肽核酸研究的现状与未来

肽核酸（PNA）是DNA的类似物，具有由氨乙基甘氨酸单位组成的假肽内架，能以高亲和性和高生物稳定性与DNA和RNA特异性杂交，PNA以链侵占方式与DNA结合，抑制转录或提供人工强启动子促进转录。与mRNA结合，阻止蛋白质的合成，此外，PNA还能导向核糖核蛋白的RNA部分，抑制其酶活性，肽核酸的其它特点如抗核酸酶和蛋白质酶作用，方便而灵活的固相合成法（SPS）等，使其有望成为一个基因靶向药物，该文综述了近年有关肽核酸研究的生物化学特性及其应用前景。     

肽核酸在分子生物学技术和疾病治疗方面的应用（综述）

肽核酸是一种以多肽为骨架，类似核苷酸的物质，肽核酸与DNA或PNA有高度的亲和力和特异性，能够抑制基因的转录和翻译过程，在分子生物和肿瘤，艾滋病，病毒感染和其它难治性疾病的治疗方面有着广泛的应用前景。     

小鼠线粒体DNA中一个新的R-loop结构的发现

哺乳动物线粒体DNA的D-loop区是其复制和转录的起始区域,其中D-loop重链RNA(DH-RNA)与复制和转录功能密切相关.但轻链RNA(DL-RNA)被认为没有重要的功能,因此几乎没有有关D-loop区的轻链RNA的研究.文中研究发现一个DL-RNA存在于小鼠线粒体D-loop区.研究表明这个DL-RNA跨越了几乎整个D-loop区,并且能够耐受RNase A和RNase T1酶的切割,但对RNase H酶敏感.在这种RNA存在的情况下,D-loop的DNA不能被HaeⅢ酶切割.这些结果意味着新发现的DL-RNA能同D-loop区的DNA形成三链结构,并且能使其对应区域的DNA不被限制性内切酶消化.在以细胞色素b基因为对照的实验中没有发现类似的结构,证明这一结构不是RNA转录过程中形成的临时结构.考虑到D-loop区是线粒体DNA复制和转录的重要调控区,这个新奇的三链RNA-DNA复合物可能在线粒体DNA复制和转录中扮演了重要角色.     

TIAR通过在DNA和RNA之间的穿梭机制调控DNA的转录活性

应用体外转录模型,即通过构建T7 及T7 TIAR 的碱基序列及部分退火的双链模型,合成了一段ODN,其包含单链的TIAR结合位点和1个T7的起始位点.通过进行RNA转录分析,TIAR的结合和替代实验,证明了TIAR可与富含T的单链DNA结合,并且TIAR与DNA的结合可因DNA的转录活性而解离.这一发现为TIAR可在DNA与RNA之间穿梭提供了证据.     

原核CRISPR-Cas系统的结构功能及应用

CRISPR-Cas系统是新近在原核生物中发现的一种抵御外来DNA入侵的免疫机制,由一个成簇规则间隔的短回文重复序列(CRISPR)和附属的蛋白质(Cas)组成,广泛分布于真细菌和古菌中.CRISPR由重复序列及其间隔序列组成,间隔序列来自于过去的入侵DNA,并插入到细菌的CRISPR排列中.一旦出现新的入侵,CRISPR转录,其RNA经过加工后与Cas蛋白质组成一个核蛋白复合体,该复合体通过RNA与入侵DNA序列之间的互补配对,结合目标序列,最后Cas蛋白质将入侵DNA降解.此外,基于CRISPR系统中的Cas9蛋白,发展了一种新的基因组编辑技术,在不同的细胞中均能获得高效的基因定点打靶,展现出巨大的潜力.     

DNA聚合与RNA转录联用分子机器的改进

建立了一个集成DNA聚合和RNA转录过程,能够重复产生RNA适体片段,并结合孔雀石绿产生荧光信号的分子机器,并探索了此分子机器在检测DNA方面的应用.转录产生的大量孔雀石绿适体序列被释放到溶液中,并可以与孔雀石绿结合产生荧光,实现信号的放大.85μL体系中的聚合转录的最适条件为：DNA聚合酶10 IU（0.118 IU·μL-1）,RNA聚合酶60 IU（0.706 IU·μL-1）,反应时间为3h.在上述条件下,荧光信号随着引发DNA用量的增加而增大.     

A label-free colorimetric assay for detection of c-Myc mRNA based on peptide nucleic acid and silver nanoparticles利用肽核酸和纳米银免标记比色检测原癌基因c-Myc mRNA

A label-free colorimetric protocol based on peptide nucleic acid/silver nanoparticles(PNA/Ag NPs) has been initially proposed for specific recognition of m RNA.Making use of the controlled silver nanoparticles aggregation/dispersion by PNA/PNA–RNA complex, proto-oncogene c-Myc m RNA detection can be achieved. Moreover, the PNA/Ag NPs platform can undergo color change in response to target c-Myc m RNA with single-base-mismatch sensitivity, which could further help in visually identify single nucleotide differences in target genes.     

