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Lu S. Zn2+ blocks annealing of complementary single-stranded DNA in a sequence-selective manner. Sci Rep 2014; 4:5464. [PMID: 24965053 PMCID: PMC4071324 DOI: 10.1038/srep05464] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 06/11/2014] [Indexed: 12/19/2022] Open
Abstract
Zinc is the second most abundant trace element essential for all living organisms. In human body, 30–40% of the total zinc ion (Zn2+) is localized in the nucleus. Intranuclear free Zn2+ sparks caused by reactive oxygen species have been observed in eukaryotic cells, but question if these free Zn2+ outrages could have affected annealing of complementary single-stranded (ss) DNA, a crucial step in DNA synthesis, repair and recombination, has never been raised. Here the author reports that Zn2+ blocks annealing of complementary ssDNA in a sequence-selective manner under near-physiological conditions as demonstrated in vitro using a low-temperature EDTA-free agarose gel electrophoresis (LTEAGE) procedure. Specifically, it is shown that Zn2+ does not block annealing of repetitive DNA sequences lacking CG/GC sites that are the major components of junk DNA. It is also demonstrated that Zn2+ blocks end-joining of double-stranded (ds) DNA fragments with 3′ overhangs mimicking double-strand breaks, and prevents renaturation of long stretches (>1 kb) of denatured dsDNA, in which Zn2+-tolerant intronic DNA provides annealing protection on otherwise Zn2+-sensitive coding DNA. These findings raise a challenging hypothesis that Zn2+-ssDNA interaction might be among natural forces driving eukaryotic genomes to maintain the Zn2+-tolerant repetitive DNA for adapting to the Zn2+-rich nucleus.
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Affiliation(s)
- Shunwen Lu
- USDA-ARS, Cereal Crops Research Unit, Fargo, ND 58102, USA
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2
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Bergquist H, Nikravesh A, Fernández RD, Larsson V, Nguyen CH, Good L, Zain R. Structure-specific recognition of Friedreich's ataxia (GAA)n repeats by benzoquinoquinoxaline derivatives. Chembiochem 2010; 10:2629-37. [PMID: 19746387 DOI: 10.1002/cbic.200900263] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Expansion of GAA triplet repeats in intron 1 of the FXN gene reduces frataxin expression and causes Friedreich's ataxia. (GAA)n repeats form non-B-DNA structures, including triple helix H-DNA and higher-order structures (sticky DNA). In the proposed mechanisms of frataxin gene silencing, central unanswered questions involve the characterization of non-B-DNA structure(s) that are strongly suggested to play a role in frataxin expression. Here we examined (GAA)n binding by triplex-stabilizing benzoquinoquinoxaline (BQQ) and the corresponding triplex-DNA-cleaving BQQ-1,10-phenanthroline (BQQ-OP) compounds. We also examined the ability of these compounds to act as structural probes for H-DNA formation within higher-order structures at pathological frataxin sequences in plasmids. DNA-complex-formation analyses with a gel-mobility-shift assay and sequence-specific probing of H-DNA-forming (GAA)n sequences by single-strand oligonucleotides and triplex-directed cleavage demonstrated that a parallel pyrimidine (rather than purine) triplex is the more stable motif formed at (GAA)n repeats under physiologically relevant conditions.
