Germann M W, Kalisch B W, Pon R T, van de Sande J H
Department of Medical Biochemistry, University of Calgary, Alberta, Canada.
Biochemistry. 1990 Oct 9;29(40):9426-32. doi: 10.1021/bi00492a017.
Parallel-stranded DNA can be formed from alternating AT segments and is not restricted exclusively to homooligomeric AT sequences. DNA oligonucleotides 3'-d(AT)nxC4(AT)n-3' (where x indicates the location of the 5'-5' phosphodiester linkage) form parallel-stranded hairpin structures at micromolar strand concentration for n = 4 or 5 but not for n = 6, 7. The spectral properties of the parallel-stranded structures are similar to those of the hairpin structures containing homooligomeric AT stems. However, parallel-stranded structures formed in alternating AT segments are significantly less stable than either their corresponding antiparallel control or the homooligomeric parallel AT hairpins as evidenced by their lower helix-coil transition enthalpy, melting temperature, and stability constant. This results in a remarkable polymorphism which is most pronounced for 3'-d(AT)5xC4(AT)5-3'. This oligonucleotide can exist as a parallel-stranded hairpin, coil, or concatameric antiparallel structure(s), depending on temperature and strand concentration. These results suggest simple guidelines for the design of parallel-stranded DNA. In addition, we present a model for the assessment of the stability of parallel-stranded duplex structures formed from AT base pairs based on their sequence.
平行链DNA可由交替的AT片段形成，并不局限于同聚寡核苷酸AT序列。DNA寡核苷酸3'-d(AT)nxC4(AT)n-3'（其中x表示5'-5'磷酸二酯键的位置）在微摩尔链浓度下，当n = 4或5时形成平行链发夹结构，但n = 6、7时则不形成。平行链结构的光谱特性与含有同聚寡核苷酸AT茎的发夹结构相似。然而，由交替AT片段形成的平行链结构明显不如其相应的反平行对照或同聚平行AT发夹稳定，这可从它们较低的螺旋-线圈转变焓、解链温度和稳定性常数得到证明。这导致了显著的多态性，对于3'-d(AT)5xC4(AT)5-3'最为明显。这种寡核苷酸可根据温度和链浓度以平行链发夹、线圈或串联反平行结构的形式存在。这些结果为平行链DNA的设计提供了简单的指导原则。此外，我们提出了一个基于序列评估由AT碱基对形成的平行链双链结构稳定性的模型。
