Measurement of anomalously high hydration of (dA)n.(dT)n double helices in dilute solution

Different DNA sequences have different physical properties, which seem to be important for their biological function. In particular, (dA)n.(dT)n has many unusual features, which include resistance to conformational changes in a variable chemical environment, an unusual thermodynamics of interaction with ligands, and the inability to reassociate into nucleosomes. Short A.T base-pair runs also play a critical role in DNA bending. It is believed that hydration of DNA is an important factor in determining the physical chemical and biological properties of different regions of DNA. Until now, however, it has not been possible to study the details of the hydration of DNA in dilute solution with sufficient sensitivity and precision. Moreover, it was not known if different base sequences differ in the extent of their hydration. Indirect evidence that (dA)n.(dT)n can be hydrated to a greater extent than other DNA sequences may be inferred from a recent study of the binding of drugs to polynucleotides. Here we used a novel high-precision technique measuring ultrasonic velocity to obtain direct estimates of the extent of hydration of various oligo- and polynucleotides in dilute solution. We report that different DNA sequences differ in their hydration, and that (dA)n.(dT)n in particular has an anomalously high level of hydration.     

Chiral selection in poly(C)-directed synthesis of oligo(G)

Theories of the origin of optical asymmetry in living systems place fundamental importance on the amplification of optical asymmetry by an autocatalytic process. The replication of a polynucleotide is one obvious choice for such an autocatalytic growth mechanism. If an optically homogeneous polynucleotide could replicate by directing the polymerization of monomers of the same handedness, while excluding monomers of the opposite handedness, its chiral descendants would come to dominate what was once an achiral environment. Recently, two highly efficient template-directed reaction systems have been developed for the oligomerization of activated guanosine mononucleotides (Fig. 1) on a poly(C) template. The synthesis of L-guanosine 5'-mononucleotide makes it possible to study chiral selection in these systems. We report here that poly(C)-directed oligomerization of activated guanosine mononucleotides proceeds readily if the monomers are of the same optical handedness as the template, and is indeed far less efficient if the monomers are of the opposite handedness. However, in template-directed reactions with a racemic mixture, monomers of the opposite handedness to the template are incorporated as chain terminators at the 2'(3') end of the products. This inhibition raises an important problem for many theories of the origin of life.     

Association of histone H1(0) with a gene repressed during liver development

Histone H1(0) has a number of unusual properties that set it apart from other H1 subtypes (for review see ref. 1). For example, H1(0) synthesis is not strictly coupled to DNA synthesis, it is absent from the embryonic liver of mice (but present shortly after birth) and its synthesis is hormone-dependent in some of the glands of adult rodents. All the H1 subtypes differ in their DNA binding properties, and H1(0) has been shown to be preferentially associated with nuclease-resistant chromatin. These features suggest that the H1(0) may have a role in developmental gene control. To investigate this further, we have fractionated the H1(0)-containing nucleosomes of chromatin from adult mouse liver. We report here that the gene for alpha-fetoprotein, which is expressed in embryonic tissue but repressed soon after birth, is preferentially associated with the H1(0)-containing nucleosomes. The related gene for albumin, which is expressed in both embryonic and adult tissues, is absent from the H1(0)-containing nucleosome fraction. These results support a role for histone H1(0) in the control of gene expression.     

DNA overwinds when stretched

DNA is often modelled as an isotropic rod, but its chiral structure suggests the possible importance of anisotropic mechanical properties, including coupling between twisting and stretching degrees of freedom. Simple physical intuition predicts that DNA should unwind under tension, as it is pulled towards a denatured structure. We used rotor bead tracking to directly measure twist-stretch coupling in single DNA molecules. Here we show that for small distortions, contrary to intuition, DNA overwinds under tension, reaching a maximum twist at a tension of approximately 30 pN. As tension is increased above this critical value, the DNA begins to unwind. The observed twist-stretch coupling predicts that DNA should also lengthen when overwound under constant tension, an effect that we quantitatively confirm. We present a simple model that explains these unusual mechanical properties, and also suggests a possible origin for the anomalously large torsional rigidity of DNA. Our results have implications for the action of DNA-binding proteins that must stretch and twist DNA to compensate for variability in the lengths of their binding sites. The requisite coupled DNA distortions are favoured by the intrinsic mechanical properties of the double helix reported here.     

