The three-dimensional structure of a DNA duplex containing looped-out bases

Unpaired bases in DNA have been assigned a possible role in the mechanism of frameshift mutagenesis in sequences with repeated base pairs. They also occur in quasipalindromic DNA sequences, which have been implicated in mutagenesis where there are no repeated base pairs, through the formation of single-stranded hairpin loops. The conformation of unpaired bases in DNA has been the subject of numerous thermodynamic as well as high resolution NMR (nuclear magnetic resonance) studies (reviewed in ref. 4). The NMR studies in solution have shown that the duplex of the tridecamer DNA fragment d(CGCAGAATTCGCG) remains intact, and that the unpaired adenosines are stacked into the duplex. Having crystallized this oligonucleotide and determined its structure, we find its conformation in the crystal is close to that of a B-DNA duplex, with the two additional adenosines looped out from the double helix and causing little disruption of the rest of the structure.     

High-resolution structure of a DNA helix containing mismatched base pairs

The concept of complementary base pairing, integral to the double-helical structure of DNA, provides an effective and elegant mechanism for the faithful transmission of genetic information. Implicit in this model, however, is the potential for incorporating non-complementary base pairs (mismatches) during replication or subsequently, for example, during genetic recombination. As such errors are usually damaging to the organism, they are generally detected and repaired. Occasionally, however, the propagation of erroneous copies of the genome confers a selective advantage, leading to genetic variation and evolutionary change. An understanding of the nature of base-pair mismatches at a molecular level, and the effect of incorporation of such errors on the secondary structure of DNA is thus of fundamental importance. We now report the first single-crystal X-ray analysis of a DNA fragment, d(GGGGCTCC), which contains two non-complementary G X T base pairs, and discuss the implications of the results for the in vivo recognition of base-pair mismatches.     

Effect of lanthanum ions on tRNAphe structure: Imino proton NMR spectroscopy

The effect of lanthanum ions on the structural and conformational change of yeast tRNA Phe was studied by 1H NMR. The results suggest that the tertiary base pair (G-15)(C-48), which was located in the terminal in the augmented dihydrouridine helix (D-helix), was markedly affected by adding La 3+ and shifted 0.33 downfield. Based pair (U-8)(A-14), which is associated with a tertiary interaction, links the base of the acceptor stem to the D-stem and anchors the elbow of the L structure, shifted 0.20 upfield. Another imino proton that may be affected by La 3+ in tRNA Phe is the tertiary base pair (G-19)(C-56). The assignment of this resonance is tentative since it is located in the region of highly overlapping resonances between 12.6 and 12.2. This base pair helps to anchor the D-loop to the TΨC loop.     

Crystal structure of the human centromeric nucleosome containing CENP-A

In eukaryotes, accurate chromosome segregation during mitosis and meiosis is coordinated by kinetochores, which are unique chromosomal sites for microtubule attachment. Centromeres specify the kinetochore formation sites on individual chromosomes, and are epigenetically marked by the assembly of nucleosomes containing the centromere-specific histone H3 variant, CENP-A. Although the underlying mechanism is unclear, centromere inheritance is probably dictated by the architecture of the centromeric nucleosome. Here we report the crystal structure of the human centromeric nucleosome containing CENP-A and its cognate α-satellite DNA derivative (147 base pairs). In the human CENP-A nucleosome, the DNA is wrapped around the histone octamer, consisting of two each of histones H2A, H2B, H4 and CENP-A, in a left-handed orientation. However, unlike the canonical H3 nucleosome, only the central 121 base pairs of the DNA are visible. The thirteen base pairs from both ends of the DNA are invisible in the crystal structure, and the αN helix of CENP-A is shorter than that of H3, which is known to be important for the orientation of the DNA ends in the canonical H3 nucleosome. A structural comparison of the CENP-A and H3 nucleosomes revealed that CENP-A contains two extra amino acid residues (Arg?80 and Gly?81) in the loop 1 region, which is completely exposed to the solvent. Mutations of the CENP-A loop 1 residues reduced CENP-A retention at the centromeres in human cells. Therefore, the CENP-A loop 1 may function in stabilizing the centromeric chromatin containing CENP-A, possibly by providing a binding site for trans-acting factors. The structure provides the first atomic-resolution picture of the centromere-specific nucleosome.     

1H MAS NMR spectra of hydroxyl species on diatomite surface

High spinning speed¹H magic-angle spinning nuclear magnetic resonance (¹H MAS NMR) was used to detect surface hydroxyl groups of diatomite, which include isolated hydroxyl groups and hydrogen-bonded hydroxyl groups, and water adsorbed on diatomite surface that include pore water and hydrogen-bonded water. The corresponding proton chemical shifts of above species are ca. 2.0, 6.0–7.1, 4.9 and 3.0 respectively. Accompanied by thermal treatment temperature ascending, the pore water and hydrogen-bonded water are desorbed successively. As a result, the relative intensities of the peaks assigned to protons of isolated hydroxyl groups and hydrogen-bonded hydroxyl groups increase gradually and reach their maxima at 1000°C. After 1100°C calcination, the hydroxyl groups that classified to strongly hydrogen-bonded ones and the isolated hydroxyl groups condense basically. But some weakly hydrogen-bonded hydroxyl groups may still persist in the micropores.     

