Highly chemo- and regioselective phosphitylation of unprotected 2′-deoxyribonucleosides

We have developed the chemo- and regioselective phosphitylation of unprotected 2′-deoxyribonucleosides by the use of di-tert-butyl N,N-diethylphosphoramidite, a sterically hindered phosphoramidite. Both N/O- and primary hydroxy group-selectivities were simultaneously achieved, and the selectivity for the 5′-hydroxy groups was up to 97% regardless of the base moiety of the 2′-deoxyribonucleosides. The 3′-O-isomers and the 5′-O-isomers were easily separated by silica gel column chromatography or crystallization to give the pure 2′-deoxyribonucleoside 5′-phosphites in moderate to good yields.     

四甲基吡啶卟啉与核酸相互作用的稳态和时间分辨光谱

采用稳态吸收和荧光光谱、圆二色谱和皮秒时间分辨荧光光谱手段, 研究了5,10,15,20-四[4-(N-甲基吡啶)]卟啉(TMPyP4)与腺嘌呤(A)、鸟嘌呤(G)、胸腺嘧啶(T)和胞嘧啶(C)等4种碱基, 以及相应的核苷、核苷酸和单链DNA的结合能力和光谱学性质. 研究结果发现, 嘌呤与TMPyP4的结合能力比嘧啶的强. 对于某一碱基系列, 结合能力强弱顺序依次为: 碱基~核苷<核苷酸<单链DNA. 时间分辨荧光谱研究发现, 除鸟嘌呤外, 核酸和TMPyP4复合物的荧光动力学均含有快(1~2 ns)和慢(约10 ns)两个衰减过程, 它们分别是由激基复合体和环境极性对激发态TMPyP4分子的影响所致. 单链DNA能诱导TMPyP4产生诱导圆二色信号, 而单分子(碱基、核苷、核苷酸)则无此功能.     

多色蓝在核酸分子上的Langmuir聚集吸附

用微相吸附-光谱修正（MPASC）新技术研究核酸与多色蓝(PCB)探针分子间的相互作用，分析核酸分子内双静电膜的形成与Langmuir吸附的关联性.通过pH 7.24的介质核酸-PCB反应的光谱研究，测定了结合产物的物理化学参数：结合比1PCB:2DNA-PCB、1PCB:3RNA-PCB, 平衡常数KDNA-PCB=5.42×104， KRNA-PCB=2.82×104,摩尔吸收系数ε(DNA-PCB, 625 nm)=5.65×103（mo1－1•L ）•cm－1， ε(RNA-PCB, 625 nm)=3.85×103 （mol－1•L）•cm－1.结果表明， RNA分子仅形成约60％双螺旋结构链，核酸双螺旋每一周期的负静电沟最大聚集10个PCB分子.该吸附反应用于核酸样品测定，结果良好.     

Near-infrared fluorimetric determination of nucleic acids by shifting the ion-association equilibrium between heptamethylene cyanine and Alcian blue 8GX

A new method based on near-infrared (near-IR) fluorescence recovery, employing a two-reagent system which is composed of an anionic heptamethylene cyanine (HMC) and a polycationic phthalocyanine dye, Alcian blue 8GX, is presented for the determination of nucleic acids. With a maximum excitation wavelength at 766 nm and a maximum emission wavelength at 796 nm, the fluorescence recovery is linear with the concentration of nucleic acids added. Factors including the acidity of the medium, the reaction time, the optimal ratio of the two reagents, as well as the influence of foreign substance were all investigated. Meanwhile, the mechanism of fluorescence recovery was also studied. Under the optimal conditions, the linear ranges of the calibration curves were 10-250 ng ml⁻¹ for calf thymus DNA (CT DNA) and 10-200 ng ml⁻¹ for yeast RNA. The detection limits were 6.8 ng ml⁻¹ for CT DNA and 6.3 ng ml⁻¹ for yeast RNA, respectively. The method has been applied to the analysis of practical samples and the recovery results were satisfactory.     