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Affiliation(s)
- Helen Bergquist
- Department of Molecular Biology and Functional Genomics, Stockholm University, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
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3
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de Castro CSP, Souzade JR, Júnior CB. The binding of zinc (II) to a double-stranded oligodeoxyribonucleotide. A voltammetric study. Biophys Chem 2005; 112:59-67. [PMID: 15501576 DOI: 10.1016/j.bpc.2004.07.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2004] [Revised: 06/29/2004] [Accepted: 07/02/2004] [Indexed: 11/28/2022]
Abstract
Binding of zinc to a 19 mer double-stranded oligodeoxyribonucleotide was investigated by anodic stripping voltammetry and cyclic voltammetry in order to understand the roles of zinc in DNA cleavage catalyzed by mung bean nuclease. These methods rely on the direct monitoring of zinc oxidation current in the absence and in the presence of the oligo. Zinc titration curves with the ds-oligodeoxyribonucleotide were obtained in concentrations ranging from 3.62 x 10(-9) to 3.62 x 10(-8) M and 4.06 x 10(-10) to 5.25 x 10(-9) M. The acquired data were used to determine the dissociation constant, stoichiometry and zinc binding sites of the complex and to understand the specific changes of ds-oligodeoxyribonucleotide secondary structure by zinc binding. The oxidation-reduction process of zinc was also investigated by cyclic voltammetry through I (oxidation current) versus v(1/2) (square root of scan rate) curves in the absence and in the presence of the double-stranded oligodeoxyribonucleotide.
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Affiliation(s)
- C S Pires de Castro
- Laboratório de Espectrometria de Massa, Embrapa Recursos Genéticos e Biotecnologia, P.O. Box 02372, 70.770-900 Brasília-DF, Brazil.
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4
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Badura D, Vahrenkamp H. Pyrazolylboratozinc Complexes of Nucleosides and Nucleoside Analogues. Eur J Inorg Chem 2003. [DOI: 10.1002/ejic.200300275] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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5
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Moroni F, Famulari A, Raimondi M, Sabat M. Stabilization of the Noncomplementary Guanine−Adenine Base Pairs by Zn(II) Ions. An ab Initio SCF-MI Study. J Phys Chem B 2003. [DOI: 10.1021/jp026315d] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Federico Moroni
- Dipartimento di Chimica Fisica ed Elettrochimica and Centro CNR-CSRSRC, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy, and Department of Chemistry, University of Virginia, McCormick Road, Charlottesville, Virginia 22904
| | - Antonino Famulari
- Dipartimento di Chimica Fisica ed Elettrochimica and Centro CNR-CSRSRC, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy, and Department of Chemistry, University of Virginia, McCormick Road, Charlottesville, Virginia 22904
| | - Mario Raimondi
- Dipartimento di Chimica Fisica ed Elettrochimica and Centro CNR-CSRSRC, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy, and Department of Chemistry, University of Virginia, McCormick Road, Charlottesville, Virginia 22904
| | - Michal Sabat
- Dipartimento di Chimica Fisica ed Elettrochimica and Centro CNR-CSRSRC, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy, and Department of Chemistry, University of Virginia, McCormick Road, Charlottesville, Virginia 22904
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6
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Badura D, Vahrenkamp H. Pyrazolylborate-zinc-nucleobase-complexes, 2:(1) preparations and structures of Tp(Cum,Me)Zn and Tp(Ph,Me)Zn complexes. Inorg Chem 2002; 41:6013-9. [PMID: 12425627 DOI: 10.1021/ic020280e] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The interactions of the nine most significant nucleobases (thymine, uracil, dihydrouracil, cytosine, adenine, guanine, diaminopurine, xanthine, hypoxanthine, in their deprotonated forms) with zinc and with themselves in pyrazolylborate zinc complexes Tp(Cum,Me)Zn-base and Tp(Ph,Me)Zn-base are described. Except for guanine, the complexes Tp*Zn-base could be isolated in all cases. Structure determinations could be performed for seven of the eight product types. Except for dihydrouracil and xanthine, the zinc ion is attached to that nitrogen of the base which in nucleosides bears the sugar moiety. In the solid state, all zinc-bound nucleobases are involved in hydrogen bonding interactions. Except for xanthine, this includes homo base pairing across a crystallographic inversion center.
