scholarly journals Selective DNA bending by a variety of bZIP proteins.

1993 ◽  
Vol 13 (9) ◽  
pp. 5479-5489 ◽  
Author(s):  
T K Kerppola ◽  
T Curran
Keyword(s):  
Dna Bending ◽  
Major Groove ◽  
Bent Dna ◽  
Dna Structures ◽  
Protein Dimers ◽  
Bzip Proteins ◽  
Related Proteins ◽  
Combinatorial Interactions ◽  
Bend Angles ◽  
Bzip Family

We have investigated DNA bending by bZIP family proteins that can bind to the AP-1 site. DNA bending is widespread, although not universal, among members of this family. Different bZIP protein dimers induced distinct DNA bends. The DNA bend angles ranged from virtually 0 to greater than 40 degrees as measured by phasing analysis and were oriented toward both the major and the minor grooves at the center of the AP-1 site. The DNA bends induced by the various heterodimeric complexes suggested that each component of the complex induced an independent DNA bend as previously shown for Fos and Jun. The Fos-related proteins Fra1 and Fra2 bent DNA in the same orientation as Fos but induced smaller DNA bend angles. ATF2 also bent DNA toward the minor groove in heterodimers formed with Fos, Fra2, and Jun. CREB and ATF1, which favor binding to the CRE site, did not induce significant DNA bending. Zta, which is a divergent member of the bZIP family, bent DNA toward the major groove. A variety of DNA structures can therefore be induced at the AP-1 site through combinatorial interactions between different bZIP family proteins. This diversity of DNA structures may contribute to regulatory specificity among the plethora of proteins that can bind to the AP-1 site.

scholarly journals Selective DNA bending by a variety of bZIP proteins

1993 ◽  
Vol 13 (9) ◽  
pp. 5479-5489
Author(s):  
T K Kerppola ◽  
T Curran
Keyword(s):  
Dna Bending ◽  
Major Groove ◽  
Bent Dna ◽  
Dna Structures ◽  
Protein Dimers ◽  
Bzip Proteins ◽  
Related Proteins ◽  
Combinatorial Interactions ◽  
Bend Angles ◽  
Bzip Family

We have investigated DNA bending by bZIP family proteins that can bind to the AP-1 site. DNA bending is widespread, although not universal, among members of this family. Different bZIP protein dimers induced distinct DNA bends. The DNA bend angles ranged from virtually 0 to greater than 40 degrees as measured by phasing analysis and were oriented toward both the major and the minor grooves at the center of the AP-1 site. The DNA bends induced by the various heterodimeric complexes suggested that each component of the complex induced an independent DNA bend as previously shown for Fos and Jun. The Fos-related proteins Fra1 and Fra2 bent DNA in the same orientation as Fos but induced smaller DNA bend angles. ATF2 also bent DNA toward the minor groove in heterodimers formed with Fos, Fra2, and Jun. CREB and ATF1, which favor binding to the CRE site, did not induce significant DNA bending. Zta, which is a divergent member of the bZIP family, bent DNA toward the major groove. A variety of DNA structures can therefore be induced at the AP-1 site through combinatorial interactions between different bZIP family proteins. This diversity of DNA structures may contribute to regulatory specificity among the plethora of proteins that can bind to the AP-1 site.

Reflections on apparent DNA bending by charge variants of bZIP proteins

Biopolymers ◽  
2003 ◽  
Vol 69 (1) ◽  
pp. 110-117 ◽  
Author(s):  
Philip R. Hardwidge ◽  
Kay M. Parkhurst ◽  
Lawrence J. Parkhurst ◽  
L. James Maher
Keyword(s):  
Dna Bending ◽  
Charge Variants ◽  
Bzip Proteins

scholarly journals Interaction of bleomycin with a bent DNA fragment

1992 ◽  
Vol 284 (3) ◽  
pp. 929-934 ◽  
Author(s):  
K P Nightingale ◽  
K R Fox
Keyword(s):  
Binding Sites ◽  
Dna Bending ◽  
Cobalt Complex ◽  
Dnase I ◽  
Cleavage Sites ◽  
Kinetoplast Dna ◽  
Bent Dna ◽  
Diethyl Pyrocarbonate ◽  
Dnase I Footprinting ◽  
Dna Fragment

The interaction of bleomycin with a kinetoplast DNA fragment has been examined using various footprinting techniques. This DNA adopts a bent structure and displays an unusually low gel mobility on account of its phased runs of adenines. The bleomycin-cobalt complex increases the mobility of this DNA fragment, in contrast with other DNAs which show a decreased rate of gel migration, suggesting that the antibiotic removes DNA bending, possibly via an unwinding mechanism. Removal of the bending is confirmed by hydroxy-radical footprinting which produces a more even ladder of bands in the presence of the ligand. Cleavage by bleomycin is at the sequence G-pyrimidine, though not all such sites are affected to the same extent and some cutting is found at GA and GG. DNase I footprinting confirms the antibiotic-binding sites but reveals that some strong cleavage sites do not yield footprints. Bleomycin renders adenines on the 3′ side of its cleavage sites (GT, GC and GA) hyper-reactive to diethyl pyrocarbonate.

scholarly journals The unusual structures of the hot-regions flanking large-scale deletions in human mitochondrial DNA

1996 ◽  
Vol 318 (3) ◽  
pp. 1065-1070 ◽  
Author(s):  
Jeng-Horng HOU ◽  
Yau-Huei WEI
Keyword(s):  
Mitochondrial Dna ◽  
Free Radicals ◽  
Large Scale ◽  
Rrna Genes ◽  
Nucleotide Position ◽  
Bent Dna ◽  
Two Dimensional Gel Electrophoresis ◽  
Dna Structures ◽  
Pcr Products ◽  
Recognition Motifs

Large-scale deletions of mitochondrial DNA (mtDNA) are common events that have been found to occur in human ageing and in patients with mitochondrial myopathies. The mechanisms by which these deletions occur remain unclear, but several mechanisms have been proposed, such as slipped-mispairing, illegitimate recombination, and oxidative reactions elicited by free radicals. In addition, the DNA topological stress and local DNA structures have been suggested as the important factors in eliciting the recombinational events. Upon examination of 128 breakpoints of human mtDNA deletions that have been published in the past 8 years, we found that these large-scale deletions often occur at some ‘hot-regions’. We thus hypothesized that there exist unusual structures in these regions of human mtDNA that are important for eliciting the deletions. To test this hypothesis, we used PCR techniques to amplify the sequences of the so-called hot-regions and analysed the PCR products by two-dimensional gel electrophoresis. We found that the sequences of nucleotide position (np) 5221–5988, np 6928–7493, np 7901–8732 and np 15327–16228 exhibited retarded mobilities like bent DNA structures; np 5989–6750, np 13282–13653 and np 13282–14850 showed increased mobilities like anti-bent DNA structures. Moreover, except for the sequences of np 1175–1766 found in 12 S and 16 S rRNA genes exhibiting abnormal mobility like bent DNA structures, we did not observe significant mobility abnormalities in the np 499–5545 region where deletions rarely occurred. We thus conclude that these hot-regions assume some kinds of unusual DNA structures, which may render these regions more sensitive to the attack of free radicals or serve as recognition motifs for certain recombination machinery that is involved in the large-scale deletions of human mtDNA.

scholarly journals Phylogenetic relationships between Arabidopsis and sugarcane bZIP transcriptional regulatory factors

2001 ◽  
Vol 24 (1-4) ◽  
pp. 55-60 ◽  
Author(s):  
Michel Vincentz ◽  
Paulo S. Schlögl ◽  
Luis Gustavo G. Corrêa ◽  
Fabiana Kühne ◽  
Adilson Leite
Keyword(s):  
Phylogenetic Relationships ◽  
Reference Genome ◽  
Transcriptional Regulators ◽  
Higher Plant ◽  
Regulatory Factors ◽  
Transcriptional Regulatory ◽  
Clusters Of Orthologous Groups ◽  
Expected Benefits ◽  
Bzip Proteins ◽  
Related Proteins

We built a complete and non-redundant database of bZIP transcriptional regulatory factors from the Arabidopsis reference genome. These Arabidopsis bZIP factors were ordered into thirteen families of evolutionary related proteins and this classification was used to identify and organize sugarcane cDNAs encoding bZIP proteins. We also show how this classification should help in defining putative clusters of orthologous groups of higher plant bZIP regulators and briefly discuss the expected benefits of this procedure to efficiently characterize sugarcane bZIP transcriptional regulators.

RIP60, a mammalian origin-binding protein, enhances DNA bending near the dihydrofolate reductase origin of replication

1990 ◽  
Vol 10 (12) ◽  
pp. 6236-6243
Author(s):  
M S Caddle ◽  
L Dailey ◽  
N H Heintz
Keyword(s):  
Dna Binding ◽  
Binding Protein ◽  
Dna Bending ◽  
Chinese Hamster ◽  
Nuclear Extract ◽  
Dna Fragments ◽  
Mobility Shift ◽  
Bent Dna ◽  
Origin Region ◽  
Gel Mobility Shift

Replication of the Chinese hamster dihydrofolate (dhfr) gene initiates near a 281-bp HaeIII fragment of stably bent DNA that binds RIP60, a 60-kDa origin-specific DNA-binding protein that has been purified from HeLa cell nuclear extract (L. Dailey, M. S. Caddle, N. Heintz, and N. H. Heintz, Mol. Cell. Biol. 10:6225-6235, 1990). Circular permutation assays showed that stable DNA bending in the dhfr origin region fragment was due to the presence of five oligo (dA)3-4 tracts, designated bend elements B1 to B5, that are spaced 10 bp apart. DNA bending directed by elements B1 to B5, as assessed by anomolous migration of DNA fragments on polyacrylamide gels, was accentuated at 4 degrees C. Bend element B5, which is in inverse orientation relative to elements B1 to B4, overlaps an ATT-rich motif that comprises the RIP60 protein-binding site. Gel mobility shift assays with circularly permuted bent DNA fragments and purified RIP60 showed that RIP60 markedly enhanced DNA bending of the dhfr origin region sequences. These results suggest that, as in many plasmids, bacteriophages, and eucaryotic viruses, mammalian DNA-binding proteins may enhance DNA bending near origins of replication during initiation of DNA synthesis.

scholarly journals RIP60, a mammalian origin-binding protein, enhances DNA bending near the dihydrofolate reductase origin of replication.

1990 ◽  
Vol 10 (12) ◽  
pp. 6236-6243 ◽  
Author(s):  
M S Caddle ◽  
L Dailey ◽  
N H Heintz
Keyword(s):  
Dna Binding ◽  
Binding Protein ◽  
Dna Bending ◽  
Chinese Hamster ◽  
Nuclear Extract ◽  
Dna Fragments ◽  
Mobility Shift ◽  
Bent Dna ◽  
Origin Region ◽  
Gel Mobility Shift

Replication of the Chinese hamster dihydrofolate (dhfr) gene initiates near a 281-bp HaeIII fragment of stably bent DNA that binds RIP60, a 60-kDa origin-specific DNA-binding protein that has been purified from HeLa cell nuclear extract (L. Dailey, M. S. Caddle, N. Heintz, and N. H. Heintz, Mol. Cell. Biol. 10:6225-6235, 1990). Circular permutation assays showed that stable DNA bending in the dhfr origin region fragment was due to the presence of five oligo (dA)3-4 tracts, designated bend elements B1 to B5, that are spaced 10 bp apart. DNA bending directed by elements B1 to B5, as assessed by anomolous migration of DNA fragments on polyacrylamide gels, was accentuated at 4 degrees C. Bend element B5, which is in inverse orientation relative to elements B1 to B4, overlaps an ATT-rich motif that comprises the RIP60 protein-binding site. Gel mobility shift assays with circularly permuted bent DNA fragments and purified RIP60 showed that RIP60 markedly enhanced DNA bending of the dhfr origin region sequences. These results suggest that, as in many plasmids, bacteriophages, and eucaryotic viruses, mammalian DNA-binding proteins may enhance DNA bending near origins of replication during initiation of DNA synthesis.

scholarly journals Bent DNA functions as a replication enhancer in Saccharomyces cerevisiae.

1988 ◽  
Vol 8 (7) ◽  
pp. 2763-2769 ◽  
Author(s):  
J S Williams ◽  
T T Eckdahl ◽  
J N Anderson
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Dna Bending ◽  
Direct Test ◽  
Wild Type ◽  
Bent Dna ◽  
Unusual Structure ◽  
Wild Type Level ◽  
Common Features ◽  
Sequence Patterns ◽  
Per Se

Previous studies have demonstrated that bent DNA is a conserved property of Saccharomyces cerevisiae autonomously replicating sequences (ARSs). Here we showed that bending elements are contained within ARS subdomains identified by others as replication enhancers. To provide a direct test for the function of this unusual structure, we analyzed the ARS activity of plasmids that contained synthetic bent DNA substituted for the natural bending element in yeast ARS1. The results demonstrated that deletion of the natural bending locus impaired ARS activity which was restored to a near wild-type level with synthetic bent DNA. Since the only obvious common features of the natural and synthetic bending elements are the sequence patterns that give rise to DNA bending, the results suggest that the bent structure per se is crucial for ARS function.

scholarly journals Designed architectural proteins that tune DNA looping in bacteria

2021 ◽  
Author(s):  
David H Tse ◽  
Nicole A Becker ◽  
Robert T Young ◽  
Wilma K Olson ◽  
Justin P Peters ◽  
...  
Keyword(s):  
Protein Binding ◽  
Double Helix ◽  
Dna Bending ◽  
Lac Repressor ◽  
Dna Looping ◽  
Transcription Activator ◽  
Dna Loops ◽  
Bent Dna ◽  
Architectural Proteins ◽  
Architectural Protein

Abstract Architectural proteins alter the shape of DNA. Some distort the double helix by introducing sharp kinks. This can serve to relieve strain in tightly-bent DNA structures. Here, we design and test artificial architectural proteins based on a sequence-specific Transcription Activator-like Effector (TALE) protein, either alone or fused to a eukaryotic high mobility group B (HMGB) DNA-bending domain. We hypothesized that TALE protein binding would stiffen DNA to bending and twisting, acting as an architectural protein that antagonizes the formation of small DNA loops. In contrast, fusion to an HMGB domain was hypothesized to generate a targeted DNA-bending architectural protein that facilitates DNA looping. We provide evidence from Escherichia coli Lac repressor gene regulatory loops supporting these hypotheses in living bacteria. Both data fitting to a thermodynamic DNA looping model and sophisticated molecular modeling support the interpretation of these results. We find that TALE protein binding inhibits looping by stiffening DNA to bending and twisting, while the Nhp6A domain enhances looping by bending DNA without introducing twisting flexibility. Our work illustrates artificial approaches to sculpt DNA geometry with functional consequences. Similar approaches may be applicable to tune the stability of small DNA loops in eukaryotes.

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