Dumbbell-shaped, double-hairpin structure of DNA: a thermodynamic investigation
The authors report the first calorimetric and spectroscopic investigation on a member of a new class of nucleic acid secondary structures in which both ends of a duplex core are closely by single-stranded loops. Such structures can be formed intramolecularly from appropriately designed base sequences. They have synthesized a 24-mer sequence, and they present calorimetric, spectroscopic, and electrophoretic evidence that it adopts a dumbbell-shaped, double-hairpin structure. Their data allow them to reach the following conclusions: (1) the phosphodiester gap in the center of the core duplex of the dumbbell does not reduce the transition enthalpy relative to that measured for the corresponding octameric duplex d(GGAATTCC)/sub 2/; (2) incorporation of a 5'-phosphate group into the gap decreases the thermal stability of the dumbbell relative to its unphosphorylated sequence; (3) the thymine residues in the loop behave both electrostatically and enthalpically like denatured single strands. Published nuclear magnetic resonance studies reveal partial stacking of thymine residues in the loops of linear hairpin structures; (4) when both ends of the nicked octameric core duplex are constrained by loops of only four thymine residues, the dumbbell structure may adopt conformations in which the 5' and 3' ends at the nick are twisted relative to the helical axis and therefore are not in phase. Such conformations would account for the observed resistance of the double-hairpin structure of ligation, since the 3'OH and 5'P would no longer be collinear.
- Research Organization:
- Rutgers-The State Univ. of New Jersey, Piscataway
- OSTI ID:
- 5403328
- Journal Information:
- Biochemistry; (United States), Vol. 26:22
- Country of Publication:
- United States
- Language:
- English
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DNA
CONFORMATIONAL CHANGES
NUCLEAR MAGNETIC RESONANCE
STRUCTURAL CHEMICAL ANALYSIS
ATP
CALORIMETRY
DICHROISM
ELECTROPHORESIS
PHOSPHORUS 32
PHOSPHORYLATION
TEMPERATURE DEPENDENCE
ULTRAVIOLET SPECTRA
BETA DECAY RADIOISOTOPES
BETA-MINUS DECAY RADIOISOTOPES
CHEMICAL REACTIONS
DAYS LIVING RADIOISOTOPES
ISOTOPES
LIGHT NUCLEI
MAGNETIC RESONANCE
NUCLEI
NUCLEIC ACIDS
NUCLEOTIDES
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ORGANIC COMPOUNDS
PHOSPHORUS ISOTOPES
RADIOISOTOPES
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550201* - Biochemistry- Tracer Techniques