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1.
基于三链核酸的DNA计算   总被引:2,自引:0,他引:2  
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。  相似文献   

2.
DNA计算机的分子生物学研究进展   总被引:7,自引:0,他引:7  
张治洲  赵健  贺林 《遗传学报》2003,30(9):886-892
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。  相似文献   

3.
随着高性能计算需求的不断增长,传统计算模式面临着前所未有的巨大挑战.在众多新兴计算技术中,DNA计算系统以其低能耗、并行化等特点而广受关注.DNA电路(DNA circuit)是实现DNA计算的基础,也是该领域重要的分子信息调控和处理技术.文中重点介绍了DNA计算的基本原理,并总结了最新的研究进展,最后讨论了基于DNA...  相似文献   

4.
基于分子信标的DNA计算   总被引:12,自引:5,他引:12  
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.  相似文献   

5.
DNA疫苗研究现状和展望   总被引:6,自引:0,他引:6  
自1992年第一次报道DNA疫苗技术以来,在短短3-4年的时间内这一技术得到飞速发展,在NDA疫苗的作用机理,如何增强DNA免疫效果以及DNA疫苗的优势和问题等方面做子大量卓有成效的探索,尽管现在人产对DNA疫苗抗原提呈作用机理还不清楚,也还没有完全也解DNA疫苗安全性问题,但是对DNA疫苗的免疫防御,免疫治疗和免疫调节作用已有了较为清晰的认识,本文拟对此作一简要概述。  相似文献   

6.
本文详细总结了近年来三螺旋DNA的结构和应用研究方面的进展,研究了各种因素对三螺肇稳定性的影响,并提出了一些在三螺肇DNA中富有挑战性的需进一步研究的问题。  相似文献   

7.
自1992年第一次报道DNA疫苗技术以来,在短短3-4年的时间内这一技术得到飞速发展,在DNA疫苗的作用机理、如何增强DNA免疫效果以及DNA疫苗的优势和问题等方面做了大量卓有成效的探索,尽管现在人们对DNA疫苗抗原提呈作用机理还不清楚,也还没有完全了解DNA疫苗安全性问题,但是对DNA疫苗的免疫防御、免疫治疗和免疫调节作用已有了较为清晰的认识。本文拟对此作一简要概述。  相似文献   

8.
三链DNA的形成抑制DNA结合蛋白与启动子的结合   总被引:4,自引:1,他引:3       下载免费PDF全文
电泳迁移分析方法及DNaseⅠ足迹实验表明21nt脱氧寡核苷酸G3TG2T GT2G5TG2TGT(CP1)与乙肝病毒(HBV)核心启动子(Cp)片段之间三链DNA的形成有较高的特异性及稳定性.凝胶滞留实验显示, 在大鼠肝细胞核提取物体外转录系统中, CP1可特异地抑制DNA结合蛋白与Cp片段的结合, 而不能与Cp结合形成三链DNA的脱氧寡核苷酸CP3(TGTG2TG5T2GTG2TG3)对蛋白与Cp的结合并无抑制作用.这些结果表明, 三链DNA的形成有可能抑制HBV DNA的转录.  相似文献   

9.
DNA计算机原理、现状及发展   总被引:1,自引:0,他引:1  
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  相似文献   

10.
本文介绍了两种预测DNA顺序上的启动子位置的计算机识别方法,方法1是基于启动子部位单核苷酸的分布不均一性,方法2是基于启动子部位二核苷酸的分布不均一性。分别用这两种方法推测了质粒pBR322DNA上启动子的位置,从而验证了化学实验的结果。  相似文献   

11.
    
Data are presented on a triplex type with two parallel homologous strands for which triplex formation is almost as strong as duplex formation at least for some sequences and even at pH 7 and 0.2 M NaCl. The evidence mainly rests upon comparing thermodynamic properties of similar systems. A paperclip oligonucleotide d(A12C4T12C4A12) with two linkers C4 obviously can form a triplex with parallel back-folded adenine strand regions, because the single melting transition of this complex splits in two transitions by introducing mismatches only in the third strand region. Respectively, a hairpin duplex d(A12C4T12) and a single strand d(A12) form a triplex as a 1:1 complex in which the second adenine strand is parallel oriented to the homologous one in the Watson-Crick paired duplex. In this system the melting temperature T(m) of the triplex is practically the same as that of the duplex d(A12)-d(T12), at least within a complex concentration range of 0.2-4.0 microM. The melting behaviour of complexes between triplex stabilizing ligand BePI and the system hairpin duplex plus single strand supports the triplex model. Non-denaturing gel electrophoresis suggests the existence of a triplex for a system in which five of the twelve A-T*A base triads are substituted by C-G*C base triads. The recognition between any substituted Watson-Crick base pair (X-Y) in the hairpin duplex d(A4XA7C4T7YT4) and the correspondingly replaced base (Z) in the third strand d(A4ZA7) is mutually selective. All triplexes with matching base substitutions (Z = X) have nearly the same stability (T(m) values from 29 to 33.5 degrees C), whereas triplexes with non-matching substitutions (Z not equal X) show a clearly reduced stability (T(m) values from 15 to 22 degrees C) at 2microM equimolar oligonucleotide concentration. Most nucleic acid triple helices hitherto known are limited to homopurine-homopyrimidine sequences in the target duplex. A stable triplex formation is demonstrated for inhomogeneous sequences tolerating at least 50% pyrimidine content in the homologous strands. On the basis of the surprisingly similar thermodynamic parameters for duplex and triplex, and of the fact that this triplex type seems to be more stable than many other natural DNA triplexes known, and on the basis of semiempirical and molecule mechanical calculations, we postulate bridging interactions of the third strand with the two other strands in the triplex according to the recombination motif. This triplex, denoted by us 'recombination-like form', tolerates heterogeneous base sequences.  相似文献   