Theory agrees with experimental thermal denaturation of short DNA restriction fragments

Experimental melting transitions of several natural DNAs of known nucleotide sequences have recently been obtained. The differential melting curves of these DNAs-phi X174 DNA, fd DNA and SV40 DNA-all show distinctive sets of peaks or fine structure. Theoretical melting curves calculated from the sequences and a few a priori parameters have not accurately predicted the experimental transitions. Although calculated fine structure resembled experimental curves in some cases, the characteristic features of a DNA's differential melting curve could not generally be produced. Azbel and Gabbarro-Arpa et al. have recently obtained good agreement between calculated and experimental curves using a different theoretical approach-only ground-state configurations of DNA were considered for temperatures inside the transition region. Their results suggest that the basic model of DNA melting, common to all theoretical approaches, is accurate. We have used here an exact theoretical approach to calculated melting curves of four DNA restriction fragments of 95-301 base pairs containing the lactose promoter region (Fig. 1). Theoretical curves agree very well with the experimental transitions published by Hardies et al. and obtained in this laboratory.     

Three-dimensional heteronuclear NMR studies of RNA.

Multidimensional heteronuclear NMR has revolutionized solution structure determinations of proteins. But this technique has not been applied to nucleic acids because of difficulties in the synthesis of isotopically (13C and/or 15N) labelled molecules. Here we report the application of three-dimensional heteronuclear NMR to the study of a uniformly 13C/15N or 15N-labelled RNA duplex of defined sequence. These experiments simplify resonance assignment and the analysis of proton-proton nuclear Overhauser effects (and therefore distance information) in the molecule. Our results show that it is now possible to determine the structures of larger and more complex RNAs using multidimensional heteronuclear NMR.     

2,2’-二取代联萘化合物的NMR研究

根据~1H NMR,同核自旋去偶和二维COSY(400MHZ)的实验结果,对四种2,2′-二取代-1,1~1-联萘化合物的萘环质了作了归属指定,指出联萘酚的H_8(H’_8)共振峰应在高场,不宜接 Sadtler标准谱图指定在低场。讨论了萘环环电流各向异性和二萘环平面二面角对萘环质子的影响。当萘环二面角变化时,H_8(H’_8)受到的影响最大,随着二面角减小,H_8(H’_8)的共振明显地移向低场。     

Structure refined to 2A of a nicked DNA octanucleotide complex with DNase I

The cutting rates of bovine pancreatic deoxyribonuclease I (DNase I) vary along a given DNA sequence, indicating that the enzyme recognizes sequence-dependent structural variations of the DNA double-helix. In an attempt to define the helical parameters determining this sequence-dependence, we have co-crystallized a complex of DNase I with a self-complementary octanucleotide and refined the crystal structure at 2 A resolution. This structure confirms the basic features of an early model, namely that an exposed loop of DNase I binds in the minor groove of B-type DNA and that interactions do occur with the backbone of both strands. Nicked octamer duplexes that have lost a dinucleotide from the 3'-end of one strand are hydrogen-bonded across a two-fold axis in the crystal to form a quasi-continuous double helix of 14 base pairs. The DNA 14-mer has a B-type conformation and shows substantial distortion of both local and overall helix parameters, induced mainly by the tight interaction of Y73 and R38 in the unusually wide minor groove. Directly coupled to the widening of the groove by approximately 3A is a 21.5 degree bend of the DNA away from the bound enzyme towards the major groove, suggesting that both DNA stiffness and groove width are important in determining the sequence-dependence of the enzyme cutting rate. A second cut of the DNA which is induced by diffusion of Mn2+ into the co-crystals suggests that there are two active sites in DNase I separated by more than 15A.     

Structural basis for recognition and repair of the endogenous mutagen 8-oxoguanine in DNA

Spontaneous oxidation of guanine residues in DNA generates 8-oxoguanine (oxoG). By mispairing with adenine during replication, oxoG gives rise to a G x C --> T x A transversion, a frequent somatic mutation in human cancers. The dedicated repair pathway for oxoG centres on 8-oxoguanine DNA glycosylase (hOGG1), an enzyme that recognizes oxoG x C base pairs, catalysing expulsion of the oxoG and cleavage of the DNA backbone. Here we report the X-ray structure of the catalytic core of hOGG1 bound to oxoG x C-containing DNA at 2.1 A resolution. The structure reveals the mechanistic basis for the recognition and catalytic excision of DNA damage by hOGG1 and by other members of the enzyme superfamily to which it belongs. The structure also provides a rationale for the biochemical effects of inactivating mutations and polymorphisms in hOGG1. One known mutation, R154H, converts hOGG1 to a promutator by relaxing the specificity of the enzyme for the base opposite oxoG.     

