First Ruthenium(II) Polypyridyl Complex As a True Molecular “Light Switch” for Triplex RNA Structure: [Ru(phen)2(mdpz)]2+ Enhances the Stability of Poly(U)·Poly(A)*Poly(U)

2012 ◽  
Vol 51 (8) ◽  
pp. 4417-4419 ◽  
Author(s):  
Li-Feng Tan ◽  
Jing Liu ◽  
Jian-Liang Shen ◽  
Xiao-hua Liu ◽  
Le-Li Zeng ◽  
...  
Keyword(s):  
Rna Structure ◽  
Polypyridyl Complex ◽  
Molecular Light Switch ◽  
The Stability

scholarly journals The effect of hairpin loop on the structure and gene expression activity of the long-loop G-quadruplex

2021 ◽  
Author(s):  
Subramaniyam Ravichandran ◽  
Maria Razzaq ◽  
Nazia Parveen ◽  
Ambarnil Ghosh ◽  
Kyeong Kyu Kim
Keyword(s):  
Gene Expression ◽  
Rna Structure ◽  
Biological Significance ◽  
Cellular Functions ◽  
Hairpin Loops ◽  
G Quadruplex ◽  
Reporter Assays ◽  
Expression Activity ◽  
The Stability ◽  
And Function

Abstract G-quadruplex (G4), a four-stranded DNA or RNA structure containing stacks of guanine tetrads, plays regulatory roles in many cellular functions. So far, conventional G4s containing loops of 1–7 nucleotides have been widely studied. Increasing experimental evidence suggests that unconventional G4s, such as G4s containing long loops (long-loop G4s), play a regulatory role in the genome by forming a stable structure. Other secondary structures such as hairpins in the loop might thus contribute to the stability of long-loop G4s. Therefore, investigation of the effect of the hairpin-loops on the structure and function of G4s is required. In this study, we performed a systematic biochemical investigation of model G4s containing long loops with various sizes and structures. We found that the long-loop G4s are less stable than conventional G4s, but their stability increased when the loop forms a hairpin (hairpin-G4). We also verified the biological significance of hairpin-G4s by showing that hairpin-G4s present in the genome also form stable G4s and regulate gene expression as confirmed by in cellulo reporter assays. This study contributes to expanding the scope and diversity of G4s, thus facilitating future studies on the role of G4s in the human genome.

scholarly journals Mutations in an essential U2 small nuclear RNA structure cause cold-sensitive U2 small nuclear ribonucleoprotein function by favoring competing alternative U2 RNA structures.

1994 ◽  
Vol 14 (3) ◽  
pp. 1689-1697 ◽  
Author(s):  
M I Zavanelli ◽  
J S Britton ◽  
A H Igel ◽  
M Ares
Keyword(s):  
Rna Structure ◽  
Cold Sensitivity ◽  
Small Nuclear Rna ◽  
Stem Loop ◽  
Alternative Structures ◽  
Small Nuclear Ribonucleoprotein ◽  
Alternative Conformation ◽  
Cold Sensitive ◽  
The Stability ◽  
Nuclear Ribonucleoprotein

Mutations in stem-loop IIa of yeast U2 RNA cause cold-sensitive growth and cold-sensitive U2 small nuclear ribonucleoprotein function in vitro. Cold-sensitive U2 small nuclear RNA adopts an alternative conformation that occludes the loop and disrupts the stem but does so at both restrictive and permissive temperatures. To determine whether alternative U2 RNA structure causes the defects, we tested second-site mutations in U2 predicted to disrupt the alternative conformation. We find that such mutations efficiently suppress the cold-sensitive phenotypes and partially restore correct U2 RNA folding. A genetic search for additional suppressors of cold sensitivity revealed two unexpected mutations in the base of an adjacent stem-loop. Direct probing of RNA structure in vivo indicates that the suppressors of cold sensitivity act to improve the stability of the essential stem relative to competing alternative structures by disrupting the alternative structures. We suggest that many of the numerous cold-sensitive mutations in a variety of RNAs and RNA-binding proteins could be a result of changes in the stability of a functional RNA conformation relative to a competing structure. The presence of an evolutionarily conserved U2 sequence positioned to form an alternative structure argues that this region of U2 is dynamic during the assembly or function of the U2 small nuclear ribonucleoprotein.

scholarly journals Dynamic Molecular Epidemiology Reveals Lineage-Associated Single-Nucleotide Variants That Alter RNA Structure in Chikungunya Virus

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 239
Author(s):  
Thomas Spicher ◽  
Markus Delitz ◽  
Adriano de Bernardi Schneider ◽  
Michael T. Wolfinger
Keyword(s):  
Molecular Epidemiology ◽  
South African ◽  
Rna Structure ◽  
Chikungunya Virus ◽  
Rna Structures ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Web Based ◽  
The Stability ◽  
Human Infections

Chikungunya virus (CHIKV) is an emerging Alphavirus which causes millions of human infections every year. Outbreaks have been reported in Africa and Asia since the early 1950s, from three CHIKV lineages: West African, East Central South African, and Asian Urban. As new outbreaks occurred in the Americas, individual strains from the known lineages have evolved, creating new monophyletic groups that generated novel geographic-based lineages. Building on a recently updated phylogeny of CHIKV, we report here the availability of an interactive CHIKV phylodynamics dataset, which is based on more than 900 publicly available CHIKV genomes. We provide an interactive view of CHIKV molecular epidemiology built on Nextstrain, a web-based visualization framework for real-time tracking of pathogen evolution. CHIKV molecular epidemiology reveals single nucleotide variants that change the stability and fold of locally stable RNA structures. We propose alternative RNA structure formation in different CHIKV lineages by predicting more than a dozen RNA elements that are subject to perturbation of the structure ensemble upon variation of a single nucleotide.

