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Transcriptional Regulation: Riboswitches01:23

Transcriptional Regulation: Riboswitches

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Riboswitches are RNA elements that regulate gene expression by altering their secondary structures in response to specific effector molecules. These elements, located in the leader regions of certain mRNAs, act as transcriptional regulators by toggling between alternative conformations to control downstream gene expression. Riboswitch-mediated regulation is a precise mechanism for modulating biosynthetic pathways, as exemplified by the riboflavin biosynthesis pathway in Bacillus...
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Riboswitches are non-coding mRNA domains that regulate the transcription and translation of downstream genes without the help of proteins. Riboswitches bind directly to a metabolite and can form unique stem-loop or hairpin structures in response to the amount of the metabolite present. They have two distinct regions – a metabolite-binding aptamer and an expression platform.
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DNA replication is initiated at sites containing predefined DNA sequences known as origins of replication. DNA is unwound at these sites by the minichromosome maintenance (MCM) helicase and other factors such as Cdc45 and the associated GINS complex.The unwound single strands are protected by replication protein A (RPA) until DNA polymerase starts synthesizing DNA at the 5’ end of the strand in the same direction as the replication fork. To prevent the replication fork from falling apart,...
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In the presence of oxidizing agents, phenols are oxidized to quinones. Quinones can be easily reduced back to phenols using mild reducing agents. The electron-donating hydroxyl group enhances the reactivity of the aromatic ring, enabling oxidation of the ring even in the absence of an α hydrogen.
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Updated: Oct 5, 2025

Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes
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Riboflavin Stabilizes Abasic, Oxidized G-Quadruplex Structures.

Rodrigo Galindo-Murillo1, Lauren Winkler1, Jingwei Ma2

  • 1Department of Medicinal Chemistry, College of Pharmacy, University of Utah, 2000 East 30 South Skaggs 306, Salt Lake City, Utah 84112, United States.

Biochemistry
|February 1, 2022
PubMed
Summary
This summary is machine-generated.

Riboflavin preferentially stabilizes G-quadruplex DNA with abasic sites when an oxidized guanine (OG) is adjacent. This preference arises because OG displaces free guanine, allowing riboflavin to bind the vacancy.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Genetics

Background:

  • G-quadruplex DNA structures are crucial in telomeres and gene promoters.
  • These guanine-rich regions are prone to oxidative damage, creating abasic sites.
  • Understanding ligand interactions with damaged G-quadruplexes is vital for genomic stability.

Purpose of the Study:

  • To investigate if abasic sites in G-quadruplexes act as specific ligand recognition sites.
  • To determine if 8-oxo-7,8-dihydroguanine (OG) adjacent to a vacancy influences ligand preference.
  • To assess riboflavin's ability to stabilize abasic site-containing G-quadruplexes.

Main Methods:

  • Molecular dynamics simulations
  • Circular dichroism spectroscopy
  • Nuclear magnetic resonance (NMR) spectroscopy
  • Structural and free energy binding analysis

Main Results:

  • Riboflavin stabilizes abasic site-containing G-quadruplexes specifically when an adjacent OG-modified base is present.
  • The presence of OG displaces free guanine from the tetrad vacancy.
  • Displaced guanine interacts with other G-quadruplex structural elements.

Conclusions:

  • Riboflavin shows a preference for binding abasic sites in OG-adjacent G-quadruplexes over free guanine.
  • This selectivity is mediated by the steric influence of the OG modification.
  • Findings highlight the role of modified bases in directing ligand binding to damaged DNA structures.