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Biochemical Society Transactions Nov 2021The glucocorticoid receptor (GR) is a steroid hormone-activated transcription factor that binds to various glucocorticoid response elements to up- or down- regulate the... (Review)
Review
The glucocorticoid receptor (GR) is a steroid hormone-activated transcription factor that binds to various glucocorticoid response elements to up- or down- regulate the transcription of thousands of genes involved in metabolism, development, stress and inflammatory responses. GR consists of two domains enabling interaction with glucocorticoids, DNA response elements and coregulators, as well as a large intrinsically disordered region that mediates condensate formation. A growing body of structural studies during the past decade have shed new light on GR interactions, providing a new understanding of the mechanisms driving context-specific GR activity. Here, we summarize the established and emerging mechanisms of action of GR, primarily from a structural perspective. This minireview also discusses how the current state of knowledge of GR function may guide future glucocorticoid design with an improved therapeutic index for different inflammatory disorders.
Topics: Animals; DNA; Glucocorticoids; Humans; Protein Binding; Protein Conformation; RNA; Receptors, Glucocorticoid
PubMed: 34709368
DOI: 10.1042/BST20210419 -
Acta Crystallographica. Section F,... May 2022The CENP-SX (MHF) complex is a conserved histone-fold protein complex that is involved in chromosome segregation and DNA repair. It can bind to DNA on its own as well as...
The CENP-SX (MHF) complex is a conserved histone-fold protein complex that is involved in chromosome segregation and DNA repair. It can bind to DNA on its own as well as in complex with other proteins such as CENP-TW and FANCM to recognize specific substrates. CENP-SX binds nonspecifically to dsDNA, similar to other histone-fold proteins. Several low-resolution structures of CENP-SX in complex with DNA are known, but a high-resolution structure is still lacking. The DNA-binding properties of CENP-SX and FANCM-CENP-SX complexes with various lengths of dsDNA were compared and the band-shift patterns and migration positions were found to differ. To confirm the DNA-binding properties in detail, CENP-SX-DNA and FANCM-CENP-SX-DNA complexes were crystallized. Analysis of the crystals revealed that they all contained the CENP-SX-DNA complex, irrespective of the complex that was used in crystallization. Detailed diffraction data analyses revealed that there were two types of crystal with different space groups, P2 and C2, where the volume of the P2 asymmetric unit is twice as large as that of the C2 asymmetric unit. Analysis of the self-rotation function revealed the presence of twofold and fourfold symmetry in both crystals. This suggests that there may be multiple molecules of CENP-SX and DNA within the asymmetric unit with respective symmetry. Structure determination of the present crystals should reveal details of the DNA-binding properties of CENP-SX.
Topics: Crystallization; Crystallography, X-Ray; DNA; DNA-Binding Proteins; Histones
PubMed: 35506764
DOI: 10.1107/S2053230X22003843 -
Molecular Cell Dec 2022CRISPR-Cas are prokaryotic adaptive immune systems. Cas nucleases generally use CRISPR-derived RNA guides to specifically bind and cleave DNA or RNA targets. Here, we...
CRISPR-Cas are prokaryotic adaptive immune systems. Cas nucleases generally use CRISPR-derived RNA guides to specifically bind and cleave DNA or RNA targets. Here, we describe the experimental characterization of a bacterial CRISPR effector protein Cas12m representing subtype V-M. Despite being less than half the size of Cas12a, Cas12m catalyzes auto-processing of a crRNA guide, recognizes a 5'-TTN' protospacer-adjacent motif (PAM), and stably binds a guide-complementary double-stranded DNA (dsDNA). Cas12m has a RuvC domain with a non-canonical catalytic site and accordingly is incapable of guide-dependent cleavage of target nucleic acids. Despite lacking target cleavage activity, the high binding affinity of Cas12m to dsDNA targets allows for interference as demonstrated by its ability to protect bacteria against invading plasmids through silencing invader transcription and/or replication. Based on these molecular features, we repurposed Cas12m by fusing it to a cytidine deaminase that resulted in base editing within a distinct window.
Topics: CRISPR-Associated Proteins; CRISPR-Cas Systems; DNA; Plasmids; RNA; RNA, Guide, CRISPR-Cas Systems
PubMed: 36427491
DOI: 10.1016/j.molcel.2022.11.003 -
Molecular Cell Jan 2023Endogenous and exogenous agents generate DNA-protein crosslinks (DPCs), whose replication-dependent degradation by the SPRTN protease suppresses aging and liver cancer....
