Splicing, Folding, and Stretching Nucleic Acids

描述(申请人提供)：单链核酸折叠成复杂而紧凑的形状。做出准确的二级结构预测有助于揭示功能和细胞活动，并且作为蛋白质折叠问题的类似物也是人们普遍感兴趣的。以下三项建议将扩大核酸构象的物理化学模型的预测能力。(1)目前的基因发现算法都是基于统计学的。我们和细胞一样，倾向于基于热力学的方法来定位剪接位点。初步结果表明，与假剪接序列相比，SnRNA与真实剪接序列结合得更好。这项工作应该会带来更好的基因识别算法和简单的剪接图片。(2)对现有模型进行修正，完善二级结构算法的功能，将有助于研究人员对核酸构象的研究。算法的进步可能会对其他相关问题有用，如反义基因治疗和基因芯片热力学分析。(A)伪结点被排除在像MFOLD这样的流行的动态规划算法之外。描述已知伪结点的“伪基”数据库将有助于选择一种算法，然后该算法将被实现。(B)目前的算法寻找最小能量构象，但二级结构可能会被动力学捕获。基于聚合物物理的折叠动力学规则，并在动态规划算法中实现，将允许研究错误折叠。(C)在当前的折叠模型中，未配对区域被忽略，即使单链堆积热容几乎等于双链形成的堆积热容。通过包含这些交互作用，折叠算法的精确度应该会提高。(D)折叠算法寻求最低自由能状态。由于几种构象之间的自由能差很小，能量预测的内在不确定性可能意味着另一种状态的能量最低。对不确定性进行表征将允许计算作为核苷酸数量函数的正确预测的可能性。(3)我们的“堆积或自由连接链”(SFJC)模型的发展将为研究由尖锐扭结引起的构象无序的聚合物提供一个新的背景。这个两态模型的计算很简单，初步结果表明，它们与最近拉伸的DNA实验相当好。SFJC还可以方便地对RNA的单链环段进行建模。

DESCRIPTION (provided by applicant): Single-stranded nucleic acids fold into complex and compact shapes. Making accurate secondary structure predictions helps uncover function and cellular activity and is also of general interest as an analog of the protein folding problem. The following three proposals will expand the predictive power of physical chemical models of nucleic acid conformations. (1) Gene finding algorithms are currently statistics based. We, like cells, favor a thermodynamics-based approach to locating splice sites. Preliminary results show that snRNA binds better to real splice sequences than false. This work should lead to better gene recognition algorithms and a simple picture of splicing. (2) Revising current models and improving the functionality of secondary structure algorithms will help researchers interested in nucleic acid conformations. Algorithmic advances will likely be useful for other related problems such as anti-sense gene therapy and gene chip thermodynamic analysis. (a) Pseudoknots are excluded from popular dynamic-programming algorithms like MFOLD. Characterizing the "PseudoBase" database of known pseudoknots will help select an algorithm, which would then be implemented. (b) Current algorithms search for minimum energy conformations, but secondary structures may be trapped kinetically. A kinetic rule for folding based in polymer physics and implemented in a dynamic programming algorithm would allow the study of misfolding. (c) Unpaired regions are ignored in current models of folding, even though single-strand stacking enthalpies are nearly equal to those of duplex formation. By including these interactions, the accuracy of folding algorithms should improve. (d) Folding algorithms seek the lowest free energy state. Since the free energy differences between several conformations is small, the intrinsic uncertainty of the energy prediction may mean another state is lowest in energy. Characterizing the uncertainty will permit calculations of the likelihood of a correct prediction as a function of the number of nucleotides. (3) The development of our "Stacked or Freely Jointed Chain" (SFJC) model will provide a new context with which to study polymers whose conformational disorder arises from sharp kinks. Calculations are straightforward for this two-state model and preliminary results suggest they compare well with recent stretched DNA experiments. The SFJC is also handy for modeling single-stranded loop sections of RNA.