公开(公告)号：WO2011126996A3

公开(公告)日：2011-10-13

申请号：PCT/US2011/031127

申请日：2011-04-04

Applicant: CALIFORNIA INSTITUTE OF TECHNOLOGY ,  PIERCE, Niles, A. ,  WOLFE, Brian, R. ,  ZADEH, Joseph

Inventor： PIERCE, Niles, A. ,  WOLFE, Brian, R. ,  ZADEH, Joseph

IPC: G06F19/10 ,  G06F19/14 ,  G06F19/22

Abstract: Described herein are systems and processes for designing the sequence of one or more interacting nucleic acid strands intended to adopt a target secondary structure at equilibrium. The target secondary structure is decomposed into a binary tree and candidate mutations are evaluated on leaf nodes of the tree. During a process of leaf optimization, defect-weighted mutation sampling is used to select each candidate, mutation position with a probability proportional to its contribution to an ensemble defect of the leaf. Subsequences of the tree are then merged, moving up the tree until a final nucleotide sequence of interest is determined that has the target secondary structure at equilibrium.

公开(公告)号：WO2011126996A2

公开(公告)日：2011-10-13

申请号：PCT/US2011031127

申请日：2011-04-04

Applicant: CALIFORNIA INST OF TECHN ,  PIERCE NILES A ,  WOLFE BRIAN R ,  ZADEH JOSEPH

Inventor： PIERCE NILES A ,  WOLFE BRIAN R ,  ZADEH JOSEPH

IPC: G06F17/10

CPC classification number: G06F19/22 ,  G06F19/16 ,  G06F19/24

Abstract: Described herein are systems and processes for designing the sequence of one or more interacting nucleic acid strands intended to adopt a target secondary structure at equilibrium. The target secondary structure is decomposed into a binary tree and candidate mutations are evaluated on leaf nodes of the tree. During a process of leaf optimization, defect-weighted mutation sampling is used to select each candidate, mutation position with a probability proportional to its contribution to an ensemble defect of the leaf. Subsequences of the tree are then merged, moving up the tree until a final nucleotide sequence of interest is determined that has the target secondary structure at equilibrium.

Abstract translation: 本文描述了用于设计在平衡时采用目标二级结构的一个或多个相互作用的核酸链的序列的系统和方法。 目标二级结构被分解为二叉树，并在树的叶节点上评估候选突变。 在叶优化过程中，使用缺陷加权突变抽样来选择每个候选者，突变位置的概率与其对叶的整体缺陷的贡献成比例。 然后将树的子序列合并，向上移动树，直到确定目标二级结构处于平衡状态的最终核心序列。