Endogenous and exogenous agents generate DNA-protein crosslinks (DPCs), whose replication-dependent degradation by the SPRTN protease suppresses aging and liver cancer. SPRTN is activated after the replicative CMG helicase bypasses a DPC and polymerase extends the nascent strand to the adduct. Here, we identify a role for the 5'-to-3' helicase FANCJ in DPC repair. In addition to supporting CMG bypass, FANCJ is essential for SPRTN activation. FANCJ binds ssDNA downstream of the DPC and uses its ATPase activity to unfold the protein adduct, which exposes the underlying DNA and enables cleavage of the adduct. FANCJ-dependent DPC unfolding is also essential for translesion DNA synthesis past DPCs that cannot be degraded. In summary, our results show that helicase-mediated protein unfolding enables multiple events in DPC repair.
Topics: DNA; DNA Damage; DNA Helicases; DNA Repair; DNA Replication; DNA-Binding Proteins; Protein Unfolding
PubMed: 36608669
DOI: 10.1016/j.molcel.2022.12.005 -
Nature May 2023Nucleotide excision repair removes DNA lesions caused by ultraviolet light, cisplatin-like compounds and bulky adducts. After initial recognition by XPC in global genome...
Nucleotide excision repair removes DNA lesions caused by ultraviolet light, cisplatin-like compounds and bulky adducts. After initial recognition by XPC in global genome repair or a stalled RNA polymerase in transcription-coupled repair, damaged DNA is transferred to the seven-subunit TFIIH core complex (Core7) for verification and dual incisions by the XPF and XPG nucleases. Structures capturing lesion recognition by the yeast XPC homologue Rad4 and TFIIH in transcription initiation or DNA repair have been separately reported. How two different lesion recognition pathways converge and how the XPB and XPD helicases of Core7 move the DNA lesion for verification are unclear. Here we report on structures revealing DNA lesion recognition by human XPC and DNA lesion hand-off from XPC to Core7 and XPA. XPA, which binds between XPB and XPD, kinks the DNA duplex and shifts XPC and the DNA lesion by nearly a helical turn relative to Core7. The DNA lesion is thus positioned outside of Core7, as would occur with RNA polymerase. XPB and XPD, which track the lesion-containing strand but translocate DNA in opposite directions, push and pull the lesion-containing strand into XPD for verification.
Topics: Humans; DNA; DNA Damage; DNA Helicases; DNA Repair; DNA-Binding Proteins; Transcription Factor TFIIH; Xeroderma Pigmentosum Group A Protein; Substrate Specificity; DNA-Directed RNA Polymerases
PubMed: 37076618
DOI: 10.1038/s41586-023-05959-z -
Nature Jun 2023Numerous studies have shown how RNA molecules can adopt elaborate three-dimensional (3D) architectures. By contrast, whether DNA can self-assemble into complex 3D folds...
Numerous studies have shown how RNA molecules can adopt elaborate three-dimensional (3D) architectures. By contrast, whether DNA can self-assemble into complex 3D folds capable of sophisticated biochemistry, independent of protein or RNA partners, has remained mysterious. Lettuce is an in vitro-evolved DNA molecule that binds and activates conditional fluorophores derived from GFP. To extend previous structural studies of fluorogenic RNAs, GFP and other fluorescent proteins to DNA, we characterize Lettuce-fluorophore complexes by X-ray crystallography and cryogenic electron microscopy. The results reveal that the 53-nucleotide DNA adopts a four-way junction (4WJ) fold. Instead of the canonical L-shaped or H-shaped structures commonly seen in 4WJ RNAs, the four stems of Lettuce form two coaxial stacks that pack co-linearly to form a central G-quadruplex in which the fluorophore binds. This fold is stabilized by stacking, extensive nucleobase hydrogen bonding-including through unusual diagonally stacked bases that bridge successive tiers of the main coaxial stacks of the DNA-and coordination of monovalent and divalent cations. Overall, the structure is more compact than many RNAs of comparable size. Lettuce demonstrates how DNA can form elaborate 3D structures without using RNA-like tertiary interactions and suggests that new principles of nucleic acid organization will be forthcoming from the analysis of complex DNAs.
