Nucleic Acids Research, Vol 25, Issue 20 4098-4105, Copyright © 1997 by Oxford University Press
CL Clark, PK Cecil, D Singh and DM Gray
Circular dichroism (CD) spectra and melting temperature (Tm) data for five
duplexes containing phosphorothioate linkages were compared with data for
four unmodified duplexes to assess the effect of phosphorothioate
modification on the structure and stability of DNA. DNA and DNA.RNA
duplexes. Nine duplexes were formed by mixing oligomers 24 nt long in 0.15
M K+(phosphate buffer), pH 7.0. Unmodified DNA.DNA and RNA.RNA duplexes
were used as reference B-form and A-form structures. The CD spectra of the
modified hybrids S-d(AC)12.r(GU)12 and r(AC)12.S-d(GT)12 differed from each
other but were essentially the same as the spectra of the respective
unmodified hybrids. They were more A-form than B-form in character. CD
spectra of duplexes S- d(AC)12.d(GT)12 and d(AC)12.S-d(GT)12 were similar
to that of d(AC)12.d(GT)12, except for a reduced long wavelength CD band.
Sulfur modifications on both strands of the DNA duplex caused a pronounced
effect on its CD spectrum. The order of thermal stability was: RNA.RNA >
DNA.DNA > DNA.RNA > S-DNA.DNA > S-DNA. RNA > S-DNA.S-DNA.
Phosphorothioation of one strand decreased the melting temperature by
7.8+/-0.6 degrees C, regardless of whether the substitution was in a hybrid
or DNA duplex. Thermodynamic parameters were obtained from a multistate
analysis of the thermal melting profiles. Interestingly, the destabilizing
effect of the phosphorothioate substitution appears to arise from a
difference in the entropy upon forming the DNA.DNA duplexes, while the
destabilizing effect in the DNA.RNA hybrids appears to come from a
difference in enthalpy.
ARTICLES
CD, absorption and thermodynamic analysis of repeating dinucleotide DNA, RNA and hybrid duplexes [d/r(AC)]12.[d/r(GT/U)]12 and the influence of phosphorothioate substitution [published erratum appears in Nucleic Acids Res 1997 Nov 1;25(21):4429]
The University of Texas at Dallas, Box 830688, Richardson, TX 75083- 0688, USA.
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