targets cytosines adequately exposed within single-stranded DNA of transcribed targeted S regions, with a specific affinity for WRCY motifs. In mammals, G-rich sequences are additionally present in S regions, forming canonical G-quadruplexes (G4s) DNA structures, which favor CSR. Small molecules interacting with G4-DNA (G4 ligands), proved able to regulate CSR in B lymphocytes, either positively (such as for nucleoside diphosphate kinase isoforms) or negatively (such as for RHPS4). G4-DNA is also implicated in the control of transcription, and due to their impact on both CSR and transcriptional regulation, G4-rich sequences likely play a role in the natural history of B cell malignancies. Since G4-DNA stands at multiple locations in the genome, notably within oncogene promoters, it remains to be clarified how it can more specifically promote legitimate CSR in physiology, rather than pathogenic translocation. The specific regulatory role of G4 structures in transcribed DNA and/or in corresponding transcripts and recombination hereby appears as a major issue for understanding immune responses and lymphomagenesis.

Crosstalk between G-quadruplex and ROS

The excessive production of reactive oxygen species (ROS) can lead to single nucleic acid base damage, DNA strand breakage, inter- and intra-strand cross-linking of nucleic acids, and protein-DNA cross-linking involved in the pathogenesis of cancer, neurodegenerative diseases, and aging. G-quadruplex (G4) is a stacked nucleic acid structure that is ubiquitous across regulatory regions of multiple genes. Abnormal formation and destruction of G4s due to multiple factors, including cations, helicases, transcription factors (TFs), G4-binding proteins, and epigenetic modifications, affect gene replication, transcription, translation, and epigenetic regulation. Due to the lower redox potential of G-rich sequences and unique structural characteristics, G4s are highly susceptible to oxidative damage. Additionally, the formation, stability, and biological regulatory role of G4s are affected by ROS. G4s are involved in regulating gene transcription, translation, and telomere length maintenance, and are therefore key players in age-related degeneration. Furthermore, G4s also mediate the antioxidant process by forming stress granules and activating Nrf2, which is suggestive of their involvement in developing ROS-related diseases. In this review, we have summarized the crosstalk between ROS and G4s, and the possible regulatory mechanisms through which G4s play roles in aging and age-related diseases.

Structures and conformational dynamics of DNA minidumbbells in pyrimidine-rich repeats associated with neurodegenerative diseases

Expansions of short tandem repeats (STRs) are associated with approximately 50 human neurodegenerative diseases. These pathogenic STRs are prone to form non-B DNA structure, which has been considered as one of the causative factors for repeat expansions. Minidumbbell (MDB) is a relatively new type of non-B DNA structure formed by pyrimidine-rich STRs. An MDB is composed of two tetraloops or pentaloops, exhibiting a highly compact conformation with extensive loop-loop interactions. The MDB structures have been found to form in CCTG tetranucleotide repeats associated with myotonic dystrophy type 2, ATTCT pentanucleotide repeats associated with spinocerebellar ataxia type 10, and the recently discovered ATTTT/ATTTC repeats associated with spinocerebellar ataxia type 37 and familial adult myoclonic epilepsy. In this review, we first introduce the structures and conformational dynamics of MDBs with a focus on the high-resolution structural information determined by nuclear magnetic resonance spectroscopy. Then we discuss the effects of sequence context, chemical environment, and nucleobase modification on the structure and thermostability of MDBs. Finally, we provide perspectives on further explorations of sequence criteria and biological functions of MDBs.

Quantitative detection of CpG methylation level on G-quadruplex and i-motif-forming DNA by recombinase polymerase amplification

Detection of CpG methylation levels holds immense potential for application in medical diagnosis of various diseases. In this study, we report the development of a recombinase polymerase amplification (RPA)-based CpG methylation level sensing system on G-quadruplex (G4) and intercalated motif (i-motif)-forming regions, which are stabilized by CpG methylation. This detection system is based on the principle that DNA polymerase is stalled at the methylated G4 and i-motif-forming region, which results in a decrease in the initial elongation efficiency of RPA. This reduction in turn affects the onset of amplification depending on the extent of CpG methylation; therefore, the methylation level is quantified by RPA. We demonstrate that the onset of amplification was delayed by CpG methylation when PCR products containing the vascular endothelial growth factor (VEGF) G4 and i-motif-forming region were used as the template. Furthermore, onset of amplification was delayed with the increase in CpG methylation of the VEGF region on genomic DNA. These results demonstrate that the sensing system is capable of directly detecting the methylation level at a constant temperature (39 °C) within 30 min without performing bisulfite conversion or affinity capture of methylated DNA.