Interaction Between DNA and Some Salicylic Acid Derivatives and Characterization of Their DNA Targets

A nanofiber polypyrrole (PPy) film was electrochemically deposited on a Pt electrode and used for immobilization of single‐stranded DNA (ssDNA) and investigation of hybridization events. Then, the interaction of DNA with four salicylic acid (SA) derivatives was studied with electrochemical methods. The oxidation peak of guanine was decreased by increasing the concentrations of salicylic acid derivatives. The binding constants of these compounds with four different sequences of DNA including different percentages of guanine‐cytosine and adenine‐thymine bases were calculated and it was clarified that sequences with higher percentage of adenine‐thymine bases have a higher binding constant in their interaction with SA derivatives.     

Error analysis of idealized nanopore sequencing

This numerical study provides an error analysis of an idealized nanopore sequencing method in which ionic current measurements are used to sequence intact single‐stranded DNA in the pore, while an enzyme controls DNA motion. Examples of systematic channel errors when more than one nucleotide affects the current amplitude are detailed, which if present will persist regardless of coverage. Absent such errors, random errors associated with tracking through homopolymer regions are shown to necessitate reading known sequences (Escherichia coli K‐12) at least 140 times to achieve 99.99% accuracy (Q40). By exploiting the ability to reread each strand at each pore in an array, arbitrary positioning on an error rate versus throughput tradeoff curve is possible if systematic errors are absent, with throughput governed by the number of pores in the array and the enzyme turnover rate.     

单细胞核酸编码扩增成像分析

单细胞成像可在单细胞水平观测目标物位置、 确定目标物含量, 在生命科学与临床医学研究领域应用广泛. 核酸编码扩增技术利用特定分子反应将待测目标识别转化为核酸条码的扩增, 具有探针种类多、 易编程、 反应条件温和及信号放大效率高等特点, 在单细胞低丰度、 高灵敏、 多目标物成像中优势显著, 为理解细胞状态、 探索生命过程提供了新思路. 本文综合评述了核酸编码扩增在单细胞荧光成像领域的研究进展, 以目标物的编码方式为分类依据, 系统阐述了固定细胞原位成像和活细胞成像中不同目标物编码与扩增成像方式的区别, 并对活细胞成像中多重检测面临的问题以及未来发展前景进行了展望.     

固相纳米孔对核酸组装的“免标记、均相”表征和应用探索

随着核酸自组装领域的飞速发展,除了作为遗传信息的载体外,核酸成为了一种具有高操作自由度和无限可能性的功能材料.基于核酸自组装原理的DNA纳米技术凭借其强大的可编辑性已经广泛应用于生物传感、纳米材料工程、医学诊疗以及分子计算机等领域.纳米孔作为一种新兴的单分子分析技术具有高分辨、高通量、免标记等特点,近年来在基因测序、分子物理化学性质分析等领域展示出了极大的应用潜力.作为一种新型高分辨表征技术,纳米孔已经在DNA纳米技术研究中崭露头角,被用于原位追踪和分析核酸分子的自组装行为.另一方面,DNA纳米技术也为纳米孔传感所面临的技术瓶颈提供了更多样化的解决思路,如借助功能核酸(Aptamer或DNAzyme)和无酶扩增核酸分子线路实现纳米孔对待测物的特异性增敏检测.本专论旨在通过对近期纳米孔技术与核酸自组装的跨领域研究成果进行系统性回顾,总结并展望纳米孔传感领域内核酸自组装的研究进展,以期为单分子生物分析、信息检索、基因分型和临床诊断等领域提供新思路和新方法.     

Specificity of Cyanine Dye L-21 Aggregation in Solutions with Nucleic Acids

Optical spectroscopy experiments were used to study the features of cyanine dye 3,3′-dimethyl-9-(2-thienyl)-thiacarbocyanine iodide (L-21) aggregation in binary solutions DMF:Tris–HCl buffer (pH = 8) containing nucleic acids (DNA or RNA). The appearance of absorption and luminescence bands associated with J-aggregates and dimers that are formed within the minor groove of DNA has been observed. The model of L-21 J-aggregate structure is proposed. It has been found that dimers are the building blocks of L-21 J-aggregates. Disorientation in dimers caused by the minor groove curvature is reason of observation of Davydov splitting in absorption spectrum of L-21 J-aggregates. In the solution containing DNA the absorption and luminescence bands of L-21 J-aggregates exhibit the specific properties that allows the dye L-21 to be used as a fluorescent probe for DNA detection.