三链DNA稳定性的影响因素

介绍了碱基组成、碱基修饰或替代、DNA骨架的修饰、DNA配体的结合及反应体系中的盐离子和pH值等因素对三链DNA稳定性的影响。对三链DNA稳定性研究中应注意的几个问题也作了讨论。     

Fluorescence correlation spectroscopy in the nanosecond time range: rotational diffusion of bovine carbonic anhydrase B

A fluorescence correlation experiment for measurement of rotational diffusion in the nanosecond time scale is described. Using this method, the rotational diffusion coefficient of bovine carbonic anhydrase B labelled with tetramethylrhodamine isothiocyanate was estimated to be D_r=(1.14±0.15)×10⁷ s^-1 at 22°C. The experiment is based on a cw argon ion laser, a microfluorimeter with local solution flow inside the sample cell, and two photon detectors. The fluorescence intensity autocorrelation function in the nanosecond time range is computed with the help of a time-to-amplitude converter and a multichannel pulse-amplitude analyser.     

Conservative substitutions in the hydrophobic core of Rhodobacter sphaeroides thioredoxin produce distinct functional effects.

The internal residue Phe 25 in Rhodobacter sphaeroides thioredoxin was changed to five amino acids (Ala, Val, Leu, Ile, Tyr) by site-directed mutagenesis, and the mutant proteins were characterized in vitro and in vivo using the mutant trxA genes in an Escherichia coli TrxA- background. The substitution F25A severely impaired the functional properties of the enzyme. Strains expressing all other mutations can grow on methionine sulfoxide with growth efficiencies of 45-60% that of the wild type at 37 degrees, and essentially identical at 42 degrees. At both temperatures, however, strains harboring the substitutions F25V and F25Y had lower growth rates and formed smaller colonies. In another in vivo assay, only the wild type and the F25I substitution allowed growth of phage T3/7 at 37 degrees, demonstrating that subtle modifications of the protein interior at position 25 Ile/Leu or Phe/Tyr) can produce significant biological effects. All F25 mutants were good substrates for E. coli thioredoxin reductase. Although turnover rates and apparent Km values were significantly lower for all mutants compared to the wild type, catalytic efficiency of thioredoxin reductase was similar for all substrates. Determination of the free energy of unfolding showed that the aliphatic substitutions (Val, Leu, Ile) significantly destabilized the protein, whereas the F25Y substitution did not affect protein stability. Thus, thermodynamic stability of R. sphaeroides thioredoxin variants is not correlated with the distinct functional effects observed both in vivo and in vitro.     

CorTectorTM SX100：一款桌面式荧光相关光谱仪的原理和应用

荧光相关光谱检测技术具有超灵敏(单分子)、快速(数秒至数分钟)和多功能(检测分子浓度、大小和相互作用)等技术优点,且无需反应物分离,因此有潜力成为一种新型均相、高敏荧光免疫检测技术,适用于在溶液中或单个活细胞内检测生物分子特性．本文首先介绍荧光相关光谱检测技术的原理和研究进展,然后结合项目团队自主研发的目前全球唯一一款可靠、易使用的桌面式荧光相关光谱仪,进一步探讨荧光相关光谱检测技术的具体实现和潜在应用．     

DNA binding activity of Anabaena sensory rhodopsin transducer probed by fluorescence correlation spectroscopy

Anabaena sensory rhodopsin transducer (ASRT) is believed to be a major player in the photo-signal transduction cascade, which is triggered by Anabaena sensory rhodopsin. Here, we characterized DNA binding activity of ASRT probed by using fluorescence correlation spectroscopy. We observed clear decrease of diffusion coefficient of DNA upon binding of ASRT. The dissociation constant, K_D, of ASRT to 20?bp-long DNA fragments lied in micro-molar range and varied moderately with DNA sequence. Our results suggest that ASRT may interact with several different regions of DNA with different binding affinity for global regulation of several genes that need to be activated depending on the light illumination.     

Characterization and quantification of triple helix formation in chromosomal DNA

DNA-binding molecules that recognize specific sequences offer a high potential for the understanding of chromatin structure and associated biological processes in addition to their therapeutic potential, e.g. as positioning agents for validated anticancer drugs. A prerequisite for the development of DNA-binding molecules is the availability of appropriate methods to assess their binding properties quantitatively at the desired target sequence in the human genome. We have further developed a capture assay to assess triplex-forming oligonucleotide (TFO) binding efficiency quantitatively. This assay is based on bifunctional, psoralen and biotin-conjugated, TFOs and real-time PCR analysis. We have applied this novel quantification method to address two issues that are relevant for DNA-binding molecules. First, we have compared directly the extent of TFO-binding in three experimental settings with increasing similarity to the situation in vivo, i.e. naked genomic DNA, isolated cell nuclei, or whole cells. This comparison allows us to characterize factors that influence genomic triplex formation, e.g. chromosomal DNA organization or intracellular milieu. In isolated nuclei, the binding was threefold lower compared to naked DNA, consistent with a decreased target accessibility int he nucleosomal environment. Binding was detected in whole cells, indicating that the TFO enters the nucleus and binds to its target in intact cells in vivo, but the efficiency was decreased (tenfold) compared to nuclei. Secondly, we applied the method to characterize the binding properties of two different TFOs targeting the same sequence. We found that an antiparallel-binding GT-containing TFO bound more efficiently, but with less target sequence selectivity compared to a parallel-binding CU-containing TFO. Collectively, a sensitive method to characterize genomic triplex formation was described. This may be useful for the determination of factors driving TFO binding efficiency and, thus, may improve the usefulness of triplex-mediated gene targeting for studies of chromatin structure as well as for therapeutic antigene strategies.     

