Formation of a stable triplex from a single DNA strand

Homopurine.homopyrimidine DNA sequences have been shown to form triple-stranded structures readily under appropriate conditions. Interest in DNA triplexes arises from potential applications of intermolecular triplexes as antisense inhibitors of gene expression and from the possibility that intramolecular triplexes may have a role in gene expression and recombination. We recently presented NMR evidence for triplex formation from the DNA oligonucleotides d(GA)4 and d(TC)4, which showed unambiguously that the second pyrimidine strand is Hoogsteen base paired and the cytosines are protonated at N3 as required. To obtain a more well defined triplex, and to provide a model for in vivo triplex structures, we have designed and synthesized a 28-base DNA oligomer with a sequence that could potentially fold to form a triplex containing both T.A.T and C+.G.C triplets. Our NMR results indicate that the conformation at pH 5.5 is an intramolecular triplex and that a significant amount of triplex remains even at pH 8.0.     

核酸光化学研究进展

讨论了近年来紫外光诱导的ＤＮＡ碱基主要光化学反应及其进展,其中包括嘧啶环丁烷二聚体、「６－４」光加成产物、光水合产物、ＤＮＡ－蛋白质光交联产物的形成以及在和嘌呤碱基之间的光化学反应,这些光反应及春产物是导致核酸光损的主要原因。     

A pyrimidine dimer-DNA glycosylase activity associated with the v gene product of bacterophage T4

Mutations in the v gene of bacteriophage T4 are associated with a marked increase in sensitivity to killing by UV radiation at 254 nm, but not to a variety of other forms of base damage to DNA. Early studies from this laboratory provided evidence for a role of the v gene in the excision of pyrimidine dimers (PD) from DNA. Specifically, it was shown that extracts of T4v+-infected Escherichia coli catalyse the formation of single-strand breaks (nicks) and/or alkali-labile sites in UIV-irradiated duplex DNA. Comparable hydrolysis of phosphodiester bonds is not observed with extracts of E. coli infected with the mutant T4v1 (ref. 5). The product of the v gene has been extensively purified in a number of laboratories; however, convincing evidence of purification to physical homogeneity has not yet been presented.     

An unusual DNA structure detected in a telomeric sequence under superhelical stress and at low pH

Telomeric sequences of DNA, which are found at the ends of linear chromosomes, have been attracting attention as potential sites for the formation of unusual DNA structures. They consist of (GnTm) or (GnATm) motifs (n greater than or equal to m) and, in the single-stranded state, form hairpins stabilized by non-canonical G.G pairs. In the duplex state and under superhelical stress they exhibit hypersensitivity to SI nuclease which by analogy with homopurine-homopyrimidine sequences may reflect the formation of an unusual structure. To determine whether this is the case we have inserted into a plasmid the Tetrahymena telomeric motif (G4T2).(A2C4) and probed it by two-dimensional gel electrophoresis, chemical modification and oligonucleotide binding. Our data demonstrate that, under superhelical stress and at low pH, the insert does indeed adopt a novel DNA conformation. We have concluded that in this structure the C-rich strand forms a hairpin stabilized by non-Watson-Crick base pairs C.C+ and A.A+, whereas the G-rich strand remains unstructured. We term this new DNA structure the (C,A)-hairpin.     

Expression of the E. coli uvrA gene is inducible

UvrA+-dependent excision repair is one of the most important systems in Escherichia coli for repairing UV-induced pyrimidine dimers and a variety of other forms of DNA damage. The uvrA protein acts in conjunction with the uvrB and uvrC gene products to introduce a nick at the of a DNA lesion and thus initiate the repair process. We have recently used the Mud(Ap, lac) operon fusion vector to identify a set of genes whose expression is induced by DNA damage. One Mud(Ap, lac) insertion mapped at the uvrA locus and made the cells sensitive to UV light. In this fusion strain, beta-galactosidase expression was induced by DNA-damaging agents in a recA+lexA+-dependent fashion. We were surprised by this result because uvrA+-dependent excision repair is observed both in cells in which protein synthesis has been inhibited and in recA- and lexA- cells, findings which have led to the conclusion that the uvrA gene product is constitutively expressed and not under the control of the complex recA+lexA+ regulatory circuitry (see below). We have investigated this possibility further and describe here the generation and characterization of a set of fusions of the lac genes to the promoter of the uvrA gene. We confirm that the uvrA gene product is induced by DNA damage in a recA+lexA+-dependent fashion.     

Stereo- and regio-selectivity in the photosensitized dimerization of 1, 3-dimethylthymine in solution

The effects of reaction pathway and temperature on stereo- and regio-selectivity of photocycloaddition of 1, 3-dimethylthymine (DMT) which gives four cyclobutane type dimers in solution using acetone as the photosensitizer, are investigated by measuring the product distribution. It is demonstrated that the ground-state aggregation between DMT molecules mainly leads to (h-t)dimers, and the diffusion-controlled triplet dimerization is favorable to the formation of (h-h) dimers.     

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.     

