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NMR and model-building studies were carried out on the duplex d(CTGGTGCGG).d(CCGCCCAG), referred to as (9+8)-mer, which contains an unpaired thymidine residue. Resonances of the base and of several sugar protons of the (9+8)-mer were assigned by means of a NOESY experiment. Interresidue NOEs between dG(4) and dT(5) as well as between dT(5) and dG(6) provided evidence that the extra dT is stacked into the duplex. Thermodynamic analysis of the chemical shift vs temperature profiles yielded an average TmD value of 334 K and delta HD of -289 kJmol-1 for the duplex in equilibrium random-coil transition. The shapes of the shift profiles as well as the thermodynamic parameters obtained for the extra dT residue and its neighbours again indicate that the unpaired dT base is incorporated inside an otherwise intact duplex. This conclusion is further supported by (a) the observation of an imino-proton resonance of the unpaired dT; (b) the relatively small dispersion in 31P chemical shifts (approximately 0.5 ppm) for the (9+8)-mer, which indicates the absence of t/g or g/t combinations for the phosphate diester torsion angles alpha/zeta. An energy-minimized model of the (9+8)-mer, which fits the present collection of experimental data, is presented.
Y T van den Hoogen, and
A A van Beuzekom, and
H van den Elst, and
G A van der Marel, and
J H van Boom, and
C Altona
February 1982,
Biochemistry,
Y T van den Hoogen, and
A A van Beuzekom, and
H van den Elst, and
G A van der Marel, and
J H van Boom, and
C Altona
March 1989,
The Journal of biological chemistry,
Y T van den Hoogen, and
A A van Beuzekom, and
H van den Elst, and
G A van der Marel, and
J H van Boom, and
C Altona
April 1997,
Biochemistry,
Y T van den Hoogen, and
A A van Beuzekom, and
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G A van der Marel, and
J H van Boom, and
C Altona
November 1990,
European journal of biochemistry,
Y T van den Hoogen, and
A A van Beuzekom, and
H van den Elst, and
G A van der Marel, and
J H van Boom, and
C Altona
December 2015,
Current protocols in nucleic acid chemistry,
Y T van den Hoogen, and
A A van Beuzekom, and
H van den Elst, and
G A van der Marel, and
J H van Boom, and
C Altona
February 1991,
Journal of biochemistry,
Y T van den Hoogen, and
A A van Beuzekom, and
H van den Elst, and
G A van der Marel, and
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C Altona
October 1994,
Nucleic acids research,
Y T van den Hoogen, and
A A van Beuzekom, and
H van den Elst, and
G A van der Marel, and
J H van Boom, and
C Altona
July 1992,
FEBS letters,
Y T van den Hoogen, and
A A van Beuzekom, and
H van den Elst, and
G A van der Marel, and
J H van Boom, and
C Altona
April 1992,
European journal of biochemistry,
Y T van den Hoogen, and
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H van den Elst, and
G A van der Marel, and
J H van Boom, and
C Altona
September 1987,
Nucleic acids research,
