title: The cellular protein nucleolin preferentially binds long-looped G-quadruplex nucleic acids.
abstract: G-quadruplexes (G4s) are four-stranded nucleic acid structures that form in G-rich sequences. Nucleolin (NCL) is a cellular protein reported for its functions upon G4 recognition, such as induction of neurodegenerative diseases, tumor and virus mechanisms activation. We here aimed at defining NCL/G4 binding determinants.
  
  
  
  Electrophoresis mobility shift assay was used to detect NCL/G4 binding; circular dichroism to assess G4 folding, topology and stability; dimethylsulfate footprinting to detect G bases involved in G4 folding.
  
  
  
  The purified full-length human NCL was initially tested on telomeric G4 target sequences to allow for modulation of loop, conformation, length, G-tract number, stability. G4s in promoter regions with more complex sequences were next employed. We found that NCL binding to G4s heavily relies on G4 loop length, independently of the conformation and oligonucleotide/loop sequence. Low stability G4s are preferred. When alternative G4 conformations are possible, those with longer loops are preferred upon binding to NCL, even if G-tracts need to be spared from G4 folding.
  
  
  
  Our data provide insight into how G4s and the associated proteins may control the ON/OFF molecular switch to several pathological processes, including neurodegeneration, tumor and virus activation. Understanding these regulatory determinants is the first step towards the development of targeted therapies.
  
  
  
  The indication that NCL binding preferentially stimulates and induces folding of G4s containing long loops suggests NCL ability to modify the overall structure and steric hindrance of the involved nucleic acid regions. This protein-induced modification of the G4 structure may represent a cellular mechanosensor mechanism to molecular signaling and disease pathogenesis. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.
authors.affiliation: Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121 Padua, Italy.
authors.forename: Sara
authors.initials: S
authors.lastname: Lago
authors.affiliation: Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121 Padua, Italy.
authors.forename: Elena
authors.initials: E
authors.lastname: Tosoni
authors.affiliation: Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121 Padua, Italy.
authors.forename: Matteo
authors.initials: M
authors.lastname: Nadai
authors.affiliation: Department of Pharmaceutical Sciences, University of Padua, via Marzolo 5, 35131 Padua, Italy.
authors.forename: Manlio
authors.initials: M
authors.lastname: Palumbo
authors.affiliation: Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121 Padua, Italy. Electronic address: sara.richter@unipd.it.
authors.forename: Sara N
authors.initials: SN
authors.lastname: Richter
mesh_terms: D001665:Binding Sites; D002942:Circular Dichroism; D024202:Electrophoretic Mobility Shift Assay; D054856:G-Quadruplexes; D005786:Gene Expression Regulation; D006151:Guanosine / Q000737:chemistry / Q000378:metabolism*; D008024:Ligands; D009691:Nucleic Acid Denaturation; D009841:Oligonucleotides / Q000737:chemistry / Q000378:metabolism*; D009857:Oncogenes; D010750:Phosphoproteins / Q000737:chemistry / Q000378:metabolism*; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D016601:RNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism*; D013329:Structure-Activity Relationship; D016615:Telomere / Q000737:chemistry / Q000378:metabolism; D000097796:Nucleolin
chemical_list: D006151:Guanosine; D008024:Ligands; D009841:Oligonucleotides; D010750:Phosphoproteins; D016601:RNA-Binding Proteins; D000097796:Nucleolin
keywords: Conformation; G-quadruplexes; Loops; Nucleic acids; Nucleolin; Protein-nucleic acid binding