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1.
Capping DNA with DNA 总被引:13,自引:0,他引:13
Twelve classes of deoxyribozymes that promote an ATP-dependent "self-capping" reaction were isolated by in vitro selection from a random-sequence pool of DNA. Each deoxyribozyme catalyzes the transfer of the AMP moiety of ATP to its 5'-terminal phosphate group, thereby forming a 5',5'-pyrophosphate linkage. An identical DNA adenylate structure is generated by the T4 DNA ligase during enzymatic DNA ligation. A 41-nucleotide class 1 deoxyribozyme requires Cu(2+) as a cofactor and adopts a structure that recognizes both the adenine and triphosphate moieties of ATP or dATP. The catalytic efficiency for this DNA, measured at 10(4) M(-1) x min(-1) using either ATP or dATP as substrate, is similar to other catalytic nucleic acids that use small substrates. Chemical probing and site-directed mutagenesis implicate the formation of guanine quartets as critical components of the active structure. The observation of ATP-dependent "self-charging" by DNA suggests that DNA could be made to perform the reactions typically associated with DNA cloning, but without the assistance of protein enzymes. 相似文献
2.
Eukaryotic DNA polymerases in DNA replication and DNA repair 总被引:16,自引:0,他引:16
Peter M. J. Burgers 《Chromosoma》1998,107(4):218-227
DNA polymerases carry out a large variety of synthetic transactions during DNA replication, DNA recombination and DNA repair.
Substrates for DNA polymerases vary from single nucleotide gaps to kilobase size gaps and from relatively simple gapped structures
to complex replication forks in which two strands need to be replicated simultaneously. Consequently, one would expect the
cell to have developed a well-defined set of DNA polymerases with each one uniquely adapted for a specific pathway. And to
some degree this turns out to be the case. However, in addition we seem to find a large degree of cross-functionality of DNA
polymerases in these different pathways. DNA polymerase α is almost exclusively required for the initiation of DNA replication
and the priming of Okazaki fragments during elongation. In most organisms no specific repair role beyond that of checkpoint
control has been assigned to this enzyme. DNA polymerase δ functions as a dimer and, therefore, may be responsible for both
leading and lagging strand DNA replication. In addition, this enzyme is required for mismatch repair and, together with DNA
polymerase ζ, for mutagenesis. The function of DNA polymerase ɛ in DNA replication may be restricted to that of Okazaki fragment
maturation. In contrast, either polymerase δ or ɛ suffices for the repair of UV-induced damage. The role of DNA polymerase
β in base-excision repair is well established for mammalian systems, but in yeast, DNA polymerase δ appears to fullfill that
function.
Received: 20 April 1998 / Accepted: 8 May 1998 相似文献
3.
DNA topoisomerases and DNA repair 总被引:5,自引:0,他引:5
C S Downes R T Johnson 《BioEssays : news and reviews in molecular, cellular and developmental biology》1988,8(6):179-184
DNA topoisomerases are enzymes that can modify, and may regulate, the topological state of DNA through concerted breaking and rejoining of the DNA strands. They have been believed to be directly involved in DNA excision repair, and perhaps to be required for the control of repair as well. The vicissitudes of this hypothesis provide a noteworthy example of the dangers of interpreting cellular phenomena without genetic information and vice versa. 相似文献
4.
D M Lilley 《Biochemical Society transactions》1986,14(2):211-213
5.
《Cell cycle (Georgetown, Tex.)》2013,12(9):1339-1340
Comment on: Witz G, et al. Proc Natl Acad Sci USA 2011; 108:3608-11. 相似文献
6.
Hans V. Westerhoff Mary H. O’Dea Anthony Maxwell Martin Gellert 《Cell biochemistry and biophysics》1988,12(1):157-181
Using purified DNA gyrase to supercoil circular plasmid pBR322 DNA, we examined how the linking number attained at the steady
state (‘static head’) varies with the concentrations of ATP and ADP, both in the absence and presence of spermidine. In the
absence of spermidine at total adenine nucleotide concentrations between 0.35 and 1.4 mM, the static-head linking number was independent of the sum concentration of ATP and ADP, but depended strongly on the ratio
of their concentrations. We established that the same linking number was attained independent of the direction from which
the steady state was approached. The decrease in linking number at static head is more extensive when spermidine is present
in the incubation, but remains a function of the [ATP]-to-[ADP] ratio.
These results are discussed in terms of various kinetic schemes for DNA gyrase. We present one kinetic scheme that accounts
for the experimental observations. According to this scheme our experimental results imply that there is significant slip
in DNA gyrase when spermidine is absent. It is possible that spermidine acts through adjustment of the degree of coupling
of DNA gyrase. 相似文献
7.
