scholarly journals On the binding modes of metal NHC complexes with DNA secondary structures: implications for therapy and imaging

2017 ◽  
Vol 53 (59) ◽  
pp. 8249-8260 ◽  
Author(s):  
Özden Karaca ◽  
Samuel M. Meier-Menches ◽  
Angela Casini ◽  
Fritz E. Kühn
Keyword(s):  
Nucleic Acids ◽  
Secondary Structures ◽  
Binding Modes ◽  
Dna Secondary Structures

This perspective review aims at providing an overview of the most representative examples of bioactive metal NHC complexes reacting with nucleic acidsviadifferent binding modes.

scholarly journals DNA secondary structures are associated with recombination in major Plasmodium falciparum variable surface antigen gene families

2013 ◽  
Vol 42 (4) ◽  
pp. 2270-2281 ◽  
Author(s):  
Adam F. Sander ◽  
Thomas Lavstsen ◽  
Thomas S. Rask ◽  
Michael Lisby ◽  
Ali Salanti ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Membrane Protein ◽  
Erythrocyte Membrane ◽  
Gene Families ◽  
Secondary Structures ◽  
Erythrocyte Membrane Protein ◽  
Sexual Stages ◽  
Dna Secondary Structures ◽  
Parasitic Pathogens ◽  
Falciparum Erythrocyte Membrane Protein

Abstract Many bacterial, viral and parasitic pathogens undergo antigenic variation to counter host immune defense mechanisms. In Plasmodium falciparum, the most lethal of human malaria parasites, switching of var gene expression results in alternating expression of the adhesion proteins of the Plasmodium falciparum-erythrocyte membrane protein 1 class on the infected erythrocyte surface. Recombination clearly generates var diversity, but the nature and control of the genetic exchanges involved remain unclear. By experimental and bioinformatic identification of recombination events and genome-wide recombination hotspots in var genes, we show that during the parasite’s sexual stages, ectopic recombination between isogenous var paralogs occurs near low folding free energy DNA 50-mers and that these sequences are heavily concentrated at the boundaries of regions encoding individual Plasmodium falciparum-erythrocyte membrane protein 1 structural domains. The recombinogenic potential of these 50-mers is not parasite-specific because these sequences also induce recombination when transferred to the yeast Saccharomyces cerevisiae. Genetic cross data suggest that DNA secondary structures (DSS) act as inducers of recombination during DNA replication in P. falciparum sexual stages, and that these DSS-regulated genetic exchanges generate functional and diverse P. falciparum adhesion antigens. DSS-induced recombination may represent a common mechanism for optimizing the evolvability of virulence gene families in pathogens.

scholarly journals Pif1 is essential for efficient replisome progression through lagging strand G-quadruplex DNA secondary structures

2018 ◽  
Vol 46 (22) ◽  
pp. 11847-11857 ◽  
Author(s):  
Danielle Dahan ◽  
Ioannis Tsirkas ◽  
Daniel Dovrat ◽  
Melanie A Sparks ◽  
Saurabh P Singh ◽  
...  
Keyword(s):  
Secondary Structures ◽  
Quadruplex Dna ◽  
G Quadruplex ◽  
Dna Secondary Structures ◽  
Lagging Strand

scholarly journals Non-B DNA Secondary Structures and Their Resolution by RecQ Helicases

2011 ◽  
Vol 2011 ◽  
pp. 1-15 ◽  
Author(s):  
Sudha Sharma
Keyword(s):  
Transcriptional Control ◽  
Molecular Targets ◽  
Secondary Structures ◽  
Special Focus ◽  
Dna Helicases ◽  
Dna Structures ◽  
Recq Helicases ◽  
Alternative Structures ◽  
Dna Secondary Structures ◽  
Secondary Dna Structures

In addition to the canonical B-form structure first described by Watson and Crick, DNA can adopt a number of alternative structures. These non-B-form DNA secondary structures form spontaneously on tracts of repeat sequences that are abundant in genomes. In addition, structured forms of DNA with intrastrand pairing may arise on single-stranded DNA produced transiently during various cellular processes. Such secondary structures have a range of biological functions but also induce genetic instability. Increasing evidence suggests that genomic instabilities induced by non-B DNA secondary structures result in predisposition to diseases. Secondary DNA structures also represent a new class of molecular targets for DNA-interactive compounds that might be useful for targeting telomeres and transcriptional control. The equilibrium between the duplex DNA and formation of multistranded non-B-form structures is partly dependent upon the helicases that unwind (resolve) these alternate DNA structures. With special focus on tetraplex, triplex, and cruciform, this paper summarizes the incidence of non-B DNA structures and their association with genomic instability and emphasizes the roles of RecQ-like DNA helicases in genome maintenance by resolution of DNA secondary structures. In future, RecQ helicases are anticipated to be additional molecular targets for cancer chemotherapeutics.

Stabilised DNA secondary structures with increasing transcription localise hypermutable bases for somatic hypermutation in IGHV3-23

2012 ◽  
Vol 64 (7) ◽  
pp. 481-496 ◽  
Author(s):  
Bhargavi Duvvuri ◽  
Venkata R. Duvvuri ◽  
Jianhong Wu ◽  
Gillian E. Wu
Keyword(s):  
Somatic Hypermutation ◽  
Secondary Structures ◽  
Dna Secondary Structures

scholarly journals Predicting Site-Binding Modes of Ions and Water to Nucleic Acids Using Molecular Solvation Theory

2019 ◽  
Vol 141 (6) ◽  
pp. 2435-2445 ◽  
Author(s):  
George M. Giambaşu ◽  
David A. Case ◽  
Darrin M. York
Keyword(s):  
Nucleic Acids ◽  
Binding Modes ◽  
Solvation Theory ◽  
Site Binding

Light-Induced Formation of G-Quadruplex DNA Secondary Structures

ChemBioChem ◽  
2005 ◽  
Vol 6 (11) ◽  
pp. 1966-1970 ◽  
Author(s):  
Günter Mayer ◽  
Lenz Kröck ◽  
Vera Mikat ◽  
Marianne Engeser ◽  
Alexander Heckel
Keyword(s):  
Secondary Structures ◽  
Quadruplex Dna ◽  
G Quadruplex ◽  
Dna Secondary Structures

scholarly journals Perspectives for Applying G-Quadruplex Structures in Neurobiology and Neuropharmacology

2019 ◽  
Vol 20 (12) ◽  
pp. 2884 ◽  
Author(s):  
Sefan Asamitsu ◽  
Masayuki Takeuchi ◽  
Susumu Ikenoshita ◽  
Yoshiki Imai ◽  
Hirohito Kashiwagi ◽  
...  
Keyword(s):  
Neurological Disorders ◽  
Neurological Diseases ◽  
Secondary Structures ◽  
Neuronal Function ◽  
Double Stranded Rna ◽  
Quadruplex Dna ◽  
Functional Roles ◽  
G Quadruplex ◽  
Dna Secondary Structures

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 these structures under physiologically- and pathologically-relevant conditions, with functional roles in vivo. In this review, we focused on DNA-G4 and RNA-G4, which may have important roles in neuronal function, and reveal mechanisms underlying neurological disorders related to synaptic dysfunction. In addition, we mention the potential of G-quadruplexes as therapeutic targets for neurological diseases.

The Secondary Structures of Nucleic Acids in Organic Solvents1

1961 ◽  
Vol 83 (1) ◽  
pp. 138-142 ◽  
Author(s):  
George K. Helmkamp ◽  
Paul O. P. Ts'o
Keyword(s):  
Nucleic Acids ◽  
Secondary Structures

scholarly journals A short peptide that preferentially binds c-MYC G-quadruplex DNA

2020 ◽  
Vol 56 (63) ◽  
pp. 8940-8943 ◽  
Author(s):  
Aisling Minard ◽  
Danielle Morgan ◽  
Federica Raguseo ◽  
Anna Di Porzio ◽  
Denise Liano ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Human Genome ◽  
Promoter Region ◽  
Secondary Structures ◽  
Quadruplex Dna ◽  
Short Peptide ◽  
G Quadruplex

G-quadruplexes are nucleic-acids secondary structures that are highly abundant in the human genome. In this work,we identified a short-peptide that displays selectivity for the G-quadruplex formed in the promoter region of the oncogene c-MYC.

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