5-氰基-2-(4’-正戊基-4-联苯基)嘧啶的合成

取代的丙二酸二乙酯与相应的脒盐缩合形成嘧啶环并经环上官能团的多步转换 而合成５－氰基－２－（４’－正　基－４－联苯基）嘧啶。所合成的化合物有较好的光、热和化学 稳定性，是一种性能优良的介晶材料。     

Preferential cis-syn thymine dimer bypass by DNA polymerase eta occurs with biased fidelity

Human DNA polymerase eta (Pol eta) modulates susceptibility to skin cancer by promoting DNA synthesis past sunlight-induced cyclobutane pyrimidine dimers that escape nucleotide excision repair (NER). Here we have determined the efficiency and fidelity of dimer bypass. We show that Pol eta copies thymine dimers and the flanking bases with higher processivity than it copies undamaged DNA, and then switches to less processive synthesis. This ability of Pol eta to sense the dimer location as synthesis proceeds may facilitate polymerase switching before and after lesion bypass. Pol eta bypasses a dimer with low fidelity and with higher error rates at the 3' thymine than at the 5' thymine. A similar bias is seen with Sulfolobus solfataricus DNA polymerase 4, which forms a Watson-Crick base pair at the 3' thymine of a dimer but a Hoogsteen base pair at the 5' thymine (ref. 3). Ultraviolet-induced mutagenesis is also higher at the 3' base of dipyrimidine sequences. Thus, in normal people and particularly in individuals with NER-defective xeroderma pigmentosum who accumulate dimers, errors made by Pol eta during dimer bypass could contribute to mutagenesis and skin cancer.     

Replication of a cis-syn thymine dimer at atomic resolution

Ultraviolet light damages DNA by catalysing covalent bond formation between adjacent pyrimidines, generating cis-syn cyclobutane pyrimidine dimers (CPDs) as the most common lesion. CPDs block DNA replication by high-fidelity DNA polymerases, but they can be efficiently bypassed by the Y-family DNA polymerase pol eta. Mutations in POLH encoding pol eta are implicated in nearly 20% of xeroderma pigmentosum, a human disease characterized by extreme sensitivity to sunlight and predisposition to skin cancer. Here we have determined two crystal structures of Dpo4, an archaeal pol eta homologue, complexed with CPD-containing DNA, where the 3' and 5' thymine of the CPD separately serves as a templating base. The 3' thymine of the CPD forms a Watson-Crick base pair with the incoming dideoxyATP, but the 5' thymine forms a Hoogsteen base pair with the dideoxyATP in syn conformation. Dpo4 retains a similar tertiary structure, but each unusual DNA structure is individually fitted into the active site for catalysis. A model of the pol eta-CPD complex built from the crystal structures of Saccharomyces cerevisiae apo-pol eta and the Dpo4-CPD complex suggests unique features that allow pol eta to efficiently bypass CPDs.     

Theoretical characterization of electronic structures and properties of C-F···H-C pseudohydrogen bonds

The weak intermolecular interactions between 2-F-tetrahydrofuran and imidazole, pyrimidine, adenine, and guanine were studied theoretically using density functional B3LYP/6-311++G** and HF/6-311++G** methods. The results showed that both conven- tional N···H hydrogen bond and C-F···H-C pseudohydrogen bond (PHB) structures coexist in the four complexes. The weak intermolecular interaction energies indicate that the relative stabilities of the four complexes are in the order guanine···F > imidazole···F > adenine···F > pyrimidine···F. The characteristics of the four PHBs were determined using geometry optimizations, stretching vibrational frequencies, and natural bond orbital and electron density topological properties calculations. The most important result is that the F group of 2-F-tetrahydrofuran can activate the C-H to accept electrons from another molecule, and C-F···H-C PHB formation is relatively favorable.     

Telomeric DNA dimerizes by formation of guanine tetrads between hairpin loops

The telomeric ends of eukaryotic chromosomes are composed of simple repeating sequences in which one DNA strand contains short tracts of guanine residues alternating with short tracts of A/T-rich sequences. The guanine-rich strand is always oriented in a 5'-3' direction towards the end of the chromosome and is extended to produce a 3' overhang of about two repeating units in species where the telomeric terminus is known. This overhang has been implicated in the formation of several unusual intra-and intermolecular DNA structures, although none of these structures has been characterized fully. We now report that oligonucleotides encoding Tetrahymena telomeres dimerize to form stable complexes in solution. This salt-dependent dimerization is mediated entirely by the 3'-terminal telomeric overhang (TT-GGGGTTGGGG) and produces complexes in which the N7 position of every guanine in the overhangs is chemically inaccessible. We therefore propose that telomeric DNA dimerizes by hydrogen bonding between two intramolecular hairpin loops, to form antiparallel quadruplexes containing cyclic guanine base tetrads. These novel hairpin dimers may be important in telomere association and recombination and could also provide a general mechanism for pairing two double helices in other recombinational processes.     

构造G-morphic环

若环R中的每个元a都满足R/Ran≌l(an),其中l(an)是an在R中左零化子,则环R叫做左G-morphic环.C是环D的子环,且R[D,C]={(d1,…,dt,c,c,…)|di∈D,c∈C,t≥1};本文主要给出了R[D,C]是左G-morphic环的一个充要条件;还给出了左[D,C]G-morphic元的定义和它的一些性质.     

Synthesis of new carbon nanomolecule： C141

A new [70]fullerene dimer consisting of 141 carbon atoms was first synthesized by a new method with neutron irradiation of [70]fullerene. The results of separation and isolation with two-step HPLC (high performance liquid chromatography) show that this odd-numbered fullerene dimer is stable in air. Laser induced dissociation of C141 mainly yields fragmental species C70 and C71. The UV-vis spectrum of C141 shows that its vis feature is diminished as compared to that of C70. Experiments indicate that this new method for synthesis of fullerene dimers with neutron irradiation has a high selectivity for formation of C2n-X-C2n type carbon nanomolecules.