Macromolecule Content

• Total Structure Weight: 4.96 kDa 
• Atom Count: 329 
• Residue Count: 16 
• Unique nucleic acid chains: 2

1NTQ

5'(dCCUCCUU)3':3'(rAGGAGGAAA)5'

• DOI: 10.2210/pdb1NTQ/pdb
• BMRB: 5775
• NDB: 1NTQ

• Classification: DNA/RNA
• Mutation(s): No 


• Deposited: 2003-01-30 Released: 2003-06-10 
• Deposition Author(s): Znosko, B.M., Barnes III, T.W., Krugh, T.R., Turner, D.H.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Submitted: 1 

Literature

NMR Studies of DNA Single Strands and DNA:RNA Hybrids With and Without 1-Propynylation at C5 of Oligopyrimidines

Znosko, B.M., Barnes III, T.W., Krugh, T.R., Turner, D.H.

(2003) J Am Chem Soc 125: 6090-6097

• PubMed: 12785839 
• DOI: 10.1021/ja021285d
• Structures With Same Primary Citation


• PubMed Abstract: 
  

The 1-propynylation at C5 of consecutive pyrimidines in DNA can enhance DNA:RNA hybrid stability at 37 degrees C by over 1 kcal/mol of substitution [Barnes, T. W., III; Turner, D. H. J. Am. Chem. Soc.2001, 123, 4107-4118]. To provide information on the structural consequences of propynylation, two-dimensional NMR spectroscopy was used to study the structures of several oligonucleotides. Intraresidue nuclear Overhauser effect spectroscopy cross peaks were observed at 30 degrees C and a 200 ms mixing time in the H6-H1' region for 5'(dC(P)C(P)U(P)C(P)C(P)U(P)U(P)) (ssPrODN) but not for 5'(dCCUCCUU) (ssODN), suggesting preorganization of the propynylated single strand. NMR structures of the duplexes 5'(dC(P)C(P)U(P)C(P)C(P)U(P)U(P))3':3'(rGAGGAGGAAAU)5' (PrODN:RNA), 5'(dCC(P)U(P)C(P)C(P)U(P)U(P))3':3'(rGAGGAGGAAAU)5' (sPrODN1:RNA), and 5'(dCCUCCUU)3':3'(rGAGGAGGAAAU)5' (ODN:RNA) indicate that their global structures are almost identical. The NMR data, however, suggest that the 5'-end of sPrODN1:RNA is more dynamic than that of PrODN:RNA. In the propynylated duplexes, the propyne group stacks on the aromatic ring of the 5'-base and extends into the major groove. The results suggest that the increased stability of the propynylated duplexes is caused by preorganization of the propynylated single strand and different interactions in the double strand. The propynyl group provides volume exclusion, enhanced stacking, and possibly different solvation.

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Related Citations: 

• Long-Range Cooperativity in Molecular Recognition of RNA by Oligodeoxynucleotides with Multiple C5-(1-Propynyl) Pyrimidines
  Barnes III, T.W., Turner, D.H.
  (2001) J Am Chem Soc 123: 4107

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Organizational Affiliation: 

Department of Chemistry, University of Rochester, New York 14627-0216, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism
5'-R(*AP*AP*AP*GP*GP*AP*GP*GP*A)-3'	A	9	N/A

Entity ID: 2
Molecule	Chains	Length	Organism
5'-D(*CP*CP*UP*CP*CP*UP*U)-3'	B	7	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Submitted: 1 
• OLDERADO: 1NTQ Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-01-30 
• Released Date: 2003-06-10 
Deposition Author(s): Znosko, B.M., Barnes III, T.W., Krugh, T.R., Turner, D.H.

Revision History 

• Version 1.0: 2003-06-10
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance