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Related Experiment Videos

An oligodeoxyribonucleotide N3'--> P5' phosphoramidate duplex forms an A-type helix in solution

D Ding1, S M Grayaznov, D H Lloyd

  • 1Department of Chemistry, Georgia State University, Atlanta, 30303, USA.

Nucleic Acids Research
|January 15, 1996
PubMed
Summary

Modified DNA duplexes with phosphoramidate linkages adopt an A-type helix conformation, distinct from DNA's B-type helix. This structural change, confirmed by spectroscopy, impacts sugar ring puckering in the modified nucleotide chains.

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Area of Science:

  • Structural Biology
  • Nucleic Acid Chemistry
  • Biophysical Chemistry

Background:

  • Understanding DNA and RNA structure is fundamental to molecular biology.
  • Modified internucleoside linkages can alter nucleic acid properties and functions.
  • Phosphoramidate linkages offer potential advantages over phosphodiester bonds in nucleic acid analogs.

Purpose of the Study:

  • To investigate the solution conformations of dinucleotides and duplexes with N3'--> P5' phosphoramidate linkages.
  • To compare the structural characteristics of these modified nucleic acids with natural DNA and RNA.
  • To elucidate the impact of phosphoramidate substitution on sugar ring conformation.

Main Methods:

  • Circular Dichroism (CD) spectroscopy to assess overall helical structure.

Related Experiment Videos

  • Nuclear Magnetic Resonance (NMR) spectroscopy, including 2D techniques (NOESY, DQF-COSY, TOCSY), for detailed structural analysis.
  • Study of model dimers (d(TpT), d(TnpT)) and a modified duplex (d(CGCGAATTCGCG)2).

    • Main Results:

    • CD spectra revealed an A-type helix conformation for the phosphoramidate duplex, similar to RNA, differing from DNA's B-type helix.
    • NMR studies on model dimers showed a shift in sugar ring conformation from C2'-endo to C3'-endo upon replacing the 3'-phosphoester with a phosphoramidate group.
    • Detailed 2D NMR analysis confirmed the A-type duplex conformation and predominant N-type sugar puckering in the 3'-aminonucleotides of the modified oligonucleotide.

    Conclusions:

    • The N3'--> P5' phosphoramidate internucleoside linkage induces an A-type helical structure in DNA duplexes.
    • This structural transition is associated with a significant change in furanose ring sugar puckering.
    • These findings are crucial for the design and application of modified nucleic acids in therapeutics and research.