A novel, label-free fluorescent aptasensor for cocaine detection based on a G-quadruplex and ruthenium polypyridyl complex molecular light switch

2016 ◽  
Vol 8 (18) ◽  
pp. 3740-3746 ◽  
Author(s):  
Songbai Zhang ◽  
Linping Wang ◽  
Meiling Liu ◽  
Yanqing Qiu ◽  
Mengna Wang ◽  
...  
Keyword(s):  
High Selectivity ◽  
Label Free ◽  
Ruthenium Polypyridyl ◽  
Polypyridyl Complex ◽  
G Quadruplex ◽  
Molecular Light Switch ◽  
Cocaine Detection ◽  
Fluorescent Aptasensor

A [Ru(bpy)2(bqdppz)]2+ ligand with high selectivity towards G-quadruplex was synthesized and introduced to serve as a prominent molecular light switch via specifically recognizing the cocaine aptamer-involved G-quadruplex.

A functionalized cobalt(III) mixed-polypyridyl complex as a newly designed DNA molecular light switch

2003 ◽  
Vol 95 (2-3) ◽  
pp. 194-198 ◽  
Author(s):  
Qian-Ling Zhang ◽  
Jian-Hong Liu ◽  
Xiang-Zhong Ren ◽  
Hong Xu ◽  
Yi Huang ◽  
...  
Keyword(s):  
Polypyridyl Complex ◽  
Molecular Light Switch

scholarly journals Mutations in an essential U2 small nuclear RNA structure cause cold-sensitive U2 small nuclear ribonucleoprotein function by favoring competing alternative U2 RNA structures

1994 ◽  
Vol 14 (3) ◽  
pp. 1689-1697
Author(s):  
M I Zavanelli ◽  
J S Britton ◽  
A H Igel ◽  
M Ares
Keyword(s):  
Rna Structure ◽  
Cold Sensitivity ◽  
Small Nuclear Rna ◽  
Stem Loop ◽  
Alternative Structures ◽  
Small Nuclear Ribonucleoprotein ◽  
Alternative Conformation ◽  
Cold Sensitive ◽  
The Stability ◽  
Nuclear Ribonucleoprotein

Mutations in stem-loop IIa of yeast U2 RNA cause cold-sensitive growth and cold-sensitive U2 small nuclear ribonucleoprotein function in vitro. Cold-sensitive U2 small nuclear RNA adopts an alternative conformation that occludes the loop and disrupts the stem but does so at both restrictive and permissive temperatures. To determine whether alternative U2 RNA structure causes the defects, we tested second-site mutations in U2 predicted to disrupt the alternative conformation. We find that such mutations efficiently suppress the cold-sensitive phenotypes and partially restore correct U2 RNA folding. A genetic search for additional suppressors of cold sensitivity revealed two unexpected mutations in the base of an adjacent stem-loop. Direct probing of RNA structure in vivo indicates that the suppressors of cold sensitivity act to improve the stability of the essential stem relative to competing alternative structures by disrupting the alternative structures. We suggest that many of the numerous cold-sensitive mutations in a variety of RNAs and RNA-binding proteins could be a result of changes in the stability of a functional RNA conformation relative to a competing structure. The presence of an evolutionarily conserved U2 sequence positioned to form an alternative structure argues that this region of U2 is dynamic during the assembly or function of the U2 small nuclear ribonucleoprotein.

scholarly journals Dynamic molecular epidemiology reveals lineage-associated single-nucleotide variants that alter RNA structure in Chikungunya virus

2021 ◽  
Author(s):  
Thomas Spicher ◽  
Markus Delitz ◽  
Adriano de Bernardi Schneider ◽  
Michael T. Wolfinger
Keyword(s):  
Molecular Epidemiology ◽  
South African ◽  
Rna Structure ◽  
Chikungunya Virus ◽  
Rna Structures ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Web Based ◽  
The Stability ◽  
Human Infections

Chikungunya virus (CHIKV) is an emerging Alphavirus which causes millions of human infections every year. Outbreaks have been reported in Africa and Asia since the early 1950s, from three CHIKV lineages: West African, East Central South African, and Asian Urban. As new outbreaks occurred in the Americas, individual strains from the known lineages have evolved, creating new monophyletic groups that generated novel geographic-based lineages. Building on a recently updated phylogeny of CHIKV, we report here the availability of an interactive CHIKV phylodynamics dataset, which is based on more than 900 publicly available CHIKV genomes. We provide an interactive view of CHIKV molecular epidemiology built on Nextstrain, a web-based visualization framework for real-time tracking of pathogen evolution. CHIKV molecular epidemiology reveals single nucleotide variants that change the stability and fold of locally stable RNA structures. We propose alternative RNA structure formation in different CHIKV lineages by predicting more than a dozen RNA elements that are subject to perturbation of the structure ensemble upon variation of a single nucleotide.

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