A COMPUTER-PROGRAM FOR CHOOSING OPTIMAL OLIGONUCLEOTIDES FOR FILTER HYBRIDIZATION, SEQUENCING AND INVITRO AMPLIFICATION OF DNA
A COMPUTER-PROGRAM FOR CHOOSING OPTIMAL OLIGONUCLEOTIDES FOR FILTER HYBRIDIZATION, SEQUENCING AND INVITRO AMPLIFICATION OF DNA
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DOI：
10.1093/nar/17.21.8543
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发表时间：
1989-11-11
影响因子：
14.9
通讯作者：
RHOADS, RE
中科院分区：
文献类型：
--
作者：
RYCHLIK, W;RHOADS, RE
提出了一种选择最佳寡脱氧核糖核苷酸作为滤膜杂交探针、测序引物或DNA扩增引物的方法。考虑决定探针质量的三个主要因素：探针和靶核酸之间形成的双链体的稳定性、探针对预期靶序列的特异性和自身互补性。DNA双链体稳定性计算基于由Breslauer等人[Proc.Natl. Acad. Sci. U.S.A.（1986），83：3746]。通过这里描述的方法预测的双链体解离的温度在0.4 ℃以内。C为十种寡核苷酸实验获得的值。探针的特异性及其自身互补性的计算基于简单的动态算法。
A method is presented for choosing optimal oligodexyribonucleotides as probes for filter hybridization, primers for sequencing, or primers for DNA amplification. Three main factors that determine the quality of a probe are considered: stability of the duplex formed between the probe and target nucleic acid, specificity of the probe for the intended target sequence, and self-complementarity. DNA duplex stability calculations are based on the nearest-neighbor thermodynamic values determined by Breslauer et al. [Proc. Natl. Acad. Sci. U.S.A. (1986), 83: 3746]. Temperatures of duplex dissociation predicted by the method described here were within 0.4.degree. C of the values obtained experimentally for ten oligonucleotides. Calculations for specificity of the probe and its self-complementarity are based on a simple dynamic algorithm.