碱性品红共振光散射法测定DNA研究

基于脱氧核糖核酸（DNA）对有机染料碱性品红的共振光散射增强效应，拟订了一种测定DNA的共振光散射法。在pH=6．75～7．25的范围内，碱性品红在594nm处的共振光散射增强与yDNA和ctDNA的浓度呈线性关系，线性范围分别为0．20～1．60μg／mL和0～1．50μg／mL，相关系数分别为0．9997和0．9994，检出限可达26．5μg／L。该方法简便、快速，用于合成样品中DNA的测定，结果满意。     

甲基紫6B共振光散射法测定脱氧核糖核酸

基于甲基紫6B与脱氧核糖核酸在酸性条件下共振光散射的增强效应,建立了测定DNA的共振光散射法。在pH值为2．0～3．0的三羟甲基氨基甲烷一盐酸缓冲溶液中,甲基紫6B与fsDNA、ctDNA分子作用后共振光散射增强,其强度增加值与DNA的浓度呈线性关系,线性范围分别为0～1．0、0～1．5mg／L,相关系数分别为0．9993、0．9997,检出限分别为15．3、12．2ug／L,用于DNA合成样品的测定,测定结果的精密度、准确度较高。     

荧光素共振光散射法测定脱氧核糖核酸

研究了咕吨类染料荧光素Fluorescein(FL)与DNA作用的共振光散射光谱。加入DNA后,在pH6～8的范围内,荧光素在DNA分子表面发生长距离自组装,在400nm处产生了增强的共振光散射峰,其发光强度与DNA的浓度呈线性关系,线性范围为0．04～3．1mg／L;检出限为16μg／L。考察了影响因素和最佳反应条件,建立了用RLS光谱测定ng级DNA的新方法。     

天青Ⅰ共振光散射法测定DNA

基于脱氧核糖核酸(DNA)对混合有机染料天青Ⅰ的共振光散射增强效应,拟定了一种测定DNA的共振光散射法。在pH9.5～10.5的范围内,天青Ⅰ在299、355、400、570、630nm附近均有较弱的共振光散射信号,随着DNA的加入,共振光散射信号大大增强。在355nm处,其散射光增强强度与DNA质量浓度呈线性关系。其线性回归方程为ΔI=-96.62 606.6ρ,线性范围为0 20～0.60μg mL,相关系数r=0.9998,检出限为11.2μg L。该方法可应用于合成样品中DNA的测定。     

两性离子表面活性剂作为共振光散射探针测定脱氧核糖核酸

将两性离子表面活性剂用于DNA的共振光散射测定。在pH值为7．96～9．40较宽的范围内,DNA与椰油酰胺丙基-2-羟基-3-磺基丙基甜菜碱(HSB)在392nm处有稳定的共振光散射增强,其强度与DNA浓度呈线性关系,建立了一种测定DNA的新方法。线性范围为0．02—4．25mg／L;检出限达1．5μg／L。该法简便、快速,用于合成样品中DNA的测定,重现性好,结果满意。同时探讨了有关机理。     

小檗碱共振光散射法测定脱氧核糖核酸

研究了小檗碱与DNA作用的共振光散射光谱，在pH＝2.0-2.8的范围内，DNA的加入导致小檗碱共振光散射的增强，在308nm处，存在一共振光散射增强峰，其强度与DNA的浓度呈线性关系，据此建立了一种测定DNA的共振光散射法。该方法的线性范围为0－600μg/L，相关系数为0.9972，检出限为19.9μg/L。将该方法用于混合样品中DNA的测定。结果令人满意。     

灿烂甲酚蓝共振光谱散射法测定脱氧核糖核酸

研究了灿烂甲酚蓝与脱氧核糖核酸（DNA）作用的共振光散射光谱,在pH＝10．8－11．5的范围内,DNA的加入导致灿烂甲酚蓝共振光散射的增强,在347nm处,存在一共振光散射增强峰,其强度与DNA的浓度呈线性关系,据此建立了一种测定DNA的共振光谱散射法。该方法的线范围为80－100μg/L,检出限为23．3μg/L.     

花菁-脱氧核糖核酸的共振光散射光谱及其分析应用

研究了一种苯并噻唑阳离子花菁与脱氧核糖核酸(DNA)作用的共振光散射光谱,在pH 6.0的六次甲基四胺-HCl缓冲介质中,痕量DNA的加入使花菁在590nm的共振光散射强度显著增强。在最佳实验条件下,增强的共振光散射强度与DNA浓度具有良好的线性关系,据此建立了一种测定DNA的共振光散射光谱法。方法的线性范围为:小牛胸腺DNA(CT DNA),0～20μg/mL,鱼精子DNA(FS DNA),0～15μg/mL;检出限分别为0.005μg/mL和0.008μg/mL。该方法已用于合成样品中DNA的测定。     