Topics: DNA; G-Quadruplexes; Nucleic Acid Conformation; RNA; Green Fluorescent Proteins; Molecular Mimicry; Crystallography, X-Ray; Cryoelectron Microscopy; Hydrogen Bonding; Cations, Divalent; Cations, Monovalent
PubMed: 37344591
DOI: 10.1038/s41586-023-06229-8 -
Chemical Reviews Jun 2017Metal ions are essential to many chemical, biological, and environmental processes. In the past two decades, many DNA-based metal sensors have emerged. While the main... (Review)
Review
Metal ions are essential to many chemical, biological, and environmental processes. In the past two decades, many DNA-based metal sensors have emerged. While the main biological role of DNA is to store genetic information, its chemical structure is ideal for metal binding via both the phosphate backbone and nucleobases. DNA is highly stable, cost-effective, easy to modify, and amenable to combinatorial selection. Two main classes of functional DNA were developed for metal sensing: aptamers and DNAzymes. While a few metal binding aptamers are known, it is generally quite difficult to isolate such aptamers. On the other hand, DNAzymes are powerful tools for metal sensing since they are selected based on catalytic activity, thus bypassing the need for metal immobilization. In the last five years, a new surge of development has been made on isolating new metal-sensing DNA sequences. To date, many important metals can be selectively detected by DNA often down to the low parts-per-billion level. Herein, each metal ion and the known DNA sequences for its sensing are reviewed. We focus on the fundamental aspect of metal binding, emphasizing the distinct chemical property of each metal. Instead of reviewing each published sensor, a high-level summary of signaling methods is made as a separate section. In principle, each signaling strategy can be applied to many DNA sequences for designing sensors. Finally, a few specific applications are highlighted, and future research opportunities are discussed.
Topics: Biosensing Techniques; DNA; Metals
PubMed: 28598605
DOI: 10.1021/acs.chemrev.7b00063 -
Frontiers in Bioscience (Landmark... Apr 2021Being polymorphic, deoxyribonucleic acid is worthy of raise a variety of structure like right-handed B to left-handed Z conformation. In left-handed contour of DNA... (Comparative Study)
Comparative Study Review
Being polymorphic, deoxyribonucleic acid is worthy of raise a variety of structure like right-handed B to left-handed Z conformation. In left-handed contour of DNA consecutive nucleotides substitute between syn-arrangement and anti-arrangement, through the chain. 2D gel electrophoresis comprising d(PCpG)n of topo isomers of a plasmid inserts d(pCpG)n, in this 'n' ranges among 8 to 21, indicate the change of B-Z DNA. The high denseness of salt is required for conversion of B configuration d(CG)n toward Z configuration. The rate of B to Z transition is measured by "Cytosine Analogues" and "Fluorescence Spectroscopy". h-ZĪ±ADAR1 that a Z-DNA's binding domain, binds and stabilizes one part in Z configuration and therefore the remaining half in B deoxyribonucleic acid configuration. At halfway point, it creates B-Z junction. "Stacking" is the main reason for the B-Z DNA junction construction. Upregulation of ADAM-12, related with Z-DNA is said to a cause for cancer, arthritis, and hypertrophy. Z-DNA forming sequence (ZFS) conjointly generates massive - scale deletion in cells from mammals.
Topics: Alzheimer Disease; Autoimmune Diseases; Biophysics; Cytosine; DNA; DNA, Z-Form; Genome, Human; Humans; Nucleic Acid Conformation; Protein Binding; Protein Domains
PubMed: 34027648
DOI: 10.52586/4922 -
Seminars in Cell & Developmental Biology Jan 2018Atomic force microscopy (AFM) has made significant contributions to the study of protein-DNA interactions by making it possible to topographically image biological... (Review)
Review
Atomic force microscopy (AFM) has made significant contributions to the study of protein-DNA interactions by making it possible to topographically image biological samples. A single protein-DNA binding reaction imaged by AFM can reveal protein binding specificity and affinity, protein-induced DNA bending, and protein binding stoichiometry. Changes in DNA structure, complex conformation, and cooperativity, can also be analyzed. In this review we highlight some important examples in the literature and discuss the advantages and limitations of these measurements. We also discuss important advances in technology that will facilitate the progress of AFM in the future.
Topics: DNA; Humans; Microscopy, Atomic Force; Proteins
PubMed: 28673677
DOI: 10.1016/j.semcdb.2017.06.028 -
ACS Chemical Biology Jul 2018DNA charge transport chemistry involves the migration of charge over long molecular distances through the aromatic base pair stack within the DNA helix. This migration... (Review)
Review
DNA charge transport chemistry involves the migration of charge over long molecular distances through the aromatic base pair stack within the DNA helix. This migration depends upon the intimate coupling of bases stacked one with another, and hence any perturbation in that stacking, through base modifications or protein binding, can be sensed electrically. In this review, we describe the many ways DNA charge transport chemistry has been utilized to sense changes in DNA, including the presence of lesions, mismatches, DNA-binding proteins, protein activity, and even reactions under weak magnetic fields. Charge transport chemistry is remarkable in its ability to sense the integrity of DNA.
Topics: Base Pair Mismatch; DNA; DNA-Binding Proteins; Electrochemical Techniques; Electrons; Intercalating Agents; Magnetic Phenomena; Nucleic Acid Conformation; Protein Binding; Static Electricity
PubMed: 29790735
DOI: 10.1021/acschembio.8b00347