派罗宁GS双峰双波长光度法测定核酸

 采用光度法研究了派罗宁GS与核酸的结合反应,结果表明在pH 6.0左右的介质中,派罗宁GS与核酸在室温下能迅速结合形成紫红色复合物,该复合物在570 nm处有正吸收峰,在540 nm处有负吸收峰.据此,建立了1个测定核酸的双峰双波长光度分析新方法.用该方法测定小牛胸腺DNA(ctDNA)、鱼精子DNA(fsDNA)、酵母RNA(yt RNA)及热变性ctDNA(Dct DNA)的检出限均低于0.011μg/mL.方法简单、快速,试剂及反应体系稳定、选择性好、准确度高,用于4个合成试样的分析,回收率为96.1%~103.0%.     

合成U3snRNA基因上游启动区构建ACC合成酶反义RNA-核酶嵌合基因的植物表达载体

利用反义 RNA和核酶进行基因表达调控是当今植物分子生物学的研究热点之一 .但在转基因植物中 ,利用 RNA聚合酶 型启动区表达效率不高 .番茄 U3sn RNA基因由 RNA聚合酶 来转录 ,具有较高的转录效率 ,为一般转录效率的 1 0 0～ 1 0 0 0倍 .我们人工合成了番茄 U3sn RNA基因上游启动区 ( 1 5 2 bp) ,构建到番茄 ACC合成酶的反义 RNA-核酶嵌合 DNA序列的上游 ,然后将“启动区 -反义 RNA-核酶嵌合 DNA序列”插入到植物双元表达载体p GA6 4 3中 ,并用三亲融合法导入农杆菌 LBA4 40 4中 ,为研究 U 3sn RNA上游启动区增强反义 RNA-核酶基因的表达奠定了基础     

RNA干涉及其在肿瘤研究中的应用

RNAi是双链RNA介导的转录后基因沉默的过程，是一种高效的高特异性抑制基因表达的新途径。通过双链小干涉RNA(siRNA)与一系列蛋白质结合形成siRNA诱导的沉默复合体(RISC)并活化，然后，RISC对靶基因进行识别、降解。与反义方法相比，siRNA具有更好的抑制效果。RNAi的应用将为癌症的基因治疗提供新的方法。     

PNA（T）.DNA（AT） triplexes with Hoogsteen base pairing are more favorable

Peptide nucleic acids (PNAs) are nucleic acid analogs with the deoxyribose phosphate backbone replaced by pseudo-peplide polymers to which the nucleobases are linked. The achiral, uncharged and rather flexible properties of the peplide backbone permit peptide nucleic acids more potential than oligonucleolides in application to antisence and antigenic reagents. The process of PNA binding to DNA duplex and forming triplex is the first step of PNA interacting with PNA. But there are no PNA.2DNA triplex crystal data up to date and little has been reported on the structure features and the force of the PNA.2DNA triplex. In this work, PNA(T).DNA(AT) triplexes are successfully built and the structures and forces to stabilize the triplex after optimizations and molecule dynamics are systematically examined, which are expected to aid in the application of PNAs as anticerise and antigene agents.     

抗－DNA免疫复合物性质的研究

用聚乙二醇（ＰＥＧ）和硫酸铵从系统性红斑狼疮（ＳＬＥ）患者血清中分离出免疫复合物（ＩＣ）和血浆核酸（ＰＮＡ）。分析结果表明，ＰＮＡ的主要成分是ＲＮＡ，仅有少量ＤＮＡ存在，并且ＰＮＡ中ＤＮＡ的ｄＧ＋ｄＣ含量（５５％）明显高于正常值（４２％）。一旦经过ＲＮａｓｅ处理，ＰＮＡ抑制抗－ＤＮＡ抗体结合ＤＮＡ的能力降低，说明抗－ＤＮＡ抗体和ＲＮＡ有交叉反应。动力学研究观察到，抗－ＤＮＡ免疫复合物中抗原抗体的分子比是１：１，结合能为３７ｋＪ／ｍｏｌ。这提示，除ＤＮＡ／抗－ＤＮＡ外，其他抗－ＤＮＡ免疫复合物也可能同ＳＬＥ患者的组织损伤有关。     

Synthesis and photo-activity of peptide nucleic acids containing an azobenzene unit

We prepared the azobenzene PNA unit and synthesized various PNAs containing an azobenzene unit by a typical tBoc method. Both the azobenzene PNA unit and PNA containing an azobenzene unit （N-PNA） showed reversible photoisomerization with UV and visible light irradiation. The hybridization of N-PNA with complementary DNA resulted in a considerable decrease of the photoisomerization rate constant of the azobenzene.     

The hybridization between peptide nucleic acid containing azobenzene and DNA labeled nanoparticle on chip surfaces studied by atomic force microscopy

Peptide nucleic acid containing azobenzene （N-PNA） was covalently bound on chip surfaces. Complementary DNA probes labeled by gold nanoparticles hybridizated with PNA on chip surfaces, The hybridization was successfully detected with AFM by the microscopy mothed. The influences of the position and the cis-trans isomerization of azobenzene unit on hybridization were investigated with AFM.     