MSAP在水稻害虫白背飞虱中的应用研究

甲基化敏感的扩增多态性分析方法 (MSAP)是在扩增片段长度多态性技术基础上建立起来的主要用来检测样品基因组DNA甲基化情况的一种方法,特别适用于全基因组范围内检测CCGG位点的胞嘧啶甲基化情况,在高等动物和许多植物上已广泛应用,但尚未有在昆虫中应用该方法的报道。从DNA提取、酶切基因组DNA用量、酶切和接头连接时间、电泳图谱显影方法等方面对MSAP方法进行了改进,并在水稻重要害虫白背飞虱上得到成功应用。这为将来在其它昆虫中使用该方法研究基因组DNA甲基化情况提供了一定借鉴和指导价值。且通过比较白背飞虱雌雄性别间和长短翅型间的MSAP图谱,发现雌雄性别间和长短翅型间的基因组DNA甲基化式样都存在明显的差异,说明DNA甲基化可能参与了性别和翅型分化的调节。     

Thiobase DNA: the chemistry and some applications in cancer studies

This article reviews the chemical methods for preparation of base-modified DNA with a particular focus on thiobases. Thiobases have certain unique properties, such as easy alkylation, ready oxidation and strong absorption in the near UV longer wavelength. These chemical and physical properties are retained in DNA containing thiobase and are useful for chemical manipulation and photo crosslinking of these modified DNA with other biomolecules of interest. The ability to make DNA containing thiobases or their functionalized analogues has added new research tools for DNA repair studies, and it is believed that such modified DNA can be of great use in many biological studies.     

Importance of DNA stiffness in protein-DNA binding specificity

From the first high-resolution structure of a repressor bound specifically to its DNA recognition sequence it has been shown that the phage 434 repressor protein binds as a dimer to the helix. Tight, local interactions are made at the ends of the binding site, causing the central four base pairs (bp) to become bent and overtwisted. The centre of the operator is not in contact with protein but repressor binding affinity can be reduced at least 50-fold in response to a sequence change there. This observation might be explained should the structure of the intervening DNA segment vary with its sequence, or if DNA at the centre of the operator resists the torsional and bending deformation necessary for complex formation in a sequence dependent fashion. We have considered the second hypothesis by demonstrating that DNA stiffness is sequence dependent. A method is formulated for calculating the stiffness of any particular DNA sequence, and we show that this predicted relationship between sequence and stiffness can explain the repressor binding data in a quantitative manner. We propose that the elastic properties of DNA may be of general importance to an understanding of protein-DNA binding specificity.     

Conservation of cytoplasmic poly (A)-containing RNA in mouse and rat.

By comparing the melting temperature of DNA-DNA duplexes between related species, it is shown that total single-copy DNA evolves at a faster rate that DNA which is transcribed into poly (A)-containing RNA. Such a comparison suggests that at least 70% of rat single-copy DNA does not code for protein.     

关于N(2,2,0)代数的稳定化子

讨论了N(2,2,0)代数的稳定化子的性质,并利用稳定化子给出了N(2,2,0)代数的一个同余分解,证明了该同余是N(2,2,0)代数同余,进而研究了商代数的代数结构,并讨论了自然同态下一类逆象的代数结构和性质.     