Thermodynamic dissection of the polymerizing and editing modes of a DNA polymerase

DNA polymerases with intrinsic proofreading activity interact with DNA primer/templates in two distinct modes, corresponding to the complexes formed during the 5'-3' polymerization or 3'-5' editing of a nascent DNA chain. Thermodynamic measurements designed to quantify the energetic contributions of individual DNA-protein contacts in either the polymerizing or editing complexes are complicated by the fact that both species exist in solution and are not resolved in conventional DNA-protein binding assays. To overcome this problem, we have developed a new binding analysis that combines information from steady-state and time-resolved fluorescence experiments and uses the Klenow fragment of Escherichia coli DNA polymerase I (KF) and fluorescently labeled primer/template oligonucleotides as a model polymerase-DNA system. Steady-state fluorescence titrations are used to evaluate the overall affinity of KF for the primer/template, while time-resolved fluorescence anisotropy is used to quantify the equilibrium fractions of the primer/template bound in the polymerizing and editing modes. From a combined analysis of both data, the equilibrium constant and hence standard free energy change associated with each binding mode can be obtained unequivocally. This method is initially used to determine the equilibrium constants describing binding of a correctly base-paired primer/template to the 5'-3' polymerase and 3'-5' exonuclease sites of KF. It is then extended to quantify the extent to which these parameters are affected by the introduction of mismatches into the primer/template, and by rearrangement of specific side-chains in the exonuclease domain of the protein. While these perturbants were originally designed to demonstrate the utility of our new approach, they are also relevant in their own right since they have helped identify some hitherto unknown determinants of polymerase fidelity.     

Fluorescence correlation spectroscopy in the nanosecond time range: Photon antibunching in dye fluorescence

Possibilities for the use of fluorescence correlation spectroscopy in the nanosecond time range are demonstrated. The experiment is based on a cw argon ion laser, a microfluorimeter, two photon detectors, and a time-to-analog converting system. Experiments using solutions of rhodamine 6G and pyronine G in water at concentrations of about 20 molecules per sample volume are reported. The photon anticorrelation component decaying with a time constant close to the excited state lifetime was observed.     

DNA浓度与其Raman光谱强度间的线性相关的分析

Ｒａｍａｎ光谱法业已广泛应用于生物医学,生物化学和分子生物学等很多领域,尤其是近年来傅立叶转换Ｒａｍａｎ光谱技术（ＦＴ—Ｒａｍａｎｓｐｅｃｔｒｏｓｃｏｐｙ）的兴起,引起人们极大兴趣。本文介绍Ｒａｍａｎ光谱技术应用的一个新领域一对溶液中ＤＮＡ浓度的测定。溶液中ＤＮＡ浓度的测定,是生物化学和生物医学上经常遇到的问题,通常采用紫外分光光度法。当要分析ＤＮＡ构型变化时,最常用的方法是Ｘ线晶体衍射,核磁共振和Ｒａｍａｎ光谱法。为了进一步研究ＤＮＡ构型变化与浓度变化之间的关系,进行了ＤＮＡ的Ｒａｍａｎ光谱强度与浓度间的线性相关研究。以ＨＰＫ１Ａ细胞ＤＮＡ的８１０ｃｍ－１Ｒａｍａｎ光谱峰作为线性相关分析的内标,实验结果表明该ＤＮＡ的Ｒａ－ｍａｎ光谱强度与浓度间存在着良好的线性相关（Ｒ＝０．９９３）。其检出限为０．１０μｇ／μｌ,标准差（ＳＤ）为０．００３（ｎ＝１１）,相对标准差（ＲＳＤ）为２．７３％。应用ＦＴ—Ｒａｍａｎ光谱术测定溶液中ＤＮＡ浓度,方法简单,样品不需特殊处理,灵敏和准确。本文详细讨论了该法的操作步骤和注意事项。     

纳米磁性粒子在DNA分离与纯化中的应用进展

纳米磁性粒子是一种新型的亲和纯析固相载体 ,其粒径小 ,具有超顺磁性 ,表面积大 ,表面可赋予多种反应基团如链霉亲和素、抗体等 ,或DNA片段 ,在磁场作用下可分离目的DNA ,已逐步应用于分子生物学领域中 ,有着极为广泛的应用前景。