Dornberger U, Behlke J, Birch-Hirschfeld E, Fritzsche H
Institut für Molekularbiologie, Friedrich-Schiller-Universität, Jena, Germany.
Nucleic Acids Res. 1997 Feb 15;25(4):822-9. doi: 10.1093/nar/25.4.822.
The 24mer deoxyoligonucleotide 3'-d(T)10-5'-5'-d(C)4- d(A)10-3'(psC4) with an uncommon 5'-p-5'phosphodiester linkage was designed to enable the formation of a hairpin structure with unusual parallel-stranded stem. As reference hairpin structure with an antiparallel-stranded stem, the 24mer 5'-d(T)10-d(C)4-d(A)10-3'(apsC4) was chosen. The behaviour of these oligonucleotides at different temperatures, DNA and salt concentrations was characterised by a combination of UV melting, CD, CD melting, infrared and Raman spectroscopy, infrared melting and analytical ultracentrifugation. The parallel-stranded hairpin structure was found to be formed by psC4 only under conditions of low DNA concentration and low salt concentration. Increase of the NaCl concentration beyond the physiological level or high DNA concentration supports the formation of intermolecular multi-stranded structures. The experimental data are in agreement with a four-stranded complex formed by two molecules of psC4. The base pairing model of this asymmetric four-stranded complex is based on the pyrimidine motif of a triple helix with two bifurcated hydrogen bonds at the O4 of the thymine each directed towards one of the amino protons of both adenines. In contrast, the reference oligonucleotide apsC4 forms only an antiparallel-stranded hairpin under all experimental conditions.
设计了具有不常见5'-p-5'磷酸二酯键的24聚体脱氧寡核苷酸3'-d(T)10-5'-5'-d(C)4-d(A)10-3'(psC4)，以使其能够形成具有不寻常平行链茎的发夹结构。作为具有反平行链茎的参考发夹结构，选择了24聚体5'-d(T)10-d(C)4-d(A)10-3'(apsC4)。通过紫外熔解、圆二色（CD）、CD熔解、红外和拉曼光谱、红外熔解以及分析超速离心等多种方法相结合，对这些寡核苷酸在不同温度、DNA和盐浓度下的行为进行了表征。发现平行链发夹结构仅在低DNA浓度和低盐浓度条件下由psC4形成。NaCl浓度超过生理水平或高DNA浓度会促进分子间多链结构的形成。实验数据与由两个psC4分子形成的四链复合物一致。这种不对称四链复合物的碱基配对模型基于三螺旋的嘧啶基序，在胸腺嘧啶的O4处有两个分叉的氢键，每个氢键都指向两个腺嘌呤的一个氨基质子。相比之下，参考寡核苷酸apsC4在所有实验条件下仅形成反平行链发夹。