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Affiliation(s)
- Dirk Badura
- Institut für Anorganische und Analytische Chemie der Universität Freiburg, Albertstr. 21, D-79104 Freiburg, Germany. vahrenka@ uni-freiburg.de
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7
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Li G, Tolstonog GV, Sabasch M, Traub P. Interaction in vitro of type III intermediate filament proteins with supercoiled plasmid DNA and modulation of eukaryotic DNA topoisomerase I and II activities. DNA Cell Biol 2002; 21:743-69. [PMID: 12443544 DOI: 10.1089/104454902760599726] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
To further characterize the interaction of cytoplasmic intermediate filament (cIF) proteins with supercoiled (sc)DNA, and to support their potential function as complementary nuclear matrix proteins, the type III IF proteins vimentin, glial fibrillary acidic protein, and desmin were analyzed for their capacities to interact with supercoiled plasmids containing a bent mouse gamma-satellite insert or inserts capable of non-B-DNA transitions into triplex, Z, and cruciform DNA, that is, DNA conformations typically bound by nuclear matrices. While agarose gel electrophoresis revealed a rough correlation between the superhelical density of the plasmids and their affinity for cIF proteins as well as cIF protein-mediated protection of the plasmid inserts from S1 nucleolytic cleavage, electron microscopy disclosed binding of the cIF proteins to DNA strand crossovers in the plasmids, in accordance with their potential to interact with both negatively and positively supercoiled DNA. In addition, the three cIF proteins were analyzed for their effects on eukaryotic DNA topoisomerases I and II. Possibly because cIF proteins interact with the same plectonemic and paranemic scDNA conformations also recognized by topoisomerases, but select the major groove of DNA for binding in contrast to topoisomerases that insert into the minor groove, the cIF proteins were able to stimulate the enzymes in their supercoil-relaxing activity on both negatively and positively supercoiled plasmids. The stimulatory effect was considerably stronger on topoisomerase I than on topoisomerase II. Moreover, cIF proteins assisted topoisomerases I and II in overwinding plasmid DNA with the formation of positive supercoils. Results obtained with the N-terminal head domain of vimentin harboring the DNA binding region and terminally truncated vimentin proteins indicated the involvement of both protein-DNA and protein-protein interactions in these activities. Based on these observations, it seems conceivable that cIF proteins participate in the control of the steady-state level of DNA superhelicity in the interphase nucleus in conjunction with such topoisomerase-controlled processes as DNA replication, transcription, recombination, maintenance of genome stability, and chromosome condensation and segregation.
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Affiliation(s)
- Guohong Li
- Max-Planck-Institut für Zellbiologie, Ladenburg, Germany
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8
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Li G, Tolstonog GV, Traub P. Interaction in vitro of type III intermediate filament proteins with triplex DNA. DNA Cell Biol 2002; 21:163-88. [PMID: 12015895 DOI: 10.1089/10445490252925422] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
As previously shown, type III intermediate filaments (IFs) select from a mixture of linear mouse genomic DNA fragments mobile and repetitive, recombinogenic sequences that have also been identified in SDS-stable crosslinkage products of vimentin and DNA isolated from intact fibroblasts. Because these sequences also included homopurine.homopyrimidine (Pu.Py) tracts known to adopt triple-helical conformation under superhelical tension, and because IF proteins are single-stranded (ss) and supercoiled DNA-binding proteins, it was of interest whether they have a particular affinity for triplex DNA. To substantiate this, IF-selected DNA fragments harboring a (Pu.Py) segment and synthetic d(GA)(n) microsatellites were inserted into a vector plasmid and the constructs analyzed for their capacity to interact with IF proteins. Band shift assays revealed a substantially higher affinity of the IF proteins for the insert-containing plasmids than for the empty vector, with an activity decreasing in the order of vimentin > glial fibrillary acidic protein > desmin. In addition, footprint analyses performed with S1 nuclease, KMnO(4), and OsO(4)/bipyridine showed that the (Pu.Py) inserts had adopted triplex conformation under the superhelical strain of the plasmids, and that the IF proteins protected the triple-helical insert sequences from nucleolytic cleavