Doktycz M J, Morris M D, Dormady S J, Beattie K L, Jacobson K B
Health Sciences Research Division, Oak Ridge National Laboratory, Tennessee 37831-6123, USA.
J Biol Chem. 1995 Apr 14;270(15):8439-45. doi: 10.1074/jbc.270.15.8439.
The use of short oligonucleotide probes is finding increased application in DNA sequencing and genome characterization techniques, but a lack of knowledge of the hybridization properties of short duplexes hinders their use. Melting data were acquired on 128 DNA duplexes based on the length proposed in sequencing by hybridization procedures and formed from the general sequences 5'-XYZTGGAC-3',5'-GTCCAXYZ-3',5'-GCXYZGAC-3', and 5'-GTCXYZGC-3' where X, Y, and Z are either A, T, G, or C. These molecules were designed to elucidate the effects of location and nearest-neighbor stacking on the stability of base pairing in short DNA duplexes. The type of base pairs present had a major effect on stability, but was insufficient to predict stability without the inclusion of nearest-neighbor terms. Furthermore, the addition of information on position, or distance from the end, of the nearest-neighbor doublets led to statistically better fitting of the melting data. However, the positionally dependent stabilization differences are small compared with the contributions of base pairing and stacking.
短寡核苷酸探针在DNA测序和基因组表征技术中的应用越来越广泛，但对短双链体杂交特性的了解不足阻碍了它们的使用。根据杂交测序程序中提出的长度，对128个DNA双链体进行了熔解数据采集，这些双链体由通用序列5'-XYZTGGAC-3'、5'-GTCCAXYZ-3'、5'-GCXYZGAC-3'和5'-GTCXYZGC-3'形成，其中X、Y和Z为A、T、G或C。设计这些分子是为了阐明位置和近邻堆积对短DNA双链体中碱基配对稳定性的影响。存在的碱基对类型对稳定性有主要影响，但在不包括近邻项的情况下不足以预测稳定性。此外，添加关于近邻双峰的位置或距末端的距离的信息导致熔解数据的统计拟合更好。然而，与碱基配对和堆积的贡献相比，位置依赖性稳定差异较小。
