Macromolecule Content

• Total Structure Weight: 5601.59 
• Atom Count: 371 
• Residue Count: 18 
• Unique nucleic acid chains: 2

1C2Q

SOLUTION STRUCTURE OF A DNA.RNA HYBRID CONTAINING AN ALPHAT-ANOMERIC THYMIDINE AND POLARITY REVERSALS

• DOI: 10.2210/pdb1C2Q/pdb
• BMRB: 4547
• NDB: 1C2Q

• Classification: DNA-RNA HYBRID


• Deposited: 1999-07-26 Released: 1999-11-29 
• Deposition Author(s): Germann, M.W., Aramini, J.M.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Submitted: 1 

Literature

Solution structure of a DNA.RNA hybrid containing an alpha-anomeric thymidine and polarity reversals: d(ATGG-3'-3'-alphaT-5'-5'-GCTC). r(gagcaccau).

Aramini, J.M., Germann, M.W.

(1999) Biochemistry 38: 15448-15458

• PubMed: 10569927 


• PubMed Abstract: 
  

We report the thermodynamic and structural properties of an alpha-containing DNA.RNA nonamer hybrid duplex, d(ATGG-3'-3'-alphaT-5'-5'-GCTC).r(gagcaccau). The RNA strand corresponds to the core of the initiation sequence for the transcript of the erbB-2 oncogene. The tandem anomeric and polarity changes in the DNA strand result in a slight decrease in thermostability (DeltaT(m) = -2.8 degrees C) compared to the unmodified control hybrid. The three-dimensional solution structure determination of the alpha-containing DNA.RNA hybrid, conducted via restrained molecular dynamics using interproton distance (nuclear Overhauser enhancement) and furanose ring torsion angle (J-based) restraints, converged to a final ensemble of structures from unique starting models. In agreement with hyperchromicity and circular dichroism data, the final average structure derived from this ensemble is consistent with an overall A-like motif featuring Watson-Crick base pairing and base stacking across the entire sequence, albeit with localized B-like traits within the DNA strand. Comparative pseudorotation analyses of the J-coupling data for this hybrid and its unmodified control reveal a surprising increase in S-puckering for two nucleotides immediately upstream of the 3'-3' linkage, and the associated narrowing of the minor groove in this portion of the hybrid. Other structural perturbations are localized to and diagnostic of the central alpha-nucleotide and juxtaposed polarity reversals. The structural information presented here has direct relevance to the design of future antisense oligonucleotides composed of these modifications.

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Related Citations: 

• NMR solution structures of [d(GCGAAT-3'-3'-(alpha-T)-5'-5'-CGC)2] and its unmodified control
  Aramini, J.M.,Mujeeb, A.,Germann, M.W.
  (1998) Nucleic Acids Res. 26: 5644




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Organizational Affiliation: 

Department of Microbiology and Immunology, Kimmel Cancer Institute, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Length	Organism
5'-D(ATGG-3'-3'-(T3P)-5'-5'-GCTC)-3'	A	9	N/A

Entity ID: 2
Molecule	Chains	Length	Organism
5'-R(GAGCACCAU)-3'	B	9	N/A

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
T3P	A	DNA LINKING	C10 H15 N2 O8 P		DT

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Submitted: 1 

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-07-26 
• Released Date: 1999-11-29 
• Deposition Author(s): Germann, M.W., Aramini, J.M.

Revision History 

• Version 1.0: 1999-11-29
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance