149D

SOLUTION STRUCTURE OF A PYRIMIDINE(DOT)PURINE(DOT) PYRIMIDINE DNA TRIPLEX CONTAINING T(DOT)AT, C+(DOT)GC AND G(DOT)TA TRIPLES

• PDB DOI:  https://doi.org/10.2210/pdb149D/pdb
• NAKB: 149D

• Classification: DNA
• Mutation(s): No 


• Deposited: 1993-11-15 Released: 1994-04-30 
• Deposition Author(s): Radhakrishnan, I., Patel, D.J.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Submitted: 14 

Literature

Solution structure of a pyrimidine.purine.pyrimidine DNA triplex containing T.AT, C+.GC and G.TA triples.

Radhakrishnan, I., Patel, D.J.

(1994) Structure 2: 17

• PubMed: 8075980 
• DOI: https://doi.org/10.1016/s0969-2126(00)00005-8
• Primary Citation of Related Structures:  
  149D


• PubMed Abstract: 
  

Under certain conditions, homopyrimidine oligonucleotides can bind to complementary homopurine sequences in homopurine-homopyrimidine segments of duplex DNA to form triple helical structures. Besides having biological implications in vivo, this property has been exploited in molecular biology applications. This approach is limited by a lack of knowledge about the recognition by the third strand of pyrimidine residues in Watson-Crick base pairs.

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Related Citations: 

• Three-Dimensional Homonuclear Noesy-Tocsy of an Intramolecular Pyrimidine(Dot)Purine(Dot)Pyrimidine DNA Triplex Containing a Central G(Dot)Ta Triple: Nonexchangeable Proton Assignments and Structural Implications
  Radhakrishnan, I., Patel, D.J., Gao, X.
  (1992) Biochemistry 31: 2514

• Solution Conformation of a G(Dot)Ta Triple in an Intramolecular Pyrimidine(Dot)Purine(Dot)Pyrimidine DNA Triplex
  Radhakrishnan, I., Patel, D.J., Veal, J.M., Gao, X.
  (1992) J Am Chem Soc 114: 6913

• NMR Structural Studies of Intramolecular (Y+)N(Dot)(R+)N(Y-)N DNA Triplexes in Solution: Imino and Amino Proton and Nitrogen Markers of G(Dot)Ta Base Triple Formation
  Radhakrishnan, I., Gao, X., De Los Santos, C., Live, D., Patel, D.J.
  (1991) Biochemistry 30: 9022

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 6.3 kDa 
• Atom Count: 417 
• Modelled Residue Count: 21 
• Deposited Residue Count: 21 
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*CP*CP*TP*AP*TP*TP*C)-3'	A	7	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*GP*AP*AP*TP*AP*GP*G)-3'	B	7	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*CP*TP*TP*GP*TP*CP*C)-3'	C	7	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Submitted: 14 

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-04-30 
Deposition Author(s): Radhakrishnan, I., Patel, D.J.

Revision History  

• Version 1.0: 1994-04-30
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-02-16
  Changes: Database references, Derived calculations, Other