A Convenient Stereochemical Notation for P‐Chiral Nucleotide Analogs

Michal Sobkowski1, Jacek Stawinski2, Adam Kraszewski1

1 Institute of Bioorganic Chemistry, Poznan, 2 Stockholm University Stockholm, Sweden and Institute of Bioorganic Chemistry, Poznan
Publication Name:  Current Protocols in Nucleic Acid Chemistry
Unit Number:  Appendix 1E
DOI:  10.1002/0471142700.nca01es28
Online Posting Date:  March, 2007
GO TO THE FULL TEXT: PDF or HTML at Wiley Online Library

Abstract

The DP/LP convention is a stereochemical notation for P‐chiral nucleotide analogs and related compounds. In contrast to the absolute RP/SP notation, the DP/LP system is based on a geometrical relationship between substituents in a dinucleoside monophosphate skeleton. The DP/LP notation is a convenient alternative to the RP/SP notation for stereochemical correlation analysis of physical, chemical, and biological properties of nucleotide and oligonucleotide analogs bearing any type of tri‐ or tetra‐coordinated phosphorus moiety.

Keywords: stereochemistry; configuration; P‐chiral; nucleotide analogs; DP/LP notation

     
 
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Table of Contents

  • General Principles
  • Applications of DP/LP Descriptors
  • Literature Cited
  • Figures
     
 
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Materials

GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Figures

Videos

Literature Cited

Literature Cited
   Cahn, R.S., Ingold, C., and Prelog, V. 1966. Specification of molecular chirality. Angew. Chem., Int. Ed. 5:385‐415.
   IUPAC Commission on the Nomenclature of Organic Chemistry (CNOC) and IUPAC‐IUB Commission on Biochemical Nomenclature (CBN). 1971. Tentative rules for carbohydrate nomenclature. Eur. J. Biochem. 21:455‐477.
   IUPAC‐IUB Joint Commission on Biochemical Nomenclature (JCBN). 1984. Nomenclature and symbolism for amino acids and peptides, recommendations 1983. Pure Appl. Chem. 56:595‐624.
   Lebedev, A.V. and Wickstrom, E. 1996. The chirality problem in P‐substituted oligonucleotides. Perspect. Drug Discov. Design 4:17‐40.
   Mata, P., Lobo, A.M., Marshall, C., and Johnson, A.P. 1993. The CIP sequence rules: Analysis and proposal for a revision. Tetrahedron Asymmetry 4:657‐668.
   Prelog, V. and Helmchen, G. 1982. Basic principles of the CIP‐system and proposals for a revision. Angew. Chem., Int. Ed. 21:567‐583.
   Sobkowski, M., Stawinski, J., and Kraszewski, A. 2005. A proposal for a new stereochemical notation for P‐chiral nucleotide analogues and related compounds. Nucleosides Nucleotides Nucleic Acids 24:1301‐1307.
   Sobkowski, M., Stawinski, J., and Kraszewski, A. 2006a. A proposal for a convenient notation for P‐chiral nucleotide analogues. Part 2. Dinucleoside monophosphate analogues. Nucleosides Nucleotides Nucleic Acids 25:1363‐1375.
   Sobkowski, M., Stawinski, J., and Kraszewski, A. 2006b. A proposal for a convenient notation for P‐chiral nucleotide analogues. Part 3. Compounds with one nucleoside residue and non‐nucleosidic derivatives. Nucleosides Nucleotides Nucleic Acids 25:1377‐1389.
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library