Specific Binding of Modified RGG Domain in TLS/FUS to G-Quadruplex RNA: Tyrosines in RGG Domain Recognize 2′-OH of the Riboses of Loops in G-Quadruplex

2013 ◽  
Vol 135 (48) ◽  
pp. 18016-18019 ◽  
Author(s):  
Kentaro Takahama ◽  
Takanori Oyoshi
Keyword(s):  
Specific Binding ◽  
G Quadruplex

scholarly journals Structural and Functional Aspects of G-Quadruplex Aptamers Which Bind a Broad Range of Influenza A Viruses

Biomolecules ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 119
Author(s):  
Anastasia A. Novoseltseva ◽  
Nikita M. Ivanov ◽  
Roman A. Novikov ◽  
Yaroslav V. Tkachev ◽  
Dmitry A. Bunin ◽  
...  
Keyword(s):  
Influenza A ◽  
Specific Binding ◽  
Dna Aptamer ◽  
Size Exclusion ◽  
Influenza A Viruses ◽  
Strain Specificity ◽  
Influenza Hemagglutinin ◽  
Functional Aspects ◽  
G Quadruplex ◽  
Exclusion Chromatography

An aptamer is a synthetic oligonucleotide with a unique spatial structure that provides specific binding to a target. To date, several aptamers to hemagglutinin of the influenza A virus have been described, which vary in affinity and strain specificity. Among them, the DNA aptamer RHA0385 is able to recognize influenza hemagglutinins with highly variable sequences. In this paper, the structure of RHA0385 was studied by circular dichroism spectroscopy, nuclear magnetic resonance, and size-exclusion chromatography, demonstrating the formation of a parallel G-quadruplex structure. Three derivatives of RHA0385 were designed in order to determine the contribution of the major loop to affinity. Shortening of the major loop from seven to three nucleotides led to stabilization of the scaffold. The affinities of the derivatives were studied by surface plasmon resonance and an enzyme-linked aptamer assay on recombinant hemagglutinins and viral particles, respectively. The alterations in the loop affected the binding to influenza hemagglutinin, but did not abolish it. Contrary to aptamer RHA0385, two of the designed aptamers were shown to be conformationally homogeneous, retaining high affinities and broad binding abilities for both recombinant hemagglutinins and whole influenza A viruses.

Specific Binding of a d ‐RNA G‐Quadruplex Structure with an l ‐RNA Aptamer

2020 ◽  
Vol 132 (13) ◽  
pp. 5331-5335
Author(s):  
Chun‐Yin Chan ◽  
Chun Kit Kwok
Keyword(s):  
Specific Binding ◽  
Rna Aptamer ◽  
Quadruplex Structure ◽  
G Quadruplex

scholarly journals Crystal structure reveals specific recognition of a G-quadruplex RNA by a β-turn in the RGG motif of FMRP

2015 ◽  
Vol 112 (39) ◽  
pp. E5391-E5400 ◽  
Author(s):  
Nikita Vasilyev ◽  
Anna Polonskaia ◽  
Jennifer C. Darnell ◽  
Robert B. Darnell ◽  
Dinshaw J. Patel ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Rna Binding ◽  
Specific Binding ◽  
Fragile X ◽  
Type I ◽  
Shape Complementarity ◽  
G Quadruplex ◽  
Rna Duplexes ◽  
Human Disorders

Fragile X Mental Retardation Protein (FMRP) is a regulatory RNA binding protein that plays a central role in the development of several human disorders including Fragile X Syndrome (FXS) and autism. FMRP uses an arginine-glycine-rich (RGG) motif for specific interactions with guanine (G)-quadruplexes, mRNA elements implicated in the disease-associated regulation of specific mRNAs. Here we report the 2.8-Å crystal structure of the complex between the human FMRP RGG peptide bound to the in vitro selected G-rich RNA. In this model system, the RNA adopts an intramolecular K+-stabilized G-quadruplex structure composed of three G-quartets and a mixed tetrad connected to an RNA duplex. The RGG peptide specifically binds to the duplex–quadruplex junction, the mixed tetrad, and the duplex region of the RNA through shape complementarity, cation–π interactions, and multiple hydrogen bonds. Many of these interactions critically depend on a type I β-turn, a secondary structure element whose formation was not previously recognized in the RGG motif of FMRP. RNA mutagenesis and footprinting experiments indicate that interactions of the peptide with the duplex–quadruplex junction and the duplex of RNA are equally important for affinity and specificity of the RGG–RNA complex formation. These results suggest that specific binding of cellular RNAs by FMRP may involve hydrogen bonding with RNA duplexes and that RNA duplex recognition can be a characteristic RNA binding feature for RGG motifs in other proteins.

scholarly journals A study on a telo21 G-quadruplex DNA specific binding ligand: enhancing the molecular recognition ability via the amino group interactions

RSC Advances ◽  
2018 ◽  
Vol 8 (36) ◽  
pp. 20222-20227 ◽  
Author(s):  
Dongli Li ◽  
Jin-Qiang Hou ◽  
Wei Long ◽  
Yu-Jing Lu ◽  
Wing-Leung Wong ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Specific Binding ◽  
Amino Group ◽  
Amino Groups ◽  
Group Interactions ◽  
Quadruplex Dna ◽  
Fluorescent Signal ◽  
Hydrogen Bonding Interactions ◽  
G Quadruplex ◽  
Recognition Ability

A significant fluorescent signal enhancement attributed to hydrogen-bonding interactions through the amino groups of a small binding ligand in the G-quartets (binding energy: −6.2 kcal mol−1).

scholarly journals Correction: A study on a telo21 G-quadruplex DNA specific binding ligand: enhancing the molecular recognition ability via the amino group interactions

RSC Advances ◽  
2018 ◽  
Vol 8 (41) ◽  
pp. 22931-22931
Author(s):  
Dongli Li ◽  
Jin-Qiang Hou ◽  
Wei Long ◽  
Yu-Jing Lu ◽  
Wing-Leung Wong ◽  
...  
Keyword(s):  
Molecular Recognition ◽  
Specific Binding ◽  
Amino Group ◽  
Group Interactions ◽  
Quadruplex Dna ◽  
G Quadruplex ◽  
Recognition Ability

Correction for ‘A study on a telo21 G-quadruplex DNA specific binding ligand: enhancing the molecular recognition ability via the amino group interactions’ by Dongli Li et al., RSC Adv., 2018, 8, 20222–20227.

scholarly journals Timeless couples G quadruplex detection with processing by DDX11 during DNA replication

2019 ◽  
Author(s):  
Leticia Koch Lerner ◽  
Sandro Holzer ◽  
Mairi L. Kilkenny ◽  
Pierre Murat ◽  
Saša Šviković ◽  
...  
Keyword(s):  
Dna Replication ◽  
Secondary Structure ◽  
Specific Binding ◽  
C Terminus ◽  
Epigenetic Instability ◽  
G Quadruplex ◽  
Fork Protection Complex ◽  
Associated Proteins ◽  
The Stability

Regions of the genome with the potential to form secondary structure pose a frequent and significant impediment to DNA replication and must be actively managed in order to preserve genetic and epigenetic integrity. The fork protection complex (FPC), a conserved group of replisome-associated proteins including Timeless, Tipin, and Claspin, plays an important role in maintaining efficient replisome activation, ensuring optimum fork rates, sister chromatid cohesion and checkpoint function. It also helps maintain the stability of sequences prone to secondary structure formation through an incompletely understood mechanism. Here, we report a previously unappreciated DNA binding domain in the C-terminus of Timeless, which exhibits specific binding to G quadruplex (G4) structures. We show that, in vivo, both the C-terminus of Timeless and the DDX11 helicase act collaboratively to ensure processive replication of G4 structures to prevent genetic and epigenetic instability.

scholarly journals Specific Binding of Anionic Porphyrin and Phthalocyanine to the G-Quadruplex with a Variety of in Vitro and in Vivo Applications

Molecules ◽  
2012 ◽  
Vol 17 (9) ◽  
pp. 10586-10613 ◽  
Author(s):  
Hidenobu Yaku ◽  
Takashi Murashima ◽  
Daisuke Miyoshi ◽  
Naoki Sugimoto
Keyword(s):  
Specific Binding ◽  
G Quadruplex
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