Thermodynamic criteria for high hit rate antisense oligonucleotide design
Thermodynamic criteria for high hit rate antisense oligonucleotide design
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DOI：
10.1093/nar/gkg710
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发表时间：
2003-09-01
影响因子：
14.9
通讯作者：
Freier, SM
中科院分区：
文献类型：
--
作者：
Matveeva, OV;Mathews, DH;Freier, SM
反义寡核苷酸用于治疗应用和功能基因组研究。然而，在实践中，许多与mRNA互补的寡核苷酸很少或没有反义活性。提高反义筛选“命中率”的理论策略将降低发现成本，并可能导致鉴定具有更高效力的反义寡核苷酸。对1000多个硫代修饰寡核苷酸实验数据的统计分析表明，与RNA形成稳定双链的寡核苷酸探针(DeltaG（37)(o)小于或等于-30 kcal/mol）具有较小的自相互作用电位，比形成不太稳定的寡核苷酸-RNA杂合体或更稳定的自结构的分子更有效。为了获得最佳的统计偏好，对于寡核苷酸间配对，自相互作用的值(DeltaG（37)(o)）大于等于-8 kcal/mol，对于分子内配对，(DeltaG（37)(o)）大于等于-1.1 kcal/mol。在分析的实验中，选择具有这些热力学值的寡核苷酸将使“命中率”提高多达6倍。
Antisense oligonucleotides are used for therapeutic applications and in functional genomic studies. In practice, however, many of the oligonucleotides complementary to an mRNA have little or no antisense activity. Theoretical strategies to improve the 'hit rate' in antisense screens will reduce the cost of discovery and may lead to identification of antisense oligonucleotides with increased potency. Statistical analysis performed on data collected from more than 1000 experiments with phosphorothioate-modified oligonucleotides revealed that the oligo-probes, which form stable duplexes with RNA (DeltaG(37)(o) less than or equal to -30 kcal/mol) and have small self-interaction potential, are more frequently efficient than molecules that form less stable oligonucleotide-RNA hybrids or more stable self-structures. To achieve optimal statistical preference, the values for self-interaction should be (DeltaG(37)(o)) greater than or equal to -8 kcal/mol for inter-oligonucleotide pairing and (DeltaG(37)(o)) greater than or equal to -1.1 kcal/mol for intra-molecular pairing. Selection of oligonucleotides with these thermodynamic values in the analyzed experiments would have increased the 'hit rate' by as much as 6-fold.