1K1H

HETERODUPLEX OF CHIRALLY PURE METHYLPHOSPHONATE/DNA DUPLEX


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of hybrid backbone methylphosphonate DNA heteroduplexes: effect of R and S stereochemistry.

Thiviyanathan, V.Vyazovkina, K.V.Gozansky, E.K.Bichenchova, E.Abramova, T.V.Luxon, B.A.Lebedev, A.V.Gorenstein, D.G.

(2002) Biochemistry 41: 827-838

  • Primary Citation of Related Structures:  1K1R

  • PubMed Abstract: 
  • Methyl phosphonate oligonucleotides have been used as antisense and antigene agents. Substitution of a methyl group for oxygen in the phosphate ester backbone introduces a new chiral center. Significant differences in physical properties and hybridiz ...

    Methyl phosphonate oligonucleotides have been used as antisense and antigene agents. Substitution of a methyl group for oxygen in the phosphate ester backbone introduces a new chiral center. Significant differences in physical properties and hybridization abilities are observed between the R(p) and S(p) diastereomers. Chirally pure methylphosphonate deoxyribooligonucleotides were synthesized, and the solution structures of duplexes formed between a single strand heptanucleotide methylphosphonate, d(Cp(Me)Cp(Me)Ap(Me)Ap(Me)Ap(Me)Cp(Me)A), hybridized to a complementary octanucleotide, d(TpGpTpTpTpGpGpC), were studied by NMR spectroscopy. Stereochemistry at the methylphosphonate center for the heptanucleotide was either RpRpRpRpRpRp (R(p) stereoisomer) or RpRpRpSpRpRp (S(p) stereoisomer, although only one of the six methylphosphonate centers has the S(p) stereochemistry). The results show that the methylphosphonate strands in the heteroduplexes exhibit increased dynamics relative to the DNA strand. Substitution of one chiral center from R(p) to S(p) has a profound effect on the hybridization ability of the methylphosphonate strand. Sugars in the phosphodiester strand exhibit C(2)(') endo sugar puckering while the sugars in the methyl phosphonate strand exhibit an intermediate C(4)(') endo puckering. Bases are well stacked on each other throughout the duplex. The hybridization of the methylphosphonate strand does not perturb the structure of the complementary DNA strand in the hetero duplexes. The sugar residue 5' to the S(p) chiral center shows A-form sugar puckering, with a C(3)(')-endo conformation. Minor groove width in the R(p) stereoisomer is considerably wider, particularly at the R(p) vs S(p) site and is attributed to either steric interactions across the minor groove or poorer metal ion coordination within the minor groove.


    Organizational Affiliation

    Sealy Center for Structural Biology and Department of Human Biological Chemistry & Genetics, University of Texas Medical Branch, Galveston, Texas 77555-1157, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*TP*GP*TP*TP*TP*GP*GP*C)-3'A8N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*CP*(CMR)P*(RMP)P*(RMP)P*(SMP)P*(CMR)P*(RMP))-3'B7N/A
Small Molecules
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
CMR
Query on CMR
B
DNA LINKINGC10 H16 N3 O6 PDC
RMP
Query on RMP
B
DNA LINKINGC11 H16 N5 O5 PDA
SMP
Query on SMP
B
DNA LINKINGC11 H16 N5 O5 PDA
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-06-19
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance