基于质粒DNA匹配问题的分子算法

给定无向图,图的最小极大匹配问题是寻找每条边都不相邻的最大集中的最小者,这个问题是著名的NP-完全问题.1994年Adleman博士首次提出用DNA计算解决NP-完全问题,以编码的DNA序列为运算对象,通过分子生物学的运算操作解决复杂的数学难题,使得NP-完全问题的求解可能得到解决.提出了基于质粒DNA的无向图的最大匹配问题的DNA分子生物算法,通过限制性内切酶的酶切和凝胶电泳完成解的产生和最终接的分离,依据分子生物学的实验手段,算法是有效并且可行的.     

DNA计算机的分子生物学研究进展

DNA(脱氧核糖核酸)计算机研究是一个新领域。从字面上看,它既包含DNA研究也包含计算机的研究,因而也包含DNA技术与计算机技术如何交融的研究。1994年,Adleman在Science上报道了首例DNA计算的研究结果;2001年,Benenson等在Nature报道了一种由DNA分子和相应的酶分子构成的、有图灵机功能的可程序试管型DNA计算机,标志着DNA计算机研究的重大进展。DNA计算机最大的特点是超大规模的并行运算能力和潜在的巨大的数据储存能力。目前DNA计算机研究已涉及许多领域,包括生物学、数学、物理、化学、计算机科学和自动化工程等具体应用,是计算概念上的一次革命。DNA计算机的研究大大促进了DNA分子操作技术尤其是在纳米尺度下操作DNA分子的研究速度。从DNA计算机的基本原理、应用形式、与基因组学研究的重要关系等方面总结和评述了相关研究进展。     

基于三链核酸的DNA计算

一种研究DNA计算的新模型——三链DNA计算模型在本文中提出。此模型是在近年三链核酸的研究成果的基础上建立的。并应用于求解可满足性问题（SAT）,这是一个困难的NP-完全问题。不同于以住的DNA计算方法,基于三链核酸的分子算法通过寡聚脱氧核苷酸（ODN）在RecA蛋白的介导下与同源的双链DNA匹配成三链DNA进行基本的运算,这样可以有效减少计算中的错误。依据分子生物学的实验方法,该算法切实可行并且有效。     

DNA分子标记技术在生态学研究中的应用

分子生物学几种常见的分子标记技术如RFLP,RAPD,微卫星法,DNA序列分析使生态学研究从宏观步入了微观领域,极大的推动了生态学的发展,对这几种分子标记技术在生态学中的应用及其进展进行了综述,并比较了这些分子生物学技术各自的优缺点.     

微生物代谢工程原理与应用

代谢工程是利用分子生物学原理系统分析细胞代谢网络,并通过DNA重组技术和应用分析生物学相关的遗传学手段对细胞进行有精确目标的基因操作,改变微生物原有的代谢或调节系统,实现目的产物代谢活性的提高。代谢工程综合了生物化学、化学工程、数学分析等多学科内容,是当前国内外学者研究热点之一。论述了微生物代谢工程的理论基础及其应用进展和前景。     

单粒干燥大豆种子基因组DNA提取的有效方法

大豆基因组DNA的提取是进行大豆分子生物学研究的基础.以大豆干燥的种子为材料,将SDS法和CTAB法结合在一起并进行了一定的改进,有效的提取了基因组DNA.通过电泳、紫外分光光度计检测和ISSR标记分析验证这种方法是提取大豆干种子基因组DNA的有效方法.     

甘蔗基因组DNA小量提取与大量提取方法研究

甘蔗的叶片中含有大量的多糖、多酚类和RNA等物质,对甘蔗分子生物学实验带来了极大的影响.本研究利用改良的CTAB对甘蔗基因组DNA进行小量提取法与大量提取方法的研究,本方法操作简单,DNA完整性好、产量高、纯度高可满足大部分分子实验的需要.     

基于PNA的最大独立集问题的DNA计算模型

肤核酸(Peptide Nucleic Acid)是人工合成的拔酸(DNA)的类似物.PNA能够特异地、稳定地与DNA杂交以及其独特的性质,使得PNA广泛应用在分子生物学中.本文提出了一种基于PNA的最大独立集问题的DNA计算模型,利用单链PNA被逐步褪火到单链DNA分子上,解决了一个最大独立集问题的实例.该模型的解空间只有一种类型的DNA分子,计算经m步生物操作产生问题的解(其中m=|E(G)|),最后利用鞭子PCR(whiplash PCR)原理以及凝胶电泳读解.     

基因操作原理(续完)——第十章 重组DNA研究的有关问题

迄今,以重组DNA研究获得最大好处的无疑是分子生物学本身了。联合应用Southern墨迹转移杂交技术和核苷酸序列快速分析法,重组DNA技术有可能对大量的真核基因结构进行详细的分析。仔细阅读本书的读者有可能了解到基因结构知识的现代进展,并将认识到这种知识的重要性。     

科学出版社科学出版中心生物分社新书推介2008-05精编分子生物学实验指南（第五版）

本书是知名度很高、不断更新的《最新分子生物学实验方法汇编》（Current Protocols in Molecular Biology）系列的精编版本。新版对原有内容进行了修订和更新,包括：大肠杆菌、质粒和噬菌体,DNA的制备和分析,DNA和RNA的酶学操作,RNA的制备和分析,重组DNA文库的构建,重组DNA文库的筛选,DNA序列测定,     

Solving the SAT problem using a DNA computing algorithm based on ligase chain reaction

A new DNA computing algorithm based on a ligase chain reaction is demonstrated to solve an SAT problem. The proposed DNA algorithm can solve an n-variable m-clause SAT problem in m steps and the computation time required is O (3m+n). Instead of generating the full-solution DNA library, we start with an empty test tube and then generate solutions that partially satisfy the SAT formula. These partial solutions are then extended step by step by the ligation of new variables using Taq DNA ligase. Correct strands are amplified and false strands are pruned by a ligase chain reaction (LCR) as soon as they fail to satisfy the conditions. If we score and sort the clauses, we can use this algorithm to markedly reduce the number of DNA strands required throughout the computing process. In a computer simulation, the maximum number of DNA strands required was 2(0.48n) when n=50, and the exponent ratio varied inversely with the number of variables n and the clause/variable ratio m/n. This algorithm is highly space-efficient and error-tolerant compared to conventional brute-force searching, and thus can be scaled-up to solve large and hard SAT problems.     

DNA supercoiling helps to unlink sister duplexes after replication

DNA supercoiling is one of the mechanisms that can help unlinking of newly replicated DNA molecules. Although DNA topoisomerases, which catalyze the strand passing of DNA segments through one another, make the unlinking problem solvable in principle, it remains difficult to complete the process that enables the separation of the sister duplexes. A few different mechanisms were developed by nature to solve the problem. Some of the mechanisms are very intuitive while the others, like topology simplification by type II DNA topoisomerases and DNA supercoiling, are not so evident. A computer simulation and analysis of linked sister plasmids formed in Escherichia coli cells with suppressed topoisomerase IV suggests an insight into the latter mechanism.     

Biomolecular computing: Is it ready to take off?

Biomolecular computing is an emerging field at the interface of computer science, biological science and engineering. It uses DNA and other biological materials as the building blocks for construction of living computational machines to solve difficult combinatorial problems. In this article, notable advances in the biomolecular computing are reviewed and challenges associated with this multidisciplinary research are addressed. Finally, several perspectives are given based on the review of biomolecular computing.     

DNA芯片在0-1规划问题中的应用

生物芯片技术和DNA计算分别是近年来生命科学与信息科学的新兴研究领域,对信息高度并行的获取与处理是二者的本质特性.而0-1规划问题作为运筹学中一个重要的问题,到目前为止还没有好的算法.在DNA计算和DNA芯片基础上,提出了基于DNA芯片解决0-1规划问题的DNA计算新模型,与以往DNA计算模型相比,该模型具有高信息量和操作易自动化的优点.同时指出DNA芯片技术有望作为新型生物计算的芯片.     

Fractal construction of constrained code words for DNA storage systems

The use of complex biological molecules to solve computational problems is an emerging field at the interface between biology and computer science. There are two main categories in which biological molecules, especially DNA, are investigated as alternatives to silicon-based computer technologies. One is to use DNA as a storage medium, and the other is to use DNA for computing. Both strategies come with certain constraints. In the current study, we present a novel approach derived from chaos game representation for DNA to generate DNA code words that fulfill user-defined constraints, namely GC content, homopolymers, and undesired motifs, and thus, can be used to build codes for reliable DNA storage systems.     

基于分子信标的DNA计算

DNA计算是解决一类难以计算问题的一种新方法,这种计算随着问题的增大可以呈指数增长．迄今为止,许多研究成果已经成功地提高了它的性能和增加了它的可行性,本文在基于表面的DNA计算中采用了分子信标编码策略,并对分子信标在与对应的补链杂交形成双链时的受力进行分析,给出3-SAT问题的另一种解法．这种方法比现有的方法更有效,更具发展前景．因为它具有编码简单;耗材底;操作时间短;技术先进等优点．本文尝试了分子生物学,光学和力学的结合．这一工作为DNA计算能解决NP一完全问题提供了更有力的依据．     

DNA计算机原理、现状及发展

DNA计算机是一种基于DNA生化反应 ,与传统计算机完全不同的新型生物计算机。本文概述了DNA计算机的原理、特点与现状。并对其发展进行展望     

分子信标芯片计算在0-1整数规划问题中的应用

生物芯片技术和DNA计算分别是近年来生命科学与信息科学的新兴研究领域,对信息高度并行的获取与处理是二者的本质特性．而0-1整数规划问题作为运筹学中一个重要的问题,到目前为止还没有好的算法．在DNA计算和DNA芯片基础上,提出了基于分子信标芯片解决0-1整数规划问题的DNA计算新模型．与以往DNA计算模型相比,该模型具有高信息量和操作易自动化的优点,同时指出分子信标芯片技术有望作为新型生物计算的芯片．     

A new fast algorithm for solving the minimum spanning tree problem based on DNA molecules computation

The minimum spanning tree (MST) problem is to find minimum edge connected subsets containing all the vertex of a given undirected graph. It is a vitally important NP-complete problem in graph theory and applied mathematics, having numerous real life applications. Moreover in previous studies, DNA molecular operations usually were used to solve NP-complete head-to-tail path search problems, rarely for NP-hard problems with multi-lateral path solutions result, such as the minimum spanning tree problem. In this paper, we present a new fast DNA algorithm for solving the MST problem using DNA molecular operations. For an undirected graph with n vertex and m edges, we reasonably design flexible length DNA strands representing the vertex and edges, take appropriate steps and get the solutions of the MST problem in proper length range and O(3m + n) time complexity. We extend the application of DNA molecular operations and simultaneity simplify the complexity of the computation. Results of computer simulative experiments show that the proposed method updates some of the best known values with very short time and that the proposed method provides a better performance with solution accuracy over existing algorithms.