DNA杂交与DNA指纹技术 总被引:1,自引:0,他引:1
Southern印迹杂交和DNA指纹技术在分子生物学研究以及疾病的诊断、亲缘关系鉴定、犯罪分子确认等过程中发挥了重要作用。回顾了2种技术的发明、发展历程和在生命科学研究中的作用,并探讨了可能的发展方向,从中可以从一个侧面了解分子生物学的发展历程和体会科学家的智慧在科学技术发展中所起的重要作用。 相似文献
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DNA supercoiling inhibits DNA knotting 总被引:1,自引:1,他引:0
Despite the fact that in living cells DNA molecules are long and highly crowded, they are rarely knotted. DNA knotting interferes with the normal functioning of the DNA and, therefore, molecular mechanisms evolved that maintain the knotting and catenation level below that which would be achieved if the DNA segments could pass randomly through each other. Biochemical experiments with torsionally relaxed DNA demonstrated earlier that type II DNA topoisomerases that permit inter- and intramolecular passages between segments of DNA molecules use the energy of ATP hydrolysis to select passages that lead to unknotting rather than to the formation of knots. Using numerical simulations, we identify here another mechanism by which topoisomerases can keep the knotting level low. We observe that DNA supercoiling, such as found in bacterial cells, creates a situation where intramolecular passages leading to knotting are opposed by the free-energy change connected to transitions from unknotted to knotted circular DNA molecules. 相似文献
10.
The DNAs of wheat and rye plants with rye B chromosomes have been compared with wheat, rye and oats DNAs by DNA/DNA hybridisation. The presence of DNA from B chromosomes made no significant difference to the proportion of repeated sequence DNA. The repeated sequence fractions of these cereal DNAs were quantitatively divided into eight different groups on the basis of the amount of DNA/DNA hybridisation occurring between the different DNAs. Rye A and B chromosomes contained similar proportions of three of the groups. These results, together with estimates of the thermal stabilities of all the renatured DNA duplexes suggest that rye B chromosome DNA is very similar to rye A chromosome DNA in the proportion and heterogeneity of its repeated sequences. 相似文献
11.
Travers A 《Current biology : CB》2006,16(19):R838-R840
The DNA in repressive loops is often tightly bent. DNA flexibility imposes significant constraints on their topology suggesting that they may exist as perturbations in plectonemic DNA. 相似文献
13.
Human placental DNA methyltransferase: DNA substrate and DNA binding specificity 总被引:9,自引:5,他引:4
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We have partially purified a DNA methyltransferase from human placenta using a novel substrate for a highly sensitive assay of methylation of hemimethylated DNA. This substrate was prepared by extensive nick translation of bacteriophage XP12 DNA, which normally has virtually all of its cytosine residues replaced by 5-methylcytosine (m5C). Micrococcus luteus DNA was just as good a substrate if it was first similarly nick translated with m5dCTP instead of dCTP in the polymerization mixture. At different stages in purification and under various conditions (including in the presence or absence of high mobility group proteins), the methylation of m5C-deficient DNA and that of hemimethylated DNA were compared. Although hemimethylated , m5C-rich DNAs were much better substrates than were m5C-deficient DNAs and normal XP12 DNA could not be methylated, all of these DNAs were bound equally well by the enzyme. In contrast, from the same placental extract, a DNA-binding protein of unknown function was isolated which binds to m5C-rich DNA in preference to the analogous m5C-poor DNA. 相似文献
14.
DNA methylation on cytosine is an epigenetic modification and is essential for gene regulation and genome stability in vertebrates. Traditionally DNA methylation was considered as the most stable of all heritable epigenetic marks. However, it has become clear that DNA methylation is reversible by enzymatic “active” DNA demethylation, with examples in plant cells, animal development and immune cells. It emerges that “pruning” of methylated cytosines by active DNA demethylation is an important determinant for the DNA methylation signature of a cell. Work in plants and animals shows that demethylation occurs by base excision and nucleotide excision repair. Far from merely protecting genomic integrity from environmental insult, DNA repair is therefore at the heart of an epigenetic activation process. 相似文献
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DNA gyrase complex with DNA: determinants for site-specific DNA breakage. 总被引:13,自引:0,他引:13
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DNA gyrase catalyses DNA supercoiling by making a transient double-stranded DNA break within its 120-150 bp binding site on DNA. Addition of the inhibitor oxolinic acid to the reaction followed by detergent traps a covalent enzyme-DNA intermediate inducing sequence-specific DNA cleavage and revealing potential sites of gyrase action on DNA. We have used site-directed mutagenesis to examine the interaction of Escherichia coli gyrase with its major cleavage site in plasmid pBR322. Point mutations have been identified within a short region encompassing the site of DNA scission that reduce or abolish gyrase cleavage in vitro. Mapping of gyrase cleavage sites in vivo reveals that the pBR322 site has the same structure as seen in vitro and is similarly sensitive to specific point changes. The mutagenesis results demonstrate conclusively that a major determinant for gyrase cleavage resides at the break site itself and agree broadly with consensus sequence studies. The gyrase cleavage sequence alone is not a good substrate, however, and requires one or other arm of flanking DNA for efficient DNA breakage. These results are discussed in relation to the mechanism and structure of the gyrase complex. 相似文献
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Stéphane Peyrégne Kay Prüfer 《BioEssays : news and reviews in molecular, cellular and developmental biology》2020,42(9):2000081
Present-day contamination can lead to false conclusions in ancient DNA studies. A number of methods are available to estimate contamination, which use a variety of signals and are appropriate for different types of data. Here an overview of currently available methods highlighting their strengths and weaknesses is provided, and a classification based on the signals used to estimate contamination is proposed. This overview aims at enabling researchers to choose the most appropriate methods for their dataset. Based on this classification, potential avenues for the further development of methods are discussed. 相似文献