Liu K, Miles H T, Frazier J, Sasisekharan V
Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland 20892.
Biochemistry. 1993 Nov 9;32(44):11802-9. doi: 10.1021/bi00095a008.
We show here for the first time that a stable parallel double helix with Hoogsteen pairing can exist independently of the triple helix of which it is a component part. The experiments employ DNA oligonucleotides with mixed sequences of normal bases. These duplexes are distinct from previously reported ribopolynucleotide helices containing bulky substituents which prevent Watson-Crick pairing as well as from parallel duplexes with Donohue, or reversed Watson-Crick, pairing. Stoichiometry is established by mixing curves and gel electrophoresis. Tm depends linearly upon pH, increasing with acidity because of the need to protonate N3 of C. The Tm of the 20-mer studied here is 52 degrees C at pH 5.2 and 0.1 M NaCl. At pH above 6, the molecule rearranges to form an antiparallel duplex with imperfect Watson-Crick pairing and loops, and the Tm is then independent of pH. The CD spectrum of the parallel duplex is very similar to that of the corresponding triple helix but quite different from that of the Watson-Crick helix. The infrared spectrum in the double bond region closely resembles that of the triple helix but, as with the CD, is quite different from that of the Watson-Crick duplex. The infrared spectra of the duplex and triple helix are also nearly identical in the region form 800 to 1000 cm-1, which is sensitive to backbone conformation. The only symmetry element present is a pseudorotational axis coincident with the helix axis of the parallel duplex as well as with the axis of the corresponding triple helix.(ABSTRACT TRUNCATED AT 250 WORDS)
我们首次在此表明，具有Hoogsteen配对的稳定平行双螺旋能够独立于其作为组成部分的三螺旋而存在。实验采用了具有正常碱基混合序列的DNA寡核苷酸。这些双链体不同于先前报道的含有庞大取代基从而阻止沃森-克里克配对的核糖多核苷酸螺旋，也不同于具有多诺休配对或反向沃森-克里克配对的平行双链体。通过混合曲线和凝胶电泳确定化学计量。熔解温度（Tm）与pH呈线性关系，由于需要使胞嘧啶的N3质子化，所以随酸度增加而升高。在此研究的20聚体在pH 5.2和0.1 M氯化钠条件下的Tm为52摄氏度。在pH高于6时，该分子重排形成具有不完全沃森-克里克配对和环的反平行双链体，此时Tm与pH无关。平行双链体的圆二色光谱与相应三螺旋的圆二色光谱非常相似，但与沃森-克里克螺旋的圆二色光谱有很大不同。双键区域的红外光谱与三螺旋的红外光谱非常相似，但与圆二色光谱一样，与沃森-克里克双链体的红外光谱有很大不同。双链体和三螺旋的红外光谱在800至1000 cm-1区域也几乎相同，该区域对主链构象敏感。唯一存在的对称元素是一个伪旋转轴，它与平行双链体的螺旋轴以及相应三螺旋的轴重合。（摘要截短至250字）
