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By means of one- and two-dimensional NMR spectroscopy the solution structures of the partly self-complementary octamer d(m5C-G-m5C-G-A-G-m5C-G) were investigated. It is shown that this DNA fragment, under conditions of high DNA concentration (8 mM DNA) and/or high ionic strength prefers to adopt a duplex structure. At low DNA concentration (0.4 mM DNA), the duplex exists in a 1:1 slow equilibrium with a monomeric hairpin form. Addition of salt destabilizes the hairpin structure in favour of the dimer. At high temperatures the hairpin form, as well as the dimer structure, exist in a fast equilibrium with the random-coil form. For the hairpin/random-coil equilibrium a Tm of 329 K and a delta H degree of -121 kJ.mol-1 were deduced. These thermodynamic parameters are independent of the DNA concentration, as is expected for a monomeric structure. For the dimer to coil transition a Tm of 359 K (1 M DNA) and a delta H degree of -285 kJ.mol duplex-1 were derived. The thermodynamic data of the hairpin-coil transition mutually agree with those recently reported for the hairpin to random coil equilibrium of the DNA octamer d(m5C-G-m5C-G-T-G-m5C-G) [Orbons, L. P. M., van der Marel, G. A., van Boom, J. H. & Altona, C. (1987) J. Biomol. Struct. Dyns. 4, 939-963]. It is demonstrated that the dimer structure exhibits B-DNA characteristics, as is witnessed by the NOESY experiments and the analysis of the proton-proton coupling data. It is shown that the base-pair formation of the G x A mismatches is anti-anti. A comparison of 1H and 31P chemical-shift data of the title compound with those of a well-characterized B-DNA structure reveals large differences in the dm5C(3)-dG(4)-dA(5) part of the mismatched dimer structure. These differences apparently indicate some major local structural changes due to the incorporation of the G x A mismatches. Under the most extreme conditions used (i.e. up to 3 M NaCl or 75% CH3OH in the presence of 10 mM MgCl2) no Z-DNA structure was observed. It is shown that the structural features of the hairpin form of the title compound mimic those of the hairpin structure of d(m5C-G-m5C-G-T-G-m5C-G). An energy-minimized model of the hairpin form is given.
L P Orbons, and
G A van der Marel, and
J H van Boom, and
C Altona
October 1986,
European journal of biochemistry,
L P Orbons, and
G A van der Marel, and
J H van Boom, and
C Altona
April 1983,
FEBS letters,
L P Orbons, and
G A van der Marel, and
J H van Boom, and
C Altona
August 1990,
Journal of biomolecular structure & dynamics,
L P Orbons, and
G A van der Marel, and
J H van Boom, and
C Altona
February 1985,
European journal of biochemistry,
L P Orbons, and
G A van der Marel, and
J H van Boom, and
C Altona
August 2007,
Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology,
L P Orbons, and
G A van der Marel, and
J H van Boom, and
C Altona
January 1983,
Cold Spring Harbor symposia on quantitative biology,
L P Orbons, and
G A van der Marel, and
J H van Boom, and
C Altona
September 2001,
Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry,
L P Orbons, and
G A van der Marel, and
J H van Boom, and
C Altona
August 1989,
The Journal of biological chemistry,
L P Orbons, and
G A van der Marel, and
J H van Boom, and
C Altona
May 1985,
Nucleic acids research,
L P Orbons, and
G A van der Marel, and
J H van Boom, and
C Altona
April 1988,
Biochemistry,
