Functional features defining the efficacy of cholesterol-conjugated, self-deliverable, chemically modified siRNAs.
Functional features defining the efficacy of cholesterol-conjugated, self-deliverable, chemically modified siRNAs.
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DOI：
10.1093/nar/gky745
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发表时间：
2018-11-16
影响因子：
14.9
通讯作者：
Wolfson AD
中科院分区：
文献类型：
--
作者：
Shmushkovich T;Monopoli KR;Homsy D;Leyfer D;Betancur-Boissel M;Khvorova A;Wolfson AD
寡核苷酸化学的进展已经产生了所用siRNA性质的转变，从配制的、最小修饰的siRNA到未配制的、重度修饰的siRNA缀合物。引入广泛的化学修饰对于缀合物介导的递送是必不可少的。修饰通过干扰RNAi酶机制的识别和加工对siRNA功效具有显著影响，严重限制了可用于siRNA设计的序列空间。许多公开可用的算法可以成功地预测未经修饰的siRNA的活性，但是用于设计重度修饰的siRNA的算法的效率从未被系统地实验评估。在这里，我们筛选了356个具有广泛修饰的胆固醇缀合的siRNA，并开发了一种基于线性回归的算法，该算法使用两个独立的数据集有效地预测siRNA活性。我们进一步证明，修饰和未修饰的siRNA的预测决定因素有很大的不同。从未修饰的siRNA数据集开发的算法对修饰的siRNA没有预测能力，反之亦然。在重度修饰的SiRNA的背景下，化学不对称性的引入完全消除了对热力学偏差的要求，而热力学偏差是未修饰的SiRNA功效的主要决定因素。最后，我们证明，除了靶位点的序列，邻近3′区域的可及性显着有助于siRNA的功效。
Progress in oligonucleotide chemistry has produced a shift in the nature of siRNA used, from formulated, minimally modified siRNAs, to unformulated, heavily modified siRNA conjugates. The introduction of extensive chemical modifications is essential for conjugate-mediated delivery. Modifications have a significant impact on siRNA efficacy through interference with recognition and processing by RNAi enzymatic machinery, severely restricting the sequence space available for siRNA design. Many algorithms available publicly can successfully predict the activity of non-modified siRNAs, but the efficiency of the algorithms for designing heavily modified siRNAs has never been systematically evaluated experimentally. Here we screened 356 cholesterol-conjugated siRNAs with extensive modifications and developed a linear regression-based algorithm that effectively predicts siRNA activity using two independent datasets. We further demonstrate that predictive determinants for modified and non-modified siRNAs differ substantially. The algorithm developed from the non-modified siRNAs dataset has no predictive power for modified siRNAs and vice versa. In the context of heavily modified siRNAs, the introduction of chemical asymmetry fully eliminates the requirement for thermodynamic bias, the major determinant for non-modified siRNA efficacy. Finally, we demonstrate that in addition to the sequence of the target site, the accessibility of the neighboring 3′ region significantly contributes to siRNA efficacy.
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影响因子：
11.4
作者：
Elbashir, SM;Martinez, J;Tuschl, T
通讯作者：
Tuschl, T
影响因子：
14.9
作者：
Amarzguioui, M;Holen, T;Prydz, H
通讯作者：
Prydz, H
影响因子：
4.5
作者：
Layzer, JM;McCaffrey, AP;Sullenger, BA
通讯作者：
Sullenger, BA
影响因子：
14.9
作者：
Hassler MR;Turanov AA;Alterman JF;Haraszti RA;Coles AH;Osborn MF;Echeverria D;Nikan M;Salomon WE;Roux L;Godinho BMDC;Davis SM;Morrissey DV;Zamore PD;Karumanchi SA;Moore MJ;Aronin N;Khvorova A
通讯作者：
Khvorova A
影响因子：
14.9
作者：
Koller E;Propp S;Murray H;Lima W;Bhat B;Prakash TP;Allerson CR;Swayze EE;Marcusson EG;Dean NM
通讯作者：
Dean NM