1SLS

IMMOBILE SLIPPED-LOOP STRUCTURE (SLS) OF DNA HOMODIMER IN SOLUTION, NMR, 9 STRUCTURES


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 
  • Conformers Submitted: 
  • Selection Criteria: SCORING FUNCTION (WEIGHTED SUM OF DISTANCE RESTRAINTS VIOLATION AND CONFORMATIONAL ENERGY) 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A pseudosquare knot structure of DNA in solution.

Ulyanov, N.B.Ivanov, V.I.Minyat, E.E.Khomyakova, E.B.Petrova, M.V.Lesiak, K.James, T.L.

(1998) Biochemistry 37: 12715-12726

  • DOI: 10.1021/bi981018d

  • PubMed Abstract: 
  • We report a high-resolution NMR structure of a homodimer formed by a synthetic 25 residue DNA oligonucleotide GCTCCCATGGTTTTTGTGCACGAGC. This structure presents a novel structural motif for single-stranded nucleic acids, called a pseudosquare knot (P ...

    We report a high-resolution NMR structure of a homodimer formed by a synthetic 25 residue DNA oligonucleotide GCTCCCATGGTTTTTGTGCACGAGC. This structure presents a novel structural motif for single-stranded nucleic acids, called a pseudosquare knot (PSQ). The oligonucleotide was originally designed to mimic a slipped-loop structure (SLS), another "unusual" DNA structure postulated as an alternative conformation for short direct repeats in double-stranded DNA. The design of the sequence is compatible with both SLS and PSQ structures, both of which possess identical sets of base-paired and unpaired nucleotides but different tertiary folds. We used deuteration of the H8 positions of purines to ascertain that the PSQ is actually formed under the conditions used. The PSQ structure was solved based on homonuclear proton nuclear Overhauser effect data using complete relaxation matrix methods. The structure essentially consists of two side-by-side helices connected by single-stranded loops. Each of the helices is well-defined; however, the relative orientation of the two remains undetermined by the NMR data. The sequences compatible with the PSQ formation are frequent in single-stranded genomes; this structure may play a role as a dimerization motif.


    Organizational Affiliation

    Department of Pharmaceutical Chemistry, University of California, San Francisco 94143-0446, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
OLIGODEOXYRIBONUCLEOTIDEA,B25N/A
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 
  • Conformers Submitted: 
  • Selection Criteria: SCORING FUNCTION (WEIGHTED SUM OF DISTANCE RESTRAINTS VIOLATION AND CONFORMATIONAL ENERGY) 
Software Package:
Software NamePurpose
DYANAmodel building
DYANArefinement
AMBERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-04-08
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance