Xodo L E, Manzini G, Quadrifoglio F, van der Marel G A, van Boom J H
Department of Biochemistry, Biophysics and Macromolecular Chemistry, University of Trieste, Italy.
Biochemistry. 1988 Aug 23;27(17):6321-6. doi: 10.1021/bi00417a018.
The secondary structures of the synthetic DNA fragments d(CGCGCGTTTTTCGCGCG) (T5), d(CGCGCGAAAAACGCGCG) (A5), d(CGCGCGTACGCGCG) (TA), and d(CGCGCGATCGCGCG) (AT) were investigated in a combined electrophoretic and spectroscopic study. All the oligomers exist, at low temperature and over a wide range of ionic strength (0.5-100 mM salt) and of nucleotide concentration [0.1-2.0 mM (phosphate)], as a mixture of two slowly interconverting species, identified as the dimeric duplex and the monomeric hairpin structure. The thermodynamic parameters for hairpin denaturation of T5, A5, TA, and AT and for duplex denaturation of d(CGCGCG) show that (a) the hairpins are more stable than the reference hexamer duplex at all accessible nucleotide concentrations; (b) the loop contributes favorably to the enthalpy change of hairpin denaturation in the four DNA fragments; (c) the base composition of the loop (A vs T) and the size of the loop (A5/T5 vs TA/AT) do not appreciably influence the enthalpic contents of the hairpins; (d) hairpins TA and AT, with two AT bases intervening in the CG self-complementary part of the molecule, exhibit a markedly higher thermal stability than hairpins T5 and A5, which is entropic in origin. These findings are consistent with the presence of two-residue loops in the tetradecamers TA and AT.
通过电泳和光谱联合研究，对合成DNA片段d(CGCGCGTTTTTCGCGCG)（T5）、d(CGCGCGAAAAACGCGCG)（A5）、d(CGCGCGTACGCGCG)（TA）和d(CGCGCGATCGCGCG)（AT）的二级结构进行了研究。在低温、宽离子强度范围（0.5 - 100 mM盐）和核苷酸浓度[0.1 - 2.0 mM（磷酸盐）]下，所有寡聚物均以两种缓慢相互转化的物种混合物形式存在，这两种物种分别被鉴定为二聚体双链体和单体发夹结构。T5、A5、TA和AT发夹变性以及d(CGCGCG)双链体变性的热力学参数表明：（a）在所有可及的核苷酸浓度下，发夹比参考六聚体双链体更稳定；（b）环对四个DNA片段中发夹变性的焓变有有利贡献；（c）环的碱基组成（A对T）和环的大小（A5/T5对TA/AT）对发夹的焓含量没有明显影响；（d）在分子的CG自互补部分插入两个AT碱基的发夹TA和AT，其热稳定性明显高于发夹T5和A5，这源于熵效应。这些发现与十四聚体TA和AT中存在两个残基的环一致。
