Comparative Circular Dichroism and Fluorescence Studies of Oligodeoxyribonucleotide and Oligodeoxyribonucleoside Methylphosphonate Pyrimidine Strands in Duplex and Triplex Formation

Daniel E. Callahan, Tina L. Trapane, Paul S. Miller, Paul O.P. Ts’o, Lou Sing Kan

Research output: Contribution to journalArticlepeer-review

Abstract

An analogue of the homopyrimidine oligodeoxyribonucleotide d(CT)8 has been synthesized. This analogue, d(CT)8 contains nonionic methylphosphonate internucleoside linkages. The pH-dependent conformational transitions of d(CT)8 have been studied and its ability to form duplexes and triplexes with the normal homopurine oligonucleotide d(AG)8 has also been investigated as a function of pH. Circular dichroism spectroscopy and ethidium bromide fluorescence enhancement have been used to monitor pH-dependent conformational transitions driven by the protonation of cytosine residues, and the different behavior of d(CT)8 and d(CT)8 has been compared. It was possible to form self-associated complexes by using either d(CT)8 or d(CT)8, and both compounds combined with d(AG)8 to form duplex or triplex DNA. At neutral pH, the CD spectrum of d(AG)8·d(CT)8 duplex was quite different from the CD spectrum of d(AG)8·d(CT)8 duplex, reflecting most likely a difference in conformation. The duplex to triplex transition characteristic of this DNA sequence occurred at a lower pH when d(CT)8 was substituted for d(CT)8; however, at pH 4.2, triplex containing d(CT)8 was similar in conformation to triplex containing d(CT)8. Several of these observations can be related to the alterations in electrostatic and steric interactions that occur when the negatively charged phosphodiester backbone of d(CT)8 is replaced with a nonionic methylphosphonate backbone.

Original languageEnglish (US)
Pages (from-to)1650-1655
Number of pages6
JournalBiochemistry
Volume30
Issue number6
DOIs
StatePublished - Feb 1 1991

ASJC Scopus subject areas

  • Biochemistry

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