Ethylation interference and X-ray crystallography identify similar interactions between 434 repressor and operator

In the crystal structure of a repressor-operator complex (the 434 repressor DNA-binding domain and its 14-base pair (bp) operator), Anderson et al. elsewhere in this issue identify six positions of likely contact between repressor protein and phosphates of the DNA backbone. At each of these positions, electron densities of protein and DNA merge. Experiments presented here indicate that intact 434 repressor approaches these phosphates very closely when it is bound to DNA in solution. Specifically, when any one of these phosphates is ethylated, repressor cannot bind to the modified operator. We also identify another position where ethylation has a significant but less dramatic effect on repressor binding, and note that in the structure, repressor closely approaches this phosphate. Our results strongly support the idea that the interactions between protein and the DNA phosphate backbone in the crystallized complex are the same as those made by intact repressor to operator DNA in solution. In addition, our results suggest that DNA is slightly bent by repressor binding.     

Structural basis for gate-DNA recognition and bending by type IIA topoisomerases

Type II topoisomerases disentangle DNA to facilitate chromosome segregation, and represent a major class of therapeutic targets. Although these enzymes have been studied extensively, a molecular understanding of DNA binding has been lacking. Here we present the structure of a complex between the DNA-binding and cleavage core of Saccharomyces cerevisiae Topo II (also known as Top2) and a gate-DNA segment. The structure reveals that the enzyme enforces a 150 degrees DNA bend through a mechanism similar to that of remodelling proteins such as integration host factor. Large protein conformational changes accompany DNA deformation, creating a bipartite catalytic site that positions the DNA backbone near a reactive tyrosine and a coordinated magnesium ion. This configuration closely resembles the catalytic site of type IA topoisomerases, reinforcing an evolutionary link between these structurally and functionally distinct enzymes. Binding of DNA facilitates opening of an enzyme dimerization interface, providing visual evidence for a key step in DNA transport.     

Mechanism of DNA translocation in a replicative hexameric helicase

The E1 protein of papillomavirus is a hexameric ring helicase belonging to the AAA + family. The mechanism that couples the ATP cycle to DNA translocation has been unclear. Here we present the crystal structure of the E1 hexamer with single-stranded DNA discretely bound within the hexamer channel and nucleotides at the subunit interfaces. This structure demonstrates that only one strand of DNA passes through the hexamer channel and that the DNA-binding hairpins of each subunit form a spiral 'staircase' that sequentially tracks the oligonucleotide backbone. Consecutively grouped ATP, ADP and apo configurations correlate with the height of the hairpin, suggesting a straightforward DNA translocation mechanism. Each subunit sequentially progresses through ATP, ADP and apo states while the associated DNA-binding hairpin travels from the top staircase position to the bottom, escorting one nucleotide of single-stranded DNA through the channel. These events permute sequentially around the ring from one subunit to the next.     

3-A resolution structure of a protein with histone-like properties in prokaryotes

The 3-A structure of DNA-binding protein II, which exhibits histone-like properties in bacteria, has been determined. The molecule is dimeric and appears to bind to the phosphate backbone of DNA through two symmetry-related arms. A mechanism by which the protein induces DNA supercoiling is proposed.     

Atomic-scale imaging of DNA using scanning tunnelling microscopy

The scanning tunnelling microscope (STM) has been used to visualize DNA under water, under oil and in air. Images of single-stranded DNA have shown that submolecular resolution is possible. Here we describe atomic-resolution imaging of duplex DNA. Topographic STM images of uncoated duplex DNA on a graphite substrate obtained in ultra-high vacuum are presented that show double-helical structure, base pairs, and atomic-scale substructure. Experimental STM profiles show excellent correlation with atomic contours of the van der Waals surface of A-form DNA derived from X-ray crystallography. A comparison of variations in the barrier to quantum mechanical tunnelling (barrier-height) with atomic-scale topography shows correlation over the phosphate-sugar backbone but anticorrelation over the base pairs. This relationship may be due to the different chemical characteristics of parts of the molecule. Further investigation of this phenomenon should lead to a better understanding of the physics of imaging adsorbates with the STM and may prove useful in sequencing DNA. The improved resolution compared with previously published STM images of DNA may be attributable to ultra-high vacuum, high data-pixel density, slow scan rate, a fortuitously clean and sharp tip and/or a relatively dilute and extremely clean sample solution. This work demonstrates the potential of the STM for characterization of large biomolecular structures, but additional development will be required to make such high resolution imaging of DNA and other large molecules routine.     

PNA-磁性纳米人工切断试剂定位水解切断DNA

制备了以二氧化硅包裹的磁性纳米粒子（MNPs）为载体，PNA（肽核酸）为识别系统，Ce（Ⅳ）／EDTA配合物为切割系统的PNA-磁性纳米切割试剂．采用TEM对制备的MNPs进行了表征，通过IP—RP—HPLC对切断产物进行了分析．结果表明，该PNA-磁性纳米人工切断试剂可以成功地结合目标DNA，并对其进行定位切断．此外，磁性纳米粒子的引入，使得切断产物的分析更加简单、快捷．