诺氟沙星与DNA的拉曼光谱研究

报道了诺氟沙星(NFX)及诺氟沙星胶囊内容物的FT-Raman光谱和在银胶基底上的表面增强拉曼光谱(SERS),归属了各个振动;研究了诺氟沙星与DNA的相互作用的SERS,结果表明:胶囊内容物的拉曼光谱图与对照品的拉曼光谱图的特征振动峰:C-F键的伸缩振动,C=C伸缩振动,O-C-O的对称伸缩振动峰值未发生变化,发生变化主要是分子骨架振动峰,诺氟沙星胶囊的辅料对拉曼光谱无实质影响,可建立拉曼光谱法检测诺氟沙星药物的分析方法;诺氟沙星可以在没有金属离子的存在下与DNA直接作用,与DNA相互作用的主要键合模式是插入作用,NFX分子中的平面结构插入DNA的双螺旋碱基平面,为深入了解喹诺酮类抗生素的抗菌机理提供可靠依据.     

DNA与组蛋白相互作用的布朗动力学研究

在真核生物中,DNA按左手手征性的方式,缠绕在组蛋白八聚体的周围,形成稳定的核小体结构.文章作者运用布朗动力学,数值模拟了DNA与组蛋白相互作用最终形成核小体的动力学过程,揭示了DNA与组蛋白相互作用的详细图景,并提出了组蛋白八聚体旋转模型,以解释这一过程.文章作者还计算了组成核小体的DNA在受到拉伸力时,组蛋白被从核小体中剥离下来的动力学过程,得到了组装和剥离过程的详细图像,给出了与前人单分子实验一致的拉伸力与拉伸长度的关系曲线和拉伸台阶.此外,还通过建立的组蛋白手征性模型,模拟了核小体手征性的形成过程,发现DNA的缠绕方向强烈依赖于组蛋白的手征性,显示出环境温度对核小体手征性有重要影响.     

基于InP@ZnS QDs/Dured纳米荧光探针的DNA检测

利用巯基丙酸包覆的In P@Zn S量子点(QDs)与Dured构建了一种检测DNA的荧光探针。在该探针中,以环境友好型带负电的In P@Zn S量子点为荧光团,与带正电的Dured通过静电结合,构建了In P@Zn S QDs/Dured纳米荧光探针。通过荧光共振能量转移(FRET)机理,量子点荧光被猝灭;当DNA存在时,Dured与DNA的特异性结合使Dured从In P@Zn S QDs表面脱附,FRET过程被打断,In P@Zn S QDs荧光恢复,以荧光"关-开"方式检测DNA。该探针检测DNA的线性范围为2.0~275.0 ng·L-1,检测限为1.0 ng·L-1,并可用于模拟生物生理条件下的DNA检测。     

谐振势阱中的布朗运动——磁镊实验与模拟

从磁镊实验和模拟角度研究了处于谐振势阱中的布朗运动. 利用实验和模拟的结果验证了理论.然后通过理论与实验的对照, 对磁镊实验中DNA分子的持久长度大小对小球位移分布的影响, 以及磁镊实验中的测力误差作了相关分析.分析指出:持久长度的变化对沿 DNA链方向上的布朗运动影响更大;小的外力作用下力的测量会出现较大误差.     

Melting and unzipping of DNA

Existing experimental studies of the thermal denaturation of DNA yield sharp steps in the melting curve suggesting that the melting transition is first order. This transition has been theoretically studied since the early sixties, mostly within an approach in which the microscopic configurations of a DNA molecule consist of an alternating sequence of non-interacting bound segments and denaturated loops. Studies of these models neglect the repulsive, self-avoiding, interaction between different loops and segments and have invariably yielded continuous denaturation transitions. In the present study we take into account in an approximate way the excluded-volume interaction between denaturated loops and the rest of the chain. This is done by exploiting recent results on scaling properties of polymer networks of arbitrary topology. We also ignore the heterogeneity of the polymer. We obtain a first-order melting transition in d = 2 dimensions and above, consistent with the experimental results. We also consider within our approach the unzipping transition, which takes place when the two DNA strands are pulled apart by an external force acting on one end. We find that the under equilibrium condition the unzipping transition is also first order. Although the denaturation and unzipping transitions are thermodynamically first order, they do exhibit critical fluctuations in some of their properties. For instance, the loop size distribution decays algebraically at the transition and the length of the denaturated end segment diverges as the transition is approached. We evaluate these critical properties within our approach. Received 21 August 2001 and Received in final form 26 January 2002     

Low dimensional chaos in the AT and GC skew profiles of DNA sequences

This paper investigates the existence of low-dimensional deterministic chaos in the AT and GC skew profiles of DNA sequences. It has taken DNA sequences from eight organisms as samples. The skew profiles are analysed using continuous wavelet transform and then nonlinear time series methods. The invariant measures of correlation dimension and the largest Lyapunov exponent are calculated. It is demonstrated that the AT and GC skew profiles of these DNA sequences all exhibit low dimensional chaotic behaviour. It suggests that chaotic properties may be ubiquitous in the DNA sequences of all organisms.     

用荧光探针签别CYP2C9*3基因

用一种基激复合物荧光探针系统来签别碱基错配的CYP2C9*3基因,该系统选择两个分开的与靶点碱基相对应的12碱基荧光标记的寡核苷酸作为探针,分别对24碱基、47碱基、质粒(3165bp)的靶点CYP2C9基因和CYP2C9*3基因进行杂交配对,结果该基激复合物荧光探针系统能有效签别各种长度的CYP2C9基因和CYP2C9*3基因,背景干扰很低,灵敏度高,可尝试用于其他基因型的遗传多态性的签别。     

基于高阶残差量化的光谱二值编码新方法

光谱二值和多值编码技术能够实现目标光谱的快速匹配、识别和分类等应用,但这类量化编码方法会损失大量的光谱细节信息,且不能解码出与原始光谱近似的重构光谱,应用有限。为了解决上述问题,提出一种高阶残差量化的光谱编码新方法HOBC(high-order binary coding)。首先,对光谱向量进行去均值的规范化处理,得到值域为(-1, 1)的光谱序列;然后,求解规范化光谱的±1编码、编码系数和残差（即一阶残差）;基于一阶残差,逐阶解算2至K阶残差的±1编码及其系数;最后得到K个编码序列及其系数,即为HOBC的编码结果。选择典型波谱库数据集,对比光谱0/1二值编码BC01(binary coding with 0 and 1)、光谱分析编码SPAM(spectral analysis manager)、二值/四值混合编码SDFC(spectral derivative feature coding)和DNA四值编码等4种方法,进行了光谱量化编码和解码重构实验,分别统计了光谱形状特征和斜率特征编码的信息熵和存储量、光谱形状特征编码与原始光谱之间的光谱矢量距离SVD (spectral vector distance)、谱间Pearson相关系数SCC (spectral correlation coefficient)和光谱角SAM (spectral angle mapping)。结果表明,在编码存储量上,HOBC的1～4阶编码分别与以上4种编码相等;在编码信息熵上,HOBC的1～2阶编码分别与BC01和SPAM相等,而HOBC的3～4阶编码分别高于SDFC和DNA编码;在SCC上,HOBC1阶编码与BC01相等,而2～4阶编码均分别优于SPAM,SDFC和DNA编码;在SAM方面,HOBC 1～4阶编码均分别明显优于4种对比方法;4种对比方法不能明确解码重构,而HOBC可简便重构出与原始光谱近似的解码序列,且SVD逐阶递减。进一步,基于临泽草地试验站公开光谱数据集,进行了10类地物目标的光谱编码和监督分类实验,实验结果表明,在Kappa系数,总体分类精度和平均分类精度等3种性能评价指标上,HOBC均明显优于4种对比方法,尤其是,HOBC 4阶编码优于原始光谱的分类性能;对样本数量较少且类间相似性较高的难分类地物,HOBC亦具有优于其他算法的鲁棒性。说明HOBC编码在大幅压缩数据量的同时,其编码序列能保留较高的信息量,且具有较高的光谱可分性,可用于光谱高精度快速识别和分类;其解码重构序列与原始光谱序列具有较高的相似性,理论上可适用于目标识别和分类等应用。     

Spectroscopic and Binding Properties of Berberine to DNA and Its Application to DNA Detection

Berberine(BER) binds to the double helical DNA with a high affinity There is only a much smaller hypochromism and no shifts in the absorption spectra when BER binds to calf thymus DNA(CT DNA) The fluorescence yields increase dramatically when BER binds to DNA, with no shifts in the emission maximum. These spectral changes are in contrast to the behavior observed with many fluorescent intercalates Groove binding rather than intercalation was suggested to be the cause of these spectral changes. Consistent with groove binding, for polyamide anion quenching studies showed that the magnitude of K_sv of the bound BER was higher than that of the free BER. The addition of salt to the solution releases the DNA-bound drug action from the groove and causes a decrease in the fluorescence yield. The results of all above studies proved the groove binding of BER to DNA. The large fluorescence enhancements observed when BER binds to DNA and the poor fluorescence yield of BER in the absence of DNA can be used for sensitive detection of DNA The linear concentration range was 0–20μg/ml The limit of detection for CT DNA was 12 ng/ml     

Markov chain order estimation with conditional mutual information

We introduce the Conditional Mutual Information (CMI) for the estimation of the Markov chain order. For a Markov chain of K$K$ symbols, we define CMI of order m$m$, _Ic(m)$I_c\left(m\right)$, as the mutual information of two variables in the chain being m$m$ time steps apart, conditioning on the intermediate variables of the chain. We find approximate analytic significance limits based on the estimation bias of CMI and develop a randomization significance test of _Ic(m)$I_c\left(m\right)$, where the randomized symbol sequences are formed by random permutation of the components of the original symbol sequence. The significance test is applied for increasing m$m$ and the Markov chain order is estimated by the last order for which the null hypothesis is rejected. We present the appropriateness of CMI-testing on Monte Carlo simulations and compare it to the Akaike and Bayesian information criteria, the maximal fluctuation method (Peres–Shields estimator) and a likelihood ratio test for increasing orders using ?$?$-divergence. The order criterion of CMI-testing turns out to be superior for orders larger than one, but its effectiveness for large orders depends on data availability. In view of the results from the simulations, we interpret the estimated orders by the CMI-testing and the other criteria on genes and intergenic regions of DNA chains.