Macromolecule Content

• Total Structure Weight: 7481.87 
• Atom Count: 497 
• Residue Count: 24 
• Unique nucleic acid chains: 2

1CX5

ANTISENSE DNA/RNA HYBRID CONTAINING MODIFIED BACKBONE

• DOI: 10.2210/pdb1CX5/pdb
• NDB: 1CX5

• Classification: DNA-RNA HYBRID


• Deposited: 1999-08-28 Released: 1999-09-14 
• Deposition Author(s): Yang, X., Han, X., Cross, C., Sanghvi, Y., Gao, X.

---

Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 9 
• Conformers Submitted: 1 
• Selection Criteria: all calculated structures submitted,back calculated data agree with experimental NOESY spectrum 

Literature

NMR structure of an antisense DNA.RNA hybrid duplex containing a 3'-CH(2)N(CH(3))-O-5' or an MMI backbone linker.

Yang, X., Han, X., Cross, C., Bare, S., Sanghvi, Y., Gao, X.

(1999) Biochemistry 38: 12586-12596

• PubMed: 10504227 


• PubMed Abstract: 
  

The solution structure of an antisense DNA.RNA hybrid duplex, d(CGCGTT-MMI-TTGCGC).r(GCGCAAAACGCG) (designated R4), containing an MMI backbone linker [3'-CH(2)N(CH(3))-O5'], is elucidated. The structural details of the MMI linker, its structural effects on the neighboring residues, and the molecular basis of the MMI effects are examined. The lipophilic N-methyl group of MMI is peripheral to the helix, assuming a conformation that is most stable with regard to the N-O torsion angle. The MMI linker promotes a 3'-endo conformation for the sugar moieties at both 3'- and 5'-adjacent positions and a backbone kink involving distant residues along the 3'-direction. Comparison of R4 with other analogous hybrid duplexes previously studied in this laboratory reveals a new family of low-energy helical conformations that can be accommodated in stable duplexes and a common feature of C3'-modified sugars for adopting a C3'-endo pucker. The results of these studies emphasize the interplay of several factors that govern the formation of stable hybrid duplexes and provide a basis for the understanding of the biological role of the MMI modifications, which are important building blocks for a family of promising chimeric antisense oligonucleotides.

---

Organizational Affiliation: 

Department of Chemistry, University of Houston, 4800 Calhoun Street, Houston, Texas 77204-5641, and ISIS Pharmaceuticals, Inc., 2280 Faraday Avenue, Carlsbad, California 92008, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Length	Organism
5'-D(*CP*GP*CP*GP*TP*T*(MMT)P*TP*GP*CP*GP*C)	A	12	N/A

Entity ID: 2
Molecule	Chains	Length	Organism
5'-R(*GP*CP*GP*CP*AP*AP*AP*AP*CP*GP*CP*G)	B	12	N/A

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MMT	A	DNA LINKING	C12 H19 N3 O5		DT

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 9 
• Conformers Submitted: 1 
• Selection Criteria: all calculated structures submitted,back calculated data agree with experimental NOESY spectrum 

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-08-28 
• Released Date: 1999-09-14 
• Deposition Author(s): Yang, X., Han, X., Cross, C., Sanghvi, Y., Gao, X.

Revision History 

• Version 1.0: 1999-09-14
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance