DNA quadruplexes participate in many biological functions. It takes up a variety of folds based on the sequence and environment. Here, a meticulous analysis of experimentally determined 437 quadruplex structures (433 PDBs) deposited in the PDB is carried out. The analysis reveals the modular representation of the quadruplex folds. Forty-eight unique quadruplex motifs (whose diversity arises out of the propeller, bulge, diagonal, and lateral loops that connect the quartets) are identified, leading to simple to complex inter/intramolecular quadruplex folds. The two-layered structural motifs are further classified into 33 continuous and 15 discontinuous motifs. While the continuous motifs can directly be extended to a quadruplex fold, the discontinuous motif requires an additional loop(s) to complete a fold, as illustrated here with examples. Similarly, higher-order quadruplex folds can also be represented by continuous or discontinuous motifs or their combinations. Such a modular representation of the quadruplex folds may assist in custom engineering of quadruplexes, designing motif-based drugs, and the prediction of the quadruplex structure. Furthermore, it could facilitate understanding of the role of quadruplexes in biological functions and diseases.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11411666 | PMC |
| http://dx.doi.org/10.1021/acsomega.4c04579 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Position-Dependent Effects of AP Sites Within an Promoter G-Quadruplex Scaffold on Quadruplex Stability and Repair Activity of the APE1 Enzyme.
Int J Mol Sci
January 2025
A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia.
Apurinic/apyrimidinic (AP) sites are endogenous DNA lesions widespread in human cells. Having no nucleobases, they are noncoding and promutagenic. AP site repair is generally initiated through strand incision by AP endonuclease 1 (APE1).
View Article and Find Full Text PDFIon-Regulated Signal Amplification Optical Microfiber Interferometric DNA Sensor.
J Biophotonics
January 2025
Faculty of Physics Science and Technology, Guangxi Normal University, Guilin, China.
Genetic information sensors play a pivotal role in the biomedical field. The detection of deoxyribonucleic acid (DNA) is achieved experimentally using an optical microfiber interferometric sensor, which operates based on an ion-regulation sensitivity enhancement mechanism. The optical microfiber is fabricated by drawing optical fiber into a diameter of less than 10 μm via the melting and tapering technique.
View Article and Find Full Text PDFHigher-Order DNA Secondary Structures and Their Transformations: The Hidden Complexities of Tetrad and Quadruplex DNA Structures, Complexes, and Modulatory Interactions Induced by Strand Invasion Events.
Biomolecules
November 2024
Department of Chemistry and Chemical Biology, Rutgers University, 123 Bevier Rd, Piscataway, NJ 08854, USA.
We demonstrate that a short oligonucleotide complementary to a G-quadruplex domain can invade this iconic, noncanonical DNA secondary structure in ways that profoundly influence the properties and differential occupancies of the resulting DNA polymorphic products. Our spectroscopic mapping of the conformational space of the associated reactants and products, both before and after strand invasion, yield unanticipated outcomes which reveal several overarching features. First, strand invasion induces the disruption of DNA secondary structural elements in both the invading strand (which can assume an iDNA tetrad structure) and the invaded species (a G-quadruplex).
View Article and Find Full Text PDFMetallo-supramolecular complexes enantioselectively target monkeypox virus RNA G-quadruplex and bolster immune responses against MPXV.
Natl Sci Rev
January 2025
Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China.
The Mpox virus (MPXV) has emerged as a formidable orthopoxvirus, posing an immense challenge to global public health. An understanding of the regulatory mechanisms of MPXV infection, replication and immune evasion will benefit the development of novel antiviral strategies. Despite the involvement of G-quadruplexes (G4s) in modulating the infection and replication processes of multiple viruses, their roles in the MPXV life cycle remain largely unknown.
View Article and Find Full Text PDFFree Energy-Based Refinement of DNA Force Field via Modification of Multiple Nonbonding Energy Terms.
J Chem Inf Model
December 2024
Department of Chemistry and Institute of Functional Materials, Pusan National University, Busan 46241, South Korea.
The amber-OL21 force field (ff) was developed to better describe noncanonical DNA, including Z-DNA. Despite its improvements for DNA simulations, this study found that OL21's scope of application was limited by embedded ff artifacts. In a benchmark set of seven DNA molecules, including two double-stranded DNAs transitioning between B- and Z-DNA and five single-stranded DNAs folding into mini-dumbbell or G-quadruplex structures, the free energy landscapes obtained using OL21 revealed several issues: Z-DNA was overly stabilized; misfolded states in mini-dumbbell DNAs were most stable; DNA GQ folding was consistently biased toward an antiparallel topology.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!