N-Acetoxy-acetylaminofluorene reacts preferentially with a control region of intracellular SV40 chromosome

Many chemical carcinogens or their metabolites react with DNA; thus it is of interest to determine what effect chromosomal structure has on these reactions. The chromosome of simian virus 40 (SV40) is well suited for such studies; like chromatin of eukaryotic cells, it is organized into nucleosomes. The nucleotide sequence of SV40 is known, together with much about the pattern of viral gene expression and DNA replication, and the structure of the viral chromosome. We have investigated the binding of the ultimate carcinogen, N-acetoxy-acetylaminofluorene (AAAF), to specific regions of the SV40 chromosome in situ in the intact infected cell. The results, reported here, indicate that a region containing regulatory functions on the intracellular SV40 chromosome has unique structural properties which render it more susceptible to attack by AAAF than the rest of the SV40 genome. The preferential binding of AAAF to regulatory regions of chromatin may have implications for the mechanism of action of this and similar carcinogens.     

Porous graphene: Properties, preparation, and potential applications

Graphene has recently emerged as an important and exciting material.Inspired by its outstanding properties,many researchers have extensively studied graphene-related materials both experimentally and theoretically.Porous graphene is a collection of graphene-related materials with nanopores in the plane.Porous graphene exhibits properties distinct from those of graphene,and it has widespread potential applications in various fields such as gas separation,hydrogen storage,DNA sequencing,and supercapacitors.In this review,we summarize recent progress in studies of the properties,preparation,and potential applications of porous graphene,and show that porous graphene is a promising material with great potential for future development.     

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.     

Isolation of a new human oncogene from a diffuse B-cell lymphoma

Utilizing DNA transfection analysis with the continuous NIH 3T3 cell line as assay cell, we and other have observed that as many as 10-50% of human haematopoietic tumours contain oncogenes, the vast majority of which are members of the ras proto-oncogene family. In addition, Cooper and co-workers have reported the detection and isolation of specific oncogenes, B-lym and T-lym, which appear to be activated in human and rodent tumours of certain B and T lymphoid cells, respectively. In surveying human haematopoietic malignancies, we observed that DNA of a primary human diffuse B-cell lymphoma induced an unusual transformed focus on transfection of NIH 3T3 cells. Here, we report the molecular cloning and physical characterization of this human oncogene, whose transforming activity was shown to reside within a human DNA sequence of 45 kilobases (kb) cloned in a cosmid vector. Its properties distinguish it from previously reported retroviral or nonretroviral oncogenes.     

甜菜高分子量核DNA的分离

研究了从甜菜中分离高分子量核DNA的方法．利用离心分离细胞核，经低融点琼脂糖块包埋、蛋白酶K原位裂解，结合低融点琼脂糖脉冲电泳去除淀粉制备高分子量核DNA．结果表明利用幼叶制备高分子量核DNA分子量高，更容易去除其中的淀粉；并且利用该方法得到的高分子量核DNA纯度高，适于部分酶切．     

Role of poly(ADP-ribose) formation in DNA repair.

The abundant nuclear enzyme poly(ADP-ribose) polymerase catalyses the synthesis of poly(ADP-ribose) from nicotinamide adenine dinucleotide (NAD+). This protein has an N-terminal DNA-binding domain containing two zinc-fingers, which is linked to the C-terminal NAD(+)-binding domain by a short region containing several glutamic acid residues that are sites of auto-poly(ADP-ribosyl)ation. The intracellular production of poly(ADP-ribose) is induced by agents that generate strand interruptions in DNA. The branched homopolymer chains may attain a size of 200-300 residues but are rapidly degraded after synthesis. The function of poly(ADP-ribose) synthesis is not clear, although it seems to be required for DNA repair. Here we describe a human cell-free system that enables the role of poly(ADP-ribose) synthesis in DNA repair to be characterized. The results indicate that unmodified polymerase molecules bind tightly to DNA strand breaks; auto-poly(ADP-ribosyl)ation of the protein then effects its release and allows access to lesions for DNA repair enzymes.     

Some structural properties of 2-walk (a, b)-linear graphs

A graph has exactly two main eigenvalues if and only if it is a 2-walk linear graph. In this paper, we show some structural properties that a 2-walk (a, b)-linear graph holds. According to these properties, we can estimate and characterize more 2-walk linear graphs that have exactly two main eigenvalues.     

一种吲哚二甲川菁染料的合成、光谱性质及其应用

目的合成一种含吲哚环的二甲川菁染料,研究光谱性质、与生物分子的相互作用及其作为荧光探针在活细胞成像中的应用。方法采用UV-vis,1H NMR,IR,HR-MS分析确证产物的结构;采用吸收光谱和荧光光谱法研究二甲川菁染料在不同溶剂中的光谱性质,以及该染料在生理条件下与鲑鱼精DNA(DNA)、牛血清白蛋白(BSA)、溶菌酶、淀粉酶、糜蛋白酶和牛血红蛋白的相互作用;采用荧光倒置显微镜观察染料对K562白血病细胞的活细胞染色。结果该染料最大吸收波长(λmax)随着溶剂介电常数的增加出现蓝移。染料与DNA相互作用较强,且荧光强度随着DNA浓度的增加而增强,而其他5种生物大分子对染料的荧光强度影响不大。该染料可以穿透活细胞膜,对细胞核染色,可以清晰地看出核仁的荧光较亮,2 h后观察细胞仍有荧光。结论合成了一种光谱性质优良的二甲川菁染料,该染料对核酸(DNA/RNA)有较强的亲和性,属于活细胞通透性染料,是一种潜在的活细胞成像荧光探针。     

自发光转录激活子样效应因子的功能分析

目的:对转录激活子样效应因子(TALE)蛋白进行特异性标记.方法:通过分子生物学技术,在TALE蛋白的C-端融合了一种具有优异光学性能的萤光素酶.结果:融合蛋白不仅可对目的 DNA进行特异性识别,还可产生萤光素酶的特征光谱.结论:萤光素酶的融合不影响TALE蛋白的正常功能,其光谱信息有望成为分析TALE蛋白与DNA相互作用的特异性检测信号.     

四川黑山羊品种(群体)的RAPD标记研究

从5组24个随机引物中筛选出16个重复性好的多态引物,对四川9个黑山羊品种(群体)共计572只个体,进行随机扩增多态DNA(RAPD)标记研究.结果表明,16个引物扩增出125条带,其中102条带呈现多态,多态率为81.61%.不同引物扩增出的DNA片段在各品种(群体)中的分布频率不同.9个黑山羊品种(群体)间相似系数为0.7533～0.9642,遗传距离指数为0.0358～0.2467.引物OPQ-06(序列为GAGCGCCTTG)未在乐至黑山羊中扩增出900bpDNA片段,而在其他8个黑山羊品种(群体)中出现率均为1,可作为区分乐至黑山羊和其他8个黑山羊品种(群体)的分子遗传标记.引物OPK-03(序列为CCAGCTTAGG)未在江安黑山羊扩增出550bpDNA片段,在其他8个黑山羊品种(群体)中出现率均为1,可用于区分江安黑山羊和其他8个黑山羊品种(群体)的分子遗传标记.     

动物线粒体DNA的RFLP在家养动物遗传多样性研究中的应用(综述)

对线粒体ＤＮＡ限制性片段长度多态性（ＲＦＬＰ）在家养动物遗传多样性研究中的应用现状进行了综述,并对其应用前景进行了展望。众多的研究表明,线粒体ＤＮＡ的ＲＦＬＰ可以作为一个可靠的母性遗传标记用于家养动物起源分化及其亲缘关系的研究方面。我国有丰富的能够适应各种不同生态条件的优良畜禽品种遗传资源,因此利用线粒体ＤＮＡ的ＲＦＬＰ研究其遗传多样性对于探讨其起源分化以及今后合理的利用和保存将有十分重要的理论和实践意义。