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Proteins targeted to the nucleus carry short stretches of amino acid sequences called the nuclear localization signal or NLS. Classical nuclear localization signals are of two types: monopartite and bipartite NLS. Monopartite classical NLS (cNLS) consists of a single cluster of 4-8 amino acids. Bipartite cNLS consists of two clusters of  2-3 amino acids and a 9-12 residue long proline-rich linker bridging the two clusters. Signal clusters are rich in positively charged amino acids such as...
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The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
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The nucleolus is the most prominent substructure of the nucleus. When it was first discovered, it was considered to be an isolated organelle that forms fibrils and granules. In 1931, the relationship between the nucleolus and chromosomes was first described by Heitz. He observed that the appearance and size of nucleolus varies depending on the stage of the cell cycle. He also noticed constricted regions on different chromosomes clustered together at definite cell cycle stages. These regions,...
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For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...
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In humans, more than 80% of the genome gets transcribed. However, only around 2% of the genome codes for proteins. The remaining part produces non-coding RNAs which includes ribosomal RNAs, transfer RNAs, telomerase RNAs, and regulatory RNAs, among other types. A large number of regulatory non-coding RNAs have been classified into two groups depending upon their length – small non-coding RNAs, such as microRNA, which are less than 200 nucleotides in length, and long non-coding RNA...
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Nuclear protein sorting is the selective trafficking of histones, polymerases, gene regulatory proteins into the nucleus and exporting RNAs and ribosomes to the cytosol. It is a tightly controlled process that regulates gene expression within a cell.
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Related Experiment Video

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Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes
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Nucleolin Discriminates Drastically between Long-Loop and Short-Loop Quadruplexes.

Abhijit Saha1,2, Patricia Duchambon1,2, Vanessa Masson3

  • 1CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, 91405 Orsay, France.

Biochemistry
|March 20, 2020
PubMed
Summary
This summary is machine-generated.

Nucleolin (NCL) protein binds strongly to long-loop G-quadruplexes (G4s) but weakly to short-loop variants. This interaction is mediated by specific protein domains, revealing a dual recognition mechanism for G4 structures.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Structural Biology

Background:

  • Nucleolin (NCL) is a multifunctional protein involved in various cellular processes.
  • G-quadruplexes (G4s) are non-canonical DNA structures implicated in gene regulation.
  • The interaction between NCL and G4s is not fully understood, particularly regarding structural determinants.

Purpose of the Study:

  • To investigate the binding affinity of NCL to G4 structures with varying loop lengths.
  • To identify the specific domains and residues of NCL involved in G4 recognition.
  • To elucidate the molecular mechanism of NCL-G4 interaction and G4 ligand efficacy.

Main Methods:

  • Synthesis of G4 sequences with diverse central loop lengths.
  • Photo-cross-linking experiments with modified G4 sequences.
  • Quantitative proteomic analysis (LC-MS/MS) for NCL contact site identification.
  • Inhibition assays using benchmark G4 ligands.

Main Results:

  • NCL exhibits strong binding to long-loop (5-9 nt) G4s and weak binding to short-loop (<3 nt) G4s.
  • The WT-CEB25-L191 (9 nt loop) G4 was identified as the optimal substrate for NCL.
  • A 15-amino acid fragment in helix α2 of NCL's RNA binding domain 2 (RBD2) was identified as a key contact site.
  • Only the potent G4 ligand PhenDC3 inhibited NCL binding, suggesting RGG domain involvement.

Conclusions:

  • NCL recognizes G4 structures through a dual mechanism involving RBD2 and RGG domains.
  • The length of the G4 central loop is a critical determinant for NCL binding.
  • A model is proposed for NCL-G4 recognition, highlighting the importance of both loop-quartet interactions.