12.
全错位排列问题的基于表面的DNA计算模型   总被引:1,自引:0,他引:1  
生物表面技术是DNA计算的一种实现方式,是近年来生命科学的新兴研究领域.而全错位排列问题作为组合数学中一个重要的问题,到目前为止还没有好的算法.在DNA表面技术的基础上,首次提出了全错位排列问题的基于表面的DNA计算模型,并对模型进行了简单的分析.  相似文献   

13.
    
Meester R  Sjerps M 《Biometrics》2003,59(3):727-732
Summary . Does the evidential strength of a DNA match depend on whether the suspect was identified through database search or through other evidence (“probable cause”)? In Balding and Donnelly (1995, Journal of the Royal Statistical Society, Series A 158, 21–53) and elsewhere, it has been argued that the evidential strength is slightly larger in a database search case than in a probable cause case, while Stockmarr (1999 , Biometrics 55, 671–677) reached the opposite conclusion. Both these approaches use likelihood ratios. By making an excursion to a similar problem, the two‐stain problem, we argue in this article that there are certain fundamental difficulties with the use of a likelihood ratio, which can be avoided by concentrating on the posterior odds. This approach helps resolving the above‐mentioned conflict.  相似文献   

14.
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.  相似文献   

15.
一种基于单分子纳米操纵的有序化测序策略   总被引:1,自引:0,他引:1       下载免费PDF全文
尽管包括人类在内的许多生物物种的基因组测序工作已经完成,但由于现有测序技术的限制,大部分复杂基因组还存在很多大大小小的缺口.缺口的填补以及对其他重复序列区域的测序迫切需要全新的思路和技术.基于在DNA单分子定位切割和拾取方面的实验进展,提出了一种基于原子力显微镜纳米操纵技术的单分子有序化测序策略.计算机模拟的结果表明,这一方法和策略是可行的,有助于解决目前测序工作中所遇到的一些棘手问题.  相似文献   

16.
D S Ray  J C Hines  M H Kim  R Imber  N Nomura 《Gene》1982,18(3):231-238
M13 cloning vectors have been developed for the selection of DNA sequences capable of directing initiation of DNA synthesis on single-stranded templates. These vectors are derived from viable M13 mutants containing large deletions in the region of the complementary strand origin. The deletion mutants are defective in the conversion of viral single strands to the duplex replicative form (SS leads to RF) both in vivo and in vitro, give a reduced phage yield and form turbid plaques. A receptor site for foreign single strand initiation determinants has been introduced into the mutants by the insertion of EcoRI linker sequences at the deletion sites. Specific cloned sequences from bacteriophage G4 RF and from Co1E1 DNA restore a clear plaque type and normal phage growth. Selection of clear-plaque isolates obtained by transfection with RF from one of these vectors, M13 delta E101, carrying inserted Co1E1 HaeIII fragments resulted in the selective cloning of one specific fragment, the HaeIII-E fragment. Insertion of either the H or L strand of the HaeIII-E fragment into the M13 delta E101 viral strand gives a clear plaque phenotype, indicating the presence of initiation determinants on both the H- and L-strands of the Co1E1 HaeIII-E fragment. These cloning vectors provide a new means for the functional dissection of replication origins and for the identification of DNA sequences that determine the enzymatic mechanism of discontinuous synthesis along the length of the bacterial chromosome. The ability to assess initiation capability on the basis of plaque morphology also provides a means for rapid genetic analysis of initiation determinants.  相似文献   

17.
Five long-timescale (10 ns) explicit-solvent molecular dynamics simulations of a DNA tetradecanucleotide dimer are performed using the GROMOS 45A4 force field and the simple-point-charge water model, in order to investigate the effect of the treatment of long-range electrostatic interactions as well as of the box shape and size on the structure and dynamics of the molecule (starting from an idealised B-DNA conformation). Long-range electrostatic interactions are handled using either a lattice-sum (LS) method (particle–particle–particle–mesh; one simulation performed within a cubic box) or a cutoff-based reaction-field (RF) method (four simulations, with long-range cutoff distances of 1.4 or 2.0 nm and performed within cubic or truncated octahedral periodic boxes). The overall double-helical structure, including Watson–Crick (WC) base-pairing, is well conserved in the simulation employing the LS scheme. In contrast, the WC base-pairing is nearly completely disrupted in the four simulations employing the RF scheme. These four simulations result in highly distorted compact (cutoff distance of 1.4 nm) or extended (cutoff distance of 2 nm) structures, irrespective of the shape and size of the computational box. These differences observed between the two schemes seem correlated with large differences in the radial distribution function between charged entities (backbone phosphate groups and sodium counterions) within the system.  相似文献   

18.
Does quantum dynamics play a role in DNA replication? What type of tests would reveal that? Some statistical checks that distinguish classical and quantum dynamics in DNA replication are proposed.  相似文献   

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