| CPC C12Q 1/6818 (2013.01) [C12N 15/113 (2013.01); C12Q 1/6806 (2013.01); C12Q 1/6876 (2013.01); G16B 5/20 (2019.02); G16B 15/00 (2019.02); G16B 30/00 (2019.02); G16B 25/10 (2019.02); G16B 25/20 (2019.02); G16B 30/10 (2019.02)] | 1 Claim |
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1. A method of screening for a compound capable of stabilizing a step-loop structure to control a function of a transcript of a target RNA among a compound to be evaluated, comprising:
calculating an existence probability of a local secondary structure comprising a stem-loop and peripheral sequences contiguous to its 5′ and 3′ ends that may exist in a target RNA sequence;
selecting a local secondary structure with a desired existence probability;
preparing a screening probe corresponding to the selected local secondary structure;
contacting the screening probe with the compound to be evaluated; and
measuring an increase in stability of a stem-loop structure of the target RNA in the presence of the compound compared to in the absence of the compound, thereby identifying the compound as capable of stabilizing the stem-loop structure to control the function of the transcript of the target RNA,
wherein calculating the existence probability of the local secondary structure comprises:
predicting a structure, comprising setting a frame n having the width of W bases by an increment of R bases starting from the 5′ terminal, wherein a number of frames obtained from a target RNA is nmax, computing a base-pair pattern which can be obtained by pattern matching for a constituent base sequence of the W bases in each frame n, applying thermodynamic stability calculations to the result, and giving ΔG for each basepair pattern,
analyzing the structure, comprising hypothesizing based on the resulting mmax(n) structures predicted in frame n and respective energy level, that the state inside the cell within which the RNA is placed is in equilibrium, calculating the existence probability of each resulting predicted structure according to the Maxwell-Boltzmann statistics, wherein the existence probability of each predicted structure result is j(n,m) for the mth predicted result from the most stable structure among the resulting predicted structures in frame n;
calculating a local existence probability, comprising setting pas a property profile of a loop and stem (characteristics of the stem loop defined by the position of base in the stem-constituting base pair) formed beginning from the absolute position x on the sequence rather than in the frame, and defining the stem-loop as motif (x, p), and defining the existence probability in frame n of the motif (x,p) as partial existence probability P_local (x,p,n), and calculating the value as sum Σj (n,m) of the j values for the prediction results of structures in which the stem loop exists among all the resulting predicted structures obtained in the frame n, wherein the local existence probability P_local (x,p,n) of motif (x,p) in the frame n is represented below:
 calculating the existence probability, comprising giving the existence probability P_global (x,p) of motif (x,p) among the entirety as ΣP_local (x,p,n)/n_all (x,p) when ΣP_local (x,p,n) is the result of sum of P_local (x,p,n) from frame 1 to nmax, and the number of frames in which the full length of the sequence constituting the stem-loop motif (x, p) is contained is n all (x,p), wherein the existence probability P_global (x, p) of motif (x,p) among the entirety is represented as below, and
 analyzing, comprising selecting a stem-loop based on the existence probability and property p, with respect to the obtained existence probability P_global (x,p) of motif (x, p).
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