溴代十六烷基三甲基铵敏化吡罗红B-核酸作用的共振光散射增强法测定核酸

基于表面活性剂溴代十六烷基三甲基铵（CTMAB）对吡罗红B-核酸作用的共振光散射增强效应有敏化作用,建立了一种高灵敏测定核酸的新方法。在pH7．4时,吡罗红B在328nm处的共振光散射的增强与核酸浓度有良好的线性关系。在最佳实验条件下,对小牛胸腺DNA（ct-DNA）、鲱鱼精DNA（fs-DNA）、酵母RNA（yeast—RNA）测定的线性范围分别为0．0～1．2mg／L、0．0～0．8mg／L和0．04～1．4mg／L。检出限分别为6．1μg／L、11．2μg／L和8．6μg／L。该法简便、快捷、重现性好,对合成样品进行了测定,结果令人满意。     

溴化十六烷基吡啶的双波长共振光散射比率法测定

应用双波长共振光散射（DW—RLS）比率法研究了溴百里酚蓝（BTB）与阳离子表面活性剂溴化十六烷基吡啶（CPB）的相互作用。在pH1．5的乙酸钠-HCl缓冲溶液中,CPB本身的共振光散射很弱,BTB有一定的共振光强度,加入CPB后BTB的共振光信号显著增强,最大散射峰位于523nm,且散射光强度与CPB的浓度呈线性关系,可以通过单波长共振光散射法检测CPB,CPB质量浓度的线性范围和检出限分别为0．05—0．60mg／L和42μg／L。使用248nm和424nm两波长处散射强度比值（I248／I424）代替单波长处的共振光散射强度测定CPB,其线性范围和检出限分别为0．03～1．0mg／L和3μg／L。与共振光散射法相比较,DW—RLS比率法受酸度、离子强度等环境条件影响较小,并且有更宽的线性范围和更低的检出限,应用于合成和实际水样中CPB的测定,获得较好的结果。     

Repair processes on deoxyribonucleic acid

Many cells have the ability to recognize and eliminate damage to their DNA, particularly thymine dimers formed by UV light. The elimination of this damage may be achieved by enzymatic, light-dependent cleavage of the dimers into the monomers (photoreactivation) or more frequently by dark repair, in which the damaged part is completely removed from the, DNA. In this repair process, the DNA is incised by an endonuclease in the immediate vicinity of the thymine dimers. Oligonucleotides containing the thymine dimer are removed hydrolytically from the DNA by the 5→3′ exonuclease activity of DNA polymerase I (Kornberg enzyme). The resulting gaps are immediately closed by a de novo synthesis with the aid of the same DNA polymerase I, the complementary strand serving as a template (excision repair). The final step is the formation of the phosphodiester bond between the newly synthesized DNA fragment and the old DNA strand by a DNA ligase. Xeroderma pigmentosum patients lack the endonuclease as a result of a genetic defect; they therefore cannot eliminate thymine dimers from their DNA, and are extremely sensitive to sunlight. All information so far suggests that genetic recombination and DNA repair are performed by the same enzyme system.     

Dissecting the differences between the alpha and beta anomers of the oxidative DNA lesion FaPydG

The oxidative DNA lesion, FaPydG rapidly anomerizes to form a mixture of the alpha and beta anomer. To investigate the mutagenic potential of both forms, we prepared stabilized bioisosteric analogues of both configurational isomers and incorporated them into oligonucleotides. These were subsequently used for thermodynamic melting-point studies and for primer-extension experiments. While the beta compound, in agreement with earlier data, prefers cytidine as the pairing partner, the alpha compound is not able form a stable base pair with any natural base. In primer-extension studies with the high-fidelity polymerase Bst Pol I, the polymerase was able to read through the lesion. The beta compound showed no strong mutagenic potential. The alpha compound, in contrast, strongly destabilized DNA duplexes and also blocked all of the tested DNA polymerases, including two low-fidelity polymerases of the Y-family.     

Selective Stabilization of Abasic Site‐Containing DNA by Insertion of Sterically Demanding Biaryl Ligands

Biaryl derivatives that consist of one DNA‐intercalating unit and a sterically demanding component exhibit a specific behavior towards abasic site‐containing DNA (AP‐DNA) as determined by thermal DNA denaturation experiments, spectrometric titrations and CD spectroscopic analysis. Specifically, these ligands strongly stabilize AP‐DNA towards dissociation, whereas they do not or only marginally affect the melting temperature of regular duplex DNA.     

Synthesis and pairing properties of alpha-tricyclo-DNA

We describe the synthesis of the phosphoramidite building blocks of alpha-tricyclo-DNA (alpha-tc-DNA) covering all four natural bases, starting from the already known corresponding alpha-tc-nucleosides. These building blocks were used for the preparation of three alpha-tc-oligonucleotide 10-mers representing a homopurine, a homopyrimidine, and a mixed purine/pyrimidine base sequence. The base-pairing properties with complementary parallel and antiparallel oriented DNA and RNA were studied by UV-melting analysis and CD spectroscopy. We found that alpha-tc-DNA binds preferentially to parallel nucleic acid complements through Watson-Crick duplex formation, with a preference for RNA over DNA. In comparison with natural DNA, alpha-tc-DNA shows equal to enhanced affinity to RNA and also pairs to antiparallel DNA or RNA complements, although with much lower affinity. In the mixed-base sequence these antiparallel duplexes are of the reversed Watson-Crick type, while in the homopurine/homopyrimidine sequences Hoogsteen and/or reversed Hoogsteen pairing is observed. Antiparallel duplex formation of two alpha-tc-oligonucleotides was also observed, although the thermal stability of this duplex was surprisingly low. The base-pairing properties of alpha-tc-DNA are discussed in the context of alpha-DNA, alpha-RNA, and alpha-LNA.     

DNA Nanotechnology-based Biocomputing

With silicon-based microelectronic technology pushed to its limit,scientists hunt to exploit biomolecules to power the bio-computer as substitutes.As a typical biomolecule,DNA now has been employed as a tool to create computing systems because of its superior parallel computing ability and outstanding data storage capability.However,the key challenges in this area lie in the human intervention during the computation process and the lack of platforms for central processor.DNA nanotechnology has created hundreds of complex and hierarchical DNA nanostructures with highly controllable motions by exploiting the unparalleled self-recognition properties of DNA molecule.These DNA nanostructures can provide platforms for central processor and reduce the human intervention during the computation process,which can offer unprecedented opportunities for biocomputing.In this review,recent advances in DNA nanotechnology are briefly summarized and the newly emerging concept of biocomputing with DNA nanostructures is introduced.     

Interlocked DNA Nanojoints for Reversible Thermal Sensing

The ability to precisely measure and monitor temperature at high resolution at the nanoscale is an important task for better understanding the thermodynamic properties of functional entities at the nanoscale in complex systems, or at the level of a single cell. However, the development of high‐resolution and robust thermal nanosensors is challenging. The design, assembly, and characterization of a group of thermal‐responsive deoxyribonucleic acid (DNA) joints, consisting of two interlocked double‐stranded DNA (dsDNA) rings, is described. The DNA nanojoints reversibly switch between the static and mobile state at different temperatures without a special annealing process. The temperature response range of the DNA nanojoint can be easily tuned by changing the length or the sequence of the hybridized region in its structure, and because of its interlocked structure the temperature response range of the DNA nanojoint is largely unaffected by its own concentration; this contrasts with systems that consist of separated components.     

Nick sealing by T4 DNA ligase on a modified DNA template: tethering a functional molecule on D-threoninol

Efficient DNA nick sealing catalyzed by T4 DNA ligase was carried out on a modified DNA template in which an intercalator such as azobenzene had been introduced. The intercalator was attached to a D-threoninol linker inserted into the DNA backbone. Although the structure of the template at the point of ligation was completely different from that of native DNA, two ODNs could be connected with yields higher than 90% in most cases. A systematic study of sequence dependence demonstrated that the ligation efficiency varied greatly with the base pairs adjacent to the azobenzene moiety. Interestingly, when the introduced azobenzene was photoisomerized to the cis form on subjection to UV light (320-380 nm), the rates of ligation were greatly accelerated for all sequences investigated. These unexpected ligations might provide a new approach for the introduction of functional molecules into long DNA strands in cases in which direct PCR cannot be used because of blockage of DNA synthesis by the introduced functional molecule. The biological significance of this unexpected enzymatic action is also discussed on the basis of kinetic analysis.     

Energetics,Conformation, and Recognition of DNA Duplexes Modified by Methylated Analogues of [PtCl(dien)]+

Monodentate DNA binding of [PtCl(dien)]⁺ (dien=diethylenetriamine) complexes may considerably affect the biophysical properties of DNA and consequently downstream cellular processes as a result of a large increase in the bulkiness of the nonleaving ligand by multiple methylation (see illustration).

     

Development of a multiplex system to assess DNA persistence in taphonomic studies

In this study, we have developed a PCR multiplex that can be used to assess DNA degradation and at the same time monitor for inhibition: primers have been designed to amplify human, pig, and rabbit DNA, allowing pig and rabbit to be used as experimental models for taphonomic research, but also enabling studies on human DNA persistence in forensic evidence. Internal amplified controls have been added to monitor for inhibition, allowing the effects of degradation and inhibition to be differentiated. Sequence data for single‐copy nuclear recombination activation gene (RAG‐1) from human, pig, and rabbit were aligned to identify conserved regions and primers were designed that targeted amplicons of 70, 194, 305, and 384 bp. Robust amplification in all three species was possible using as little as 0.3 ng of template DNA. These have been combined with primers that will amplify a bacterial DNA template within the PCR. The multiplex has been evaluated in a series of experiments to gain more knowledge of DNA persistence in soft tissues, which can be important when assessing what material to collect following events such as mass disasters or conflict, when muscle or bone material can be used to aid with the identification of human remains. The experiments used pigs as a model species. When whole pig bodies were exposed to the environment in Northwest England, DNA in muscle tissue persisted for over 24 days in the summer and over 77 days in the winter, with full profiles generated from these samples. In addition to time, accumulated degree days (ADD) were also used as a measure that combines both time and temperature—24 days was in summer equivalent to 295 ADD whereas 77 days in winter was equivalent to 494 ADD.