The Experts below are selected from a list of 40911 Experts worldwide ranked by ideXlab platform
Carl O Pabo - One of the best experts on this subject based on the ideXlab platform.
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zif268 protein DNA complex refined at 1 6 a a model system for understanding zinc finger DNA interactions
Structure, 1996Co-Authors: Monicia Elroderickson, Mark A Rould, Lena Nekludova, Carl O PaboAbstract:Abstract Background Zinc fingers of the Cys 2 His 2 class recognize a wide variety of different DNA sequences and are one of the most abundant DNA-binding motifs found in eukaryotes. The previously determined 2.1 a structure of a complex containing the three zinc fingers from Zif268 has served as a basis for many modeling and design studies, and Zif268 has proved to be a very useful model system for studying how TFIIIA-like zinc fingers recognize DNA. Results We have refined the structure of the Zif268 protein–DNA complex at 1.6 a resolution. Our structure confirms all the basic features of the previous model and allows us to focus on some critical details at the protein–DNA interface. In particular, our refined structure helps explain the roles of several acidic residues located in the recognition helices and shows that the zinc fingers make a number of water-mediated contacts with bases and phosphates. Modeling studies suggest that the distinctive DNA Conformation observed in the Zif268–DNA complex is correlated with finger–finger interactions and the length of the linkers between adjacent fingers. Circular dichroism studies indicate that at least some of the features of this distinctive DNA Conformation are induced upon complex formation. Conclusions Our 1.6 a structure should provide an excellent framework for analyzing the effects of Zif268 mutations, for modeling related zinc finger–DNA complexes, and for designing and selecting Zif268 variants that will recognize other DNA sites.
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distinctive DNA Conformation with enlarged major groove is found in zn finger DNA and other protein DNA complexes
Proceedings of the National Academy of Sciences of the United States of America, 1994Co-Authors: Lena Nekludova, Carl O PaboAbstract:We have analyzed DNA Conformations in a series of protein-DNA complexes, and we find that a distinctive Conformation--with an enlarged major groove--occurs in a number of different complexes. During this analysis, we also developed a simplified model of DNA structure that illustrates the relative position of (i) the base pairs, (ii) the phosphate backbone, and (iii) the double-helical axis. This model highlights the key structural features of each duplex, facilitating the analysis and comparison of structures that are distinct from canonical A-DNA or B-DNA. Comparing DNA Conformations in this way revealed that an otherwise unrelated set of protein-DNA complexes have interesting structural similarities, including an enlarged major groove. We refer to this class of structures as Beg-DNA (where eg means enlarged groove). Since related features occur in such a diverse set of protein-DNA complexes, we suggest that this Conformation may have a significant role in protein-DNA recognition.
Lena Nekludova - One of the best experts on this subject based on the ideXlab platform.
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zif268 protein DNA complex refined at 1 6 a a model system for understanding zinc finger DNA interactions
Structure, 1996Co-Authors: Monicia Elroderickson, Mark A Rould, Lena Nekludova, Carl O PaboAbstract:Abstract Background Zinc fingers of the Cys 2 His 2 class recognize a wide variety of different DNA sequences and are one of the most abundant DNA-binding motifs found in eukaryotes. The previously determined 2.1 a structure of a complex containing the three zinc fingers from Zif268 has served as a basis for many modeling and design studies, and Zif268 has proved to be a very useful model system for studying how TFIIIA-like zinc fingers recognize DNA. Results We have refined the structure of the Zif268 protein–DNA complex at 1.6 a resolution. Our structure confirms all the basic features of the previous model and allows us to focus on some critical details at the protein–DNA interface. In particular, our refined structure helps explain the roles of several acidic residues located in the recognition helices and shows that the zinc fingers make a number of water-mediated contacts with bases and phosphates. Modeling studies suggest that the distinctive DNA Conformation observed in the Zif268–DNA complex is correlated with finger–finger interactions and the length of the linkers between adjacent fingers. Circular dichroism studies indicate that at least some of the features of this distinctive DNA Conformation are induced upon complex formation. Conclusions Our 1.6 a structure should provide an excellent framework for analyzing the effects of Zif268 mutations, for modeling related zinc finger–DNA complexes, and for designing and selecting Zif268 variants that will recognize other DNA sites.
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distinctive DNA Conformation with enlarged major groove is found in zn finger DNA and other protein DNA complexes
Proceedings of the National Academy of Sciences of the United States of America, 1994Co-Authors: Lena Nekludova, Carl O PaboAbstract:We have analyzed DNA Conformations in a series of protein-DNA complexes, and we find that a distinctive Conformation--with an enlarged major groove--occurs in a number of different complexes. During this analysis, we also developed a simplified model of DNA structure that illustrates the relative position of (i) the base pairs, (ii) the phosphate backbone, and (iii) the double-helical axis. This model highlights the key structural features of each duplex, facilitating the analysis and comparison of structures that are distinct from canonical A-DNA or B-DNA. Comparing DNA Conformations in this way revealed that an otherwise unrelated set of protein-DNA complexes have interesting structural similarities, including an enlarged major groove. We refer to this class of structures as Beg-DNA (where eg means enlarged groove). Since related features occur in such a diverse set of protein-DNA complexes, we suggest that this Conformation may have a significant role in protein-DNA recognition.
Karsten Rippe - One of the best experts on this subject based on the ideXlab platform.
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the effect of the DNA Conformation on the rate of ntrc activated transcription of escherichia coli rna polymerase σ54 holoenzyme
Journal of Molecular Biology, 2000Co-Authors: Alexandra Schulz, Jörg Langowski, Karsten RippeAbstract:Abstract The transcription activator protein NtrC (nitrogen regulatory protein C) can catalyze the transition of Escherichia coli RNA polymerase complexed with the sigma 54 factor (RNAP·σ54) from the closed complex (RNAP·σ54 bound at the promoter) to the open complex (melting of the promoter DNA). This process involves phosphorylation of NtrC (NtrC-P), assembly of an octameric NtrC-P complex at the enhancer sequence, interaction of this complex with promoter-bound RNAP·σ54via DNA looping, and hydrolysis of ATP. We have used this system to study the influence of the DNA Conformation on the transcription activation rate in single-round transcription experiments with superhelical plasmids as well as linearized templates. Most of the templates had an intrinsically curved DNA sequence between the enhancer and the promoter and differed with respect to the location of the curvature and the distance between the two DNA sites. The following results were obtained: (i) a ten- to 60-fold higher activation rate was observed with the superhelical templates as compared to the linearized Conformation; (ii) the presence of an intrinsically curved DNA sequence increased the activation rate of linear templates about five times; (iii) no systematic effect for the presence and/or location of the inserted curved sequence was observed for the superhelical templates. However, the transcription activation rate varied up to a factor of 10 between some of the constructs. (iv) Differences in the distance between enhancer and promoter had little effect for the superhelical templates studied. The results were compared with theoretical calculations for the dependence of the contact probability between enhancer and promoter expressed as the molar local concentration jM. A correlation of jM with the transcription activation rate was observed for values of 10−8 M
Bayden R Wood - One of the best experts on this subject based on the ideXlab platform.
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the application of atr ftir spectroscopy and the reversible DNA Conformation as a sensor to test the effectiveness of platinum ii anticancer drugs
2018Co-Authors: Khansa Aljorani, Anja Ruther, Miguela Martin, Rukshani Haputhanthri, Glen B Deacon, Bayden R WoodAbstract:Platinum(II) complexes have been found to be effective against cancer cells. Cisplatin curbs cell replication by interacting with the deoxyribonucleic acid (DNA), reducing cell proliferation and eventually leading to cell death. In order to investigate the ability of platinum complexes to affect cancer cells, two examples from the class of polyfluorophenylorganoamidoplatinum(II) complexes were synthesised and tested on isolated DNA. The two compounds trans-[N,N′-bis(2,3,5,6-tetrafluorophenyl)ethane-1,2-diaminato(1-)](2,3,4,5,6-pentafluorobenzoato)(pyridine)platinum(II) (PFB) and trans-[N,N′-bis(2,3,5,6-tetrafluorophenyl)ethane-1,2-diaminato(1-)](2,4,6-trimethylbenzoato)(pyridine)platinum(II) (TMB) were compared with cisplatin through their reaction with DNA. Attenuated Total Reflection Fourier Transform Infrared (ATR-FTIR) spectroscopy was applied to analyse the interaction of the Pt(II) complexes with DNA in the hydrated, dehydrated and rehydrated states. These were compared with control DNA in acetone/water (PFB, TMB) and isotonic saline (cisplatin) under the same conditions. Principle Component Analysis (PCA) was applied to compare the ATR-FTIR spectra of the untreated control DNA with spectra of PFB and TMB treated DNA samples. Disruptions in the Conformation of DNA treated with the Pt(II) complexes upon rehydration were mainly observed by monitoring the position of the IR-band around 1711 cm−1 assigned to the DNA base-stacking vibration. Furthermore, other intensity changes in the phosphodiester bands of DNA at ~1234 cm−1 and 1225 cm−1 and shifts in the dianionic phosphodiester vibration at 966 cm−1 were observed. The isolated double stranded DNA (dsDNA) or single stranded DNA (ssDNA) showed different structural changes when incubated with the studied compounds. PCA confirmed PFB had the most dramatic effect by denaturing both dsDNA and ssDNA. Both compounds, along with cisplatin, induced changes in DNA bands at 1711, 1088, 1051 and 966 cm−1 indicative of DNA Conformation changes. The ability to monitor Conformational change with infrared spectroscopy paves the way for a sensor to screen for new anticancer therapeutic agents.
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the importance of hydration and DNA Conformation in interpreting infrared spectra of cells and tissues
Chemical Society Reviews, 2016Co-Authors: Bayden R WoodAbstract:Since Watson and Crick's historical papers on the structure and function of DNA based on Rosalind Franklin's and Maurice Wilkin's X-ray diffraction patterns tremendous scientific curiosity has been aroused by the unique and dynamic structure of the molecule of life. A-DNA and B-DNA represent different Conformations of the DNA molecule, which is stabilised by hydrogen interactions between base pairs, stacking interactions between neighboring bases and long-range intra- and inter-backbone forces. This review highlights the contribution Fourier transform infrared (FTIR) spectroscopy has made to the understanding of DNA Conformation in relation to hydration and its potential role in clinical diagnostics. The review will first begin by elucidating the main forms of DNA Conformation found in nature and the general structures of the A, B and Z forms. This is followed by a detailed critique on infrared spectroscopy applied to DNA Conformation highlighting pivotal studies on isolated DNA, polynucleotides, nucleoprotein and nucleohistone complexes. A discussion on the potential of diagnosing cancer using FTIR spectroscopy based on the detection of DNA bands in cells and tissues will ensue, highlighting the recent studies investigating the Conformation of DNA in hydrated and dehydrated cells. The method of hydration as a way to facilitate DNA Conformational band assignment will be discussed and the Conformational change to the A-form upon dehydration will be used to explain the reason for the apparent lack of FTIR DNA signals observed in fixed or air-dried cells and tissues. The advantages of investigating B-DNA in the hydrated state, as opposed to A-DNA in the dehydrated state, are exemplified in a series of studies that show: (1) improved quantification of DNA in cells; (2) improved discrimination and reproducibility of FTIR spectra recorded of cells progressing through the cell cycle; (3) insights into the biological significance of A-DNA as evidenced by an interesting study on bacteria, which can survive desiccation and at the same time undergo the B–A–B transition. Finally, the importance of preserving the B-DNA Conformation for the diagnosis of cancer is put forward as way to improve the sensitivity of this powerful technique.
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monitoring the reversible b to a like transition of DNA in eukaryotic cells using fourier transform infrared spectroscopy
Nucleic Acids Research, 2011Co-Authors: Donna R Whelan, Keith R Bambery, Philip Heraud, Mark J Tobin, Max Diem, Donald Mcnaughton, Bayden R WoodAbstract:The ability to detect DNA Conformation in eukaryotic cells is of paramount importance in understanding how some cells retain functionality in response to environmental stress. It is anticipated that the B to A transition might play a role in resistance to DNA damage such as heat, desiccation and toxic damage. To this end, Conformational detail about the molecular structure of DNA has been derived primarily from in vitro experiments on extracted or synthetic DNA. Here, we report that a B- to A-like DNA Conformational change can occur in the nuclei of intact cells in response to dehydration. This transition is reversible upon rehydration in air-dried cells. By systematically monitoring the dehydration and rehydration of single and double-stranded DNA, RNA, extracted nuclei and three types of eukaryotic cells including chicken erythrocytes, mammalian lymphocytes and cancerous rodent fibroblasts using Fourier transform infrared (FTIR) spectroscopy, we unequivocally assign the important DNA Conformation marker bands within these cells. We also demonstrate that by applying FTIR spectroscopy to hydrated samples, the DNA bands become sharper and more intense. This is anticipated to provide a methodology enabling differentiation of cancerous from non-cancerous cells based on the increased DNA content inherent to dysplastic and neoplastic tissue.
Takashi Ohyama - One of the best experts on this subject based on the ideXlab platform.
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curved DNA and transcription in eukaryotes
2005Co-Authors: Takashi OhyamaAbstract:Intrinsically curved DNA structures are often found in or around transcriptional control regions of eukaryotic genes, and curved DNA may be common to all class I gene promoters. Although not all class II gene promoters contain curved DNA structures, both TATA-box-containing and TATA-box-less promoters often contain such structures. Furthermore, several studies have suggested that the TATA box itself adopts a curved DNA Conformation. Curved DNA structures are likely to function in transcription in several ways. These include acting as a Conformational signal for transcription factor binding; juxtaposition of the basal machinery with effector domains on upstream-bound factors; regulation of transcription in association with transcription-factor-induced bending of DNA; and organization of local chromatin structure to increase the accessibility of cis-DNA elements. This chapter presents a concise overview of studies of these functions.
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bent DNA in the human adenovirus type 2 e1a enhancer is an architectural element for transcription stimulation
Journal of Biological Chemistry, 1996Co-Authors: Takashi OhyamaAbstract:Abstract The upstream half of the human adenovirus type 2 enhancer adopts a curved DNA structure. Most of the enhancer elements are within the curvature, suggesting that this unusual structure is linked to enhancer function. To verify this experimentally, I constructed in vitro transcription assay systems which could distinguish any effects generated by Conformational changes in a DNA template. The curved DNA Conformation in the enhancer clearly affected the extent of the stimulation of the E1A gene transcription: assays using the wild-type DNA template showed that the moderately curved enhancer was superior to the highly curved enhancer in transcriptional stimulation. In additional experiments, the enhancer region was substituted with a curved DNA derived from the bacteriophage λ origin of replication. Assays using this mutant revealed that this curved segment could also act as an enhancer when it had the proper Conformation. Consequently, DNA Conformation may play a general role in transcriptional stimulation.