Recognition of DNA damage by the Rad4 nucleotide excision repair protein

Mutations in the nucleotide excision repair (NER) pathway can cause the xeroderma pigmentosum skin cancer predisposition syndrome. NER lesions are limited to one DNA strand, but otherwise they are chemically and structurally diverse, being caused by a wide variety of genotoxic chemicals and ultraviolet radiation. The xeroderma pigmentosum C (XPC) protein has a central role in initiating global-genome NER by recognizing the lesion and recruiting downstream factors. Here we present the crystal structure of the yeast XPC orthologue Rad4 bound to DNA containing a cyclobutane pyrimidine dimer (CPD) lesion. The structure shows that Rad4 inserts a beta-hairpin through the DNA duplex, causing the two damaged base pairs to flip out of the double helix. The expelled nucleotides of the undamaged strand are recognized by Rad4, whereas the two CPD-linked nucleotides become disordered. These findings indicate that the lesions recognized by Rad4/XPC thermodynamically destabilize the Watson-Crick double helix in a manner that facilitates the flipping-out of two base pairs.     

N，N′-双（x-甲氧基水杨醛叉缩胺乙基）草酰胺的合成

目的设计合成2种新型的对称草酰胺、席夫碱桥连配体。方法用草酸二乙酯和乙二胺合成N,N′-二（2-氨乙基）-乙二酰胺,然后再与邻香兰素、香兰素反应合成了两种最终化合物。结果合成了化合物：N,N′-双（3-甲氧基水杨醛叉缩胺乙基）草酰胺（H4Lc）和N,N′-双（4-甲氧基水杨醛叉缩胺乙基）草酰胺（H4Ld）。结论利用元素分析、红外光谱、核磁谱图、紫外光谱、熔点测定等表征手段,最终确定了两种化合物的组成结构。     

Molecular structure of a left-handed double helical DNA fragment at atomic resolution

The DNA fragment d(CpGpCpGpCpG) crystallises as a left-handed double helical molecule with Watson-Crick base pairs and an antiparallel organisation of the sugar phosphate chains. The helix has two nucleotides in the asymmetric unit and contains twelve base pairs per turn. It differs significantly from right-handed B-DNA.     

3,4-二芳基吡咯的合成

卟啉化合物及其金属配合物是一类极具潜力、环境友好的光电转换材料而成为国际上人们研究的热点,3,4-二芳基吡咯作为构建该卟啉类化合物的中心体,其合成方法的研究很少。本文以亚氨基二乙酸为原料,经酯化和酰基化2步反应得到N-乙酰基-亚胺基二乙酸二甲酯,再将得到反应物在甲醇钠溶液中与二芳基乙二酮发生缩合反应得到3,4-二芳基吡咯-2,5-二甲酸,最后将3,4-二芳基吡咯-2,5-二甲酸在乙醇胺中回流脱羧制得3,4-二芳基吡咯,其结构经1H NMR、13C NMR和元素分析得以确证。该合成方法具有反应条件温和、反应速度快、产率较高、操作简单等优点。     

A highly basic histone H4 domain bound to the sharply bent region of nucleosomal DNA

A nucleosomal core particle is composed of two each of histones H2A, H2B, H3 and H4 located inside the particle with approximately 47 base pairs (bp) of DNA wrapped around the octamer in about 1.8 turns of a left-handed superhelix. The path of the superhelix is not smooth; the DNA is sharply bent, or kinked, at positions symmetrically disposed at a distance of about one and four double-helical turns in both directions from the nucleosomal dyad axis (designated as sites +/- 1 and +/- 4 respectively). This non-uniform bending is considered archetypal to other DNA-protein complexes, but its mechanism is not clear (reviewed in ref. 4). DNA-histone chemical cross-linking within the core particle has revealed strong binding of each of the two histone H4 molecules to DNA at a distance of 1.5 helical turns either side of the nucleosomal dyad axis (sites +/- 1.5). In each of these sites, a single flexible domain of H4 was previously shown to contact three points, at about nucleotides 55 and 65 on one strand and nucleotide 88 on the complementary strand, numbering from the 5' terminus of each 147-base strand; these three locations are closely juxtaposed across the highly compressed minor and major grooves (Fig. 1). Here we report that the amino-acid residue of histone H4 cross-linked at the 1.5 site is histidine-18, embedded in a highly basic cluster Lys-Arg-His-Arg-Lys-Val-Leu-Arg which is probably involved in the sharp bending of the DNA double helix at the +/- 1 sites.     

水溶液中的环状DNA超螺旋空间构象

质粒DNA水溶液的喇曼光谱研究表明,854和1-083-cm-1特征峰反映了DNA主链骨架三级结构的振动状态;表征脱氧核糖中C-C伸缩振动的969-cm-1峰,其相对强度值介于线性DNA在水溶液和在纤维状态下所得数值之间(0.46＜0.83＜1.10);DNA中胸腺嘧啶的堆积反应活性增加,A-T间氢键能减弱.这些参数是辨认环状DNA分子三级结构的有效依据.