Genomes and Genes
Summary: Proteins conjugated with deoxyribonucleic acids (DNA) or specific DNA.
- Gillette T, Lusky M, Borowiec J. Induction of structural changes in the bovine papillomavirus type 1 origin of replication by the viral E1 and E2 proteins. Proc Natl Acad Sci U S A. 1994;91:8846-50 pubmed..Higher levels of E1 were required for binding to the adjacent ori AT-rich region. Thus, these data suggest that E2 can order the stepwise binding of E1 to ori...
- Rosenstein B, Lai L, Ducore J, Rosenstein R. DNA-protein crosslinking in normal and solar UV-sensitive ICR 2A frog cell lines exposed to solar UV-radiation. Mutat Res. 1989;217:219-26 pubmed..These results suggests that this enhancement in DPC may be indicative of a process that plays a role in cellular survival following solar UV-irradiation. ..
- Beamer L, Pabo C. Refined 1.8 A crystal structure of the lambda repressor-operator complex. J Mol Biol. 1992;227:177-96 pubmed
- Escarmis C, Gomez A, Garcia E, Ronda C, Lopez R, Salas M. Nucleotide sequence at the termini of the DNA of Streptococcus pneumoniae phage Cp-1. Virology. 1984;133:166-71 pubmed..More than 50% of the nucleotides of the sequenced regions are involved in repeats of a minimum of 8 nucleotides. Three promoter-like sequences were also found at each end of Cp-1 DNA. ..
- Young H, Ghosh P, Ye J, Lederer J, Lichtman A, Gerard J, et al. Differentiation of the T helper phenotypes by analysis of the methylation state of the IFN-gamma gene. J Immunol. 1994;153:3603-10 pubmed
- Holley W, Chatterjee A. Clusters of DNA induced by ionizing radiation: formation of short DNA fragments. I. Theoretical modeling. Radiat Res. 1996;145:188-99 pubmed..Theoretical results in combination with experimental data on fragmentation spectra may help determine the consensus or average structure of the chromatin fibers in mammalian DNA. ..
- Friedman J, Fredericks W, Jensen D, Speicher D, Huang X, Neilson E, et al. KAP-1, a novel corepressor for the highly conserved KRAB repression domain. Genes Dev. 1996;10:2067-78 pubmed..We propose that KAP-1 may be a universal corepressor for the large family of KRAB domain-containing transcription factors. ..
- Brown M, Schroth G, Gottesfeld J, Bazett Jones D. Protein and DNA requirements for the transcription factor IIIA-induced distortion of the 5 S rRNA gene promoter. J Mol Biol. 1996;262:600-14 pubmed
- Lett J, Peters E. Deoxyribonucleoprotein structure and radiation injury: cellular radiosensitivity is determined by LET infinity -dependent DNA damage in hydrated deoxyribonucleoproteins and the extent of its repair. Adv Space Res. 1992;12:51-8 pubmed..For the charged particles encountered in deep space, both the types of DNA damage caused in cellular deoxyribonucleoproteins and the efficacies of their repair are dependent on linear energy transfer (LET infinity), and repair ..
- Izaurralde E, Kas E, Laemmli U. Highly preferential nucleation of histone H1 assembly on scaffold-associated regions. J Mol Biol. 1989;210:573-85 pubmed..SARs may control the conformation of chromatin domains via a regulated H1 assembly and set up the potential transcriptional repertoire of the cell. ..
- Khenokh M, Pershina V. The effect of extreme cooling on globular and fibrillar proteins. Life Sci Space Res. 1968;6:123-9 pubmed..From a series of investigations for the present communication, we have chosen data demonstrating the action of one of such factors, low and super low temperatures, on biomacromolecules in vitro. ..
- Chandran U, Attardi B, Friedman R, Zheng Z, Roberts J, DeFranco D. Glucocorticoid repression of the mouse gonadotropin-releasing hormone gene is mediated by promoter elements that are recognized by heteromeric complexes containing glucocorticoid receptor. J Biol Chem. 1996;271:20412-20 pubmed..In contrast, Oct-1 does not appear to be a component of the GR-containing protein complex that is bound to the proximal nGRE. ..
- Nicholson W, Setlow B, Setlow P. Ultraviolet irradiation of DNA complexed with alpha/beta-type small, acid-soluble proteins from spores of Bacillus or Clostridium species makes spore photoproduct but not thymine dimers. Proc Natl Acad Sci U S A. 1991;88:8288-92 pubmed..It is suggested that as these factors diffuse out in the first minutes of spore germination, spore photoproduct yields become similar to those observed for irradiation of SASP/DNA complexes in vitro. ..
- Ebneth A, Schweers O, Thole H, Fagin U, Urbanke C, Maass G, et al. Biophysical characterization of the c-Myb DNA-binding domain. Biochemistry. 1994;33:14586-93 pubmed..Therefore, R1 might serve as an important element required for secondary structure alteration upon binding and its stabilization as well as for better discrimination between specific and related DNA sequences. ..
- Friche E, Danks M, Schmidt C, Beck W. Decreased DNA topoisomerase II in daunorubicin-resistant Ehrlich ascites tumor cells. Cancer Res. 1991;51:4213-8 pubmed..Furthermore, we note that a single cell line can express features of both P-glycoprotein-associated multidrug resistance and altered topoisomerase II-associated multidrug resistance. ..
- Keeney S, Kleckner N. Covalent protein-DNA complexes at the 5' strand termini of meiosis-specific double-strand breaks in yeast. Proc Natl Acad Sci U S A. 1995;92:11274-8 pubmed..We propose that the DSB-associated protein is the catalytic subunit of the meiotic recombination initiation nuclease and that it cleaves DNA via a covalent protein-DNA intermediate. ..
- Christova R, Bach I, Galcheva Gargova Z. Sequences of DNA fragments contacting the nuclear lamina in vivo. DNA Cell Biol. 1992;11:627-36 pubmed
- Shin C, Snapka R. Patterns of strongly protein-associated simian virus 40 DNA replication intermediates resulting from exposures to specific topoisomerase poisons. Biochemistry. 1990;29:10934-9 pubmed..The protein associated with form I DNA may represent a drug-stabilized "topological complex" between type II topoisomerase and SV40 DNA. ..
- Kurochkina L, Kolomijtseva G. Photo-induced crosslinking of histones H3 and H1 to DNA in deoxyribonucleoprotein: implication in studying histone-DNA interactions. Biochem Biophys Res Commun. 1992;187:261-7 pubmed..This type of UV-crosslinking is most probably the only type for histone H3 and, possibly, for H1. ..
- Hsieh P, Camerini Otero C, Camerini Otero R. The synapsis event in the homologous pairing of DNAs: RecA recognizes and pairs less than one helical repeat of DNA. Proc Natl Acad Sci U S A. 1992;89:6492-6 pubmed
- Pai S, Bird R. Interaction of the Rb tumor suppressor protein with the c-fos promoter in c-fos transfected cells overexpressing c-fos and Rb. Anticancer Res. 1997;17:3265-72 pubmed..These results suggested the presence of Rb and/or Rb-like peptides involved in complex formation and the presence of multiple variants of RCE-binding complexes in response to c-fos over-expression. ..
- Liu B, Kissinger C, Pabo C. Crystallization and preliminary X-ray diffraction studies of the engrailed homeodomain and of an engrailed homeodomain/DNA complex. Biochem Biophys Res Commun. 1990;171:257-9 pubmed..The cocrystals form in space group C2 with a = 131.2 A, b = 45.5 A, c = 72.9 A and beta = 119.0 degrees. These crystals diffract to 2.6 A resolution. ..
- Matl I, Haskova V, Dostal C, Kaslik J. [Antibodies against deoxyribonucleoproteins in circulating immune complexes in the blood of patients with autoimmune diseases]. Cas Lek Cesk. 1990;129:622-4 pubmed..In SLE they may be important for evaluation of the activity of the disease, in particular if estimated concurrently in serum and in CIC. ..
- Chartier F, Laine B, Sautiere P. Characterization of the chromosomal protein MC1 from the thermophilic archaebacterium Methanosarcina sp. CHTI 55 and its effect on the thermal stability of DNA. Biochim Biophys Acta. 1988;951:149-56 pubmed..Moreover, our studies indicate that one molecule of protein MC1 protects eight base pairs of DNA. ..
- Engelhorn M, Boccard F, Murtin C, Prentki P, Geiselmann J. In vivo interaction of the Escherichia coli integration host factor with its specific binding sites. Nucleic Acids Res. 1995;23:2959-65 pubmed..The occupancy of binding sites varies with the concentration of IHF in the cell and allows to estimate the concentration of free IHF protein in the cell. ..
- Murphy L, Zimmerman S. Macromolecular crowding effects on the interaction of DNA with Escherichia coli DNA-binding proteins: a model for bacterial nucleoid stabilization. Biochim Biophys Acta. 1994;1219:277-84 pubmed..Crowding-enhancement of DNA condensation by promoting the binding of proteins to the DNA provides a model for the stabilization of systems such as the bacterial nucleoid or kinetoplast DNA. ..
- Cote J, Peterson C, Workman J. Perturbation of nucleosome core structure by the SWI/SNF complex persists after its detachment, enhancing subsequent transcription factor binding. Proc Natl Acad Sci U S A. 1998;95:4947-52 pubmed..These results indicate that SWI/SNF can act transiently in the remodeling of chromatin structure, even before interactions of transcription factors. ..
- Re R, Cook J. Suppression of cellular proliferation using p53 DNA recognition site-related oligonucleotides. Am J Med Sci. 1996;311:65-72 pubmed..On the basis of these studies, p53 analogues may be used therapeutically to selectively modify proliferation of transformed cells. ..
- Jackson D, Bartlett J, Cook P. Sequences attaching loops of nuclear and mitochondrial DNA to underlying structures in human cells: the role of transcription units. Nucleic Acids Res. 1996;24:1212-9 pubmed..These results are consistent with transcription being responsible for ever-changing attachments in both nuclei and mitochondria. ..
- Wang Z, Droge P. Long-range effects in a supercoiled DNA domain generated by transcription in vitro. J Mol Biol. 1997;271:499-510 pubmed..coli is bound to multiple sites within the phage lambda attachment region. We discuss implications of our in vitro findings with respect to possible in vivo functions of the dynamic nature of transcription-induced supercoiling. ..
- Braun B, Kassavetis G, Geiduschek E. Bending of the Saccharomyces cerevisiae 5S rRNA gene in transcription factor complexes. J Biol Chem. 1992;267:22562-9 pubmed..Fully assembled transcription factor complexes bend the 5S rRNA gene in the same net direction as does TFIIIB alone. ..
- Barber A, Zhurkin V, Adhya S. CRP-binding sites: evidence for two structural classes with 6-bp and 8-bp spacers. Gene. 1993;130:1-8 pubmed..These would cause displacement of the two recognition sequences with respect to the two symmetrically located alpha-helices of the CRP dimer, if there is no change in the DNA conformation.(ABSTRACT TRUNCATED AT 250 WORDS) ..
- Nardulli A, Grobner C, Cotter D. Estrogen receptor-induced DNA bending: orientation of the bend and replacement of an estrogen response element with an intrinsic DNA bending sequence. Mol Endocrinol. 1995;9:1064-76 pubmed..However, DNA bending may be required to provide the architecture needed for modulation of target genes. ..
- Kuyl Yeheskiely E, Dreef Tromp C, Geluk A, van der Marel G, van Boom J. Synthesis of the nucleopeptides H-Phe-Tyr(pGC)-NH2 and H-Phe-Ser(pGC)-Ala-OH via a phosphotriester approach. Nucleic Acids Res. 1989;17:2897-905 pubmed
- Imaoka K, Yoshikawa Y, Kanai Y, Yamanouchi K. Characterization of antinuclear antibodies induced in rabbits by rinderpest virus infection. Arch Virol. 1988;102:111-8 pubmed..The results indicate that DNA and nucleohistone are the major target antigens for ANAs. In addition, antibodies against nucleoli and extractable nuclear antigens were induced in some rabbits...
- Peak M, Peak J, Blaumueller C, Elespuru R. Photosensitized DNA breaks and DNA-to-protein crosslinks induced in human cells by antitumor agent gilvocarcin V. Chem Biol Interact. 1988;67:267-74 pubmed..5 X 10(-9) M. These results indicate a possible potential for use of GV in human tumor photochemotherapy. ..
- Svaren J, Klebanow E, Sealy L, Chalkley R. Analysis of the competition between nucleosome formation and transcription factor binding. J Biol Chem. 1994;269:9335-44 pubmed..The relevance of these results is discussed in terms of a kinetic model for successful factor competition during the replication of the factor binding site in the cell. ..
- Paterczyk B, Lugowska A, Kwiatkowski Z. Small, heat-stable, DNA-binding proteins from Caulobacter crescentus. Microbios. 1990;61:135-43 pubmed..An abundant, heat-stable, basic and DNA-binding protein, termed HCc, which has a molecular weight of 13.4 kD may be an analogue of the HU-histone-like protein from Escherichia coli. ..
- Walter P, Owen Hughes T, Cote J, Workman J. Stimulation of transcription factor binding and histone displacement by nucleosome assembly protein 1 and nucleoplasmin requires disruption of the histone octamer. Mol Cell Biol. 1995;15:6178-87 pubmed..Thus, histone displacement in this instance occurred by transfer of complete histone octamers, a mechanism distinct from that mediated by the histone-binding proteins nucleoplasmin and NAP-1. ..
- Takeda Y, Ross P, Mudd C. Thermodynamics of Cro protein-DNA interactions. Proc Natl Acad Sci U S A. 1992;89:8180-4 pubmed..iii) The variations in the values of the thermodynamic parameters are in general accord with our knowledge of the structure of the Cro-DNA complex. ..
- Paull T, Haykinson M, Johnson R. The nonspecific DNA-binding and -bending proteins HMG1 and HMG2 promote the assembly of complex nucleoprotein structures. Genes Dev. 1993;7:1521-34 pubmed..A general role for HMG1 and HMG2 in chromatin structure is also suggested by their ability to wrap DNA duplexes into highly compact forms. ..
- Rieber M, Urbina C, Rieber M. DNA on membrane receptors: a target for monoclonal anti-DNA antibody induced by a nucleoprotein shed in systemic lupus erythematosus. Biochem Biophys Res Commun. 1989;159:1441-7 pubmed..Our data suggests that anti ds DNA antibody reactions in SLE may be triggered by circulating nucleoproteins and directed toward membrane receptors capable of interacting with extracellular DNA. ..
- Kuo C, Zou A, Jayaram M, Getzoff E, Harshey R. DNA-protein complexes during attachment-site synapsis in Mu DNA transposition. EMBO J. 1991;10:1585-91 pubmed..Three of these sites are loosely held and can be emptied of A upon challenge with heparin. A synaptic complex with only three sites occupied is stable and is fully competent in the subsequent strand-transfer step of transposition...
- Hergersberg M. Biological aspects of cytosine methylation in eukaryotic cells. Experientia. 1991;47:1171-85 pubmed..Structural and functional properties of the eukaryotic DNA cytosine methyltransferase are also reviewed. ..
- Chiang S, Welch J, Rauscher F, Beerman T. Effect of DNA-binding drugs on early growth response factor-1 and TATA box-binding protein complex formation with the herpes simplex virus latency promoter. J Biol Chem. 1996;271:23999-4004 pubmed..TFIIA.DNA complex and restored the EGR1.DNA complex. We conclude that the binding motif and sequence preference of DNA-interactive drugs are manifested in their ability to inhibit the transcription factor-DNA complexes. ..
- Pil P, Chow C, Lippard S. High-mobility-group 1 protein mediates DNA bending as determined by ring closures. Proc Natl Acad Sci U S A. 1993;90:9465-9 pubmed..These findings indicate that the role of HMG1 could involve both structure-specific recognition of prebent DNA and distortion of the DNA helix by bending and that the HMG-box domain may actually be responsible for this activity. ..
- Wong M, Hsu M. Involvement of topoisomerases in replication, transcription, and packaging of the linear adenovirus genome. J Virol. 1990;64:691-9 pubmed..Together, these data provide evidence for the requirement of topoisomerase activities in the replication, transcription, and packaging of the linear adenovirus genome. ..
- Avramova Z, Mikhailov I, Tsanev R. Metabolic behaviour of a stable DNA-protein complex. Int J Biochem. 1988;20:61-5 pubmed..3. Labelling experiments showed that the protein component was metabolically stable. ..
- Hockings S, Kahn J, Crothers D. Characterization of the ATF/CREB site and its complex with GCN4. Proc Natl Acad Sci U S A. 1998;95:1410-5 pubmed..Our results agree with recent electrophoretic and crystallographic studies and demonstrate that cyclization and simulation can characterize subtle changes in DNA structure and flexibility. ..
- Lee K, Myung K, Kook H. A clinical study of topical mucopolysaccharides & polydeoxyribonucleoprotein (Foltene) therapy in alopecia. J Korean Med Sci. 1987;2:157-65 pubmed..The side effects were as followed: itching sensation developed in 2 patients (6.7%); tingling sensation in 3 patients (10.0%); burning sensation in 1 patient (3.3%); erythema in 3 patients (10.0%). ..
- Walther A, Bjerke M, Wold M. A novel assay for examining the molecular reactions at the eukaryotic replication fork: activities of replication protein A required during elongation. Nucleic Acids Res. 1999;27:656-64 pubmed..We have used this system to show that both RPA-protein and RPA-DNA interactions are important for RPA's function in elongation. ..
- Bacsi S, Hankinson O. Functional characterization of DNA-binding domains of the subunits of the heterodimeric aryl hydrocarbon receptor complex imputing novel and canonical basic helix-loop-helix protein-DNA interactions. J Biol Chem. 1996;271:8843-50 pubmed..The apparent bipartite nature of the DNA binding region of AHR and the identity of those of its amino acids that apparently make DNA contacts impute a novel protein-DNA binding behavior for AHR. ..
- Rozek D, Pfeifer G. In vivo protein-DNA interactions at the c-jun promoter: preformed complexes mediate the UV response. Mol Cell Biol. 1993;13:5490-9 pubmed..Smeal, and M. Karin, Cell 71:1081-1091, 1992). Taken together, these data suggest that modification of the transactivating domain of DNA-bound c-Jun or a closely related factor may trigger the rapid induction of the c-jun gene. ..