Denman R B
New York State Institute of Basic Research in Developmental Disabilities, Staten Island.
Biotechniques. 1993 Dec;15(6):1090-5.
A computer-assisted method for screening the relative activity of small catalytic RNAs is described. A series of four cis-acting variant sequence files are constructed based upon the RNA sequence of a trans-acting catalytic RNA under consideration. These files are individually folded into their lowest energy structure using a standard RNA folding algorithm. The compiled structures are assessed for their ability to form recognizable catalytic RNA secondary structure motifs. We demonstrate here that RNA sequences that do not readily fold into a cis-acting hammerhead ribozyme motif have trans-acting counterparts with reduced in vitro activity. This procedure should be useful in selecting the best candidate sequences in an mRNA to target for catalytic RNA cleavage.
描述了一种用于筛选小催化RNA相对活性的计算机辅助方法。基于所考虑的反式作用催化RNA的RNA序列构建了一系列四个顺式作用变体序列文件。使用标准的RNA折叠算法将这些文件分别折叠成其最低能量结构。评估编译后的结构形成可识别的催化RNA二级结构基序的能力。我们在此证明，不容易折叠成顺式作用锤头状核酶基序的RNA序列具有体外活性降低的反式作用对应物。该程序在选择mRNA中用于催化RNA切割的最佳候选序列时应该是有用的。
