5NYS

M2 G-quadruplex dilute solution


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Pursuing origins of (poly)ethylene glycol-induced G-quadruplex structural modulations.

Trajkovski, M.Endoh, T.Tateishi-Karimata, H.Ohyama, T.Tanaka, S.Plavec, J.Sugimoto, N.

(2018) Nucleic Acids Res. 46: 4301-4315

  • DOI: 10.1093/nar/gky250
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Molecular crowding conditions provided by high concentration of cosolutes are utilized for characterization of biomolecules in cell-mimicking environment and development of drug-delivery systems. In this context, (poly)ethylene glycols are often used ...

    Molecular crowding conditions provided by high concentration of cosolutes are utilized for characterization of biomolecules in cell-mimicking environment and development of drug-delivery systems. In this context, (poly)ethylene glycols are often used for studying non-canonical DNA structures termed G-quadruplexes, which came into focus by emerging structural biology findings and new therapeutic drug design approaches. Recently, several reports were made arguing against using (poly)ethylene glycols in role of molecular crowding agents due to their direct impact on DNA G-quadruplex stability and topology. However, the available data on structural details underlying DNA interaction is very scarce and thus limits in-depth comprehension. Herein, structural and thermodynamic analyses were strategically combined to assess G-quadruplex-cosolute interactions and address previously reported variances regarding the driving forces of G-rich DNA structural transformations under molecular crowding conditions. With the use of complementary (CD, NMR and UV) spectroscopic methods and model approach we characterized DNA G-quadruplex in the presence of the smallest and one of the largest typically used (poly)ethylene glycols. Dehydration effect is the key contributor to ethylene-glycol-induced increased stability of the G-quadruplex, which is in the case of the large cosolute mainly guided by the subtle direct interactions between PEG 8000 and the outer G-quartet regions.


    Organizational Affiliation

    Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, p. p. 537, SI-1000 Ljubljana, Slovenia.,Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, Ljubljana, SI-1000, Slovenia.,Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe 650-0047, Japan.,Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan.,Department of Computational Science, Graduate School of System Informatics, Kobe University, 1-1, Rokkodai, Nada-ku, Kobe 657-8501, Japan.,EN→FIST Centre of Excellence, Trg OF 13, SI-1000 Ljubljana, Slovenia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*AP*GP*GP*GP*AP*CP*GP*GP*GP*CP*GP*GP*GP*CP*AP*GP*GP*GP*T)-3')A20synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the least restraint violations 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-04-11
    Type: Initial release
  • Version 1.1: 2018-05-09
    Type: Data collection, Database references
  • Version 1.2: 2018-05-16
    Type: Data collection, Database references
  • Version 1.3: 2018-10-03
    Type: Data collection
  • Version 1.4: 2019-05-08
    Type: Data collection
  • Version 1.5: 2019-06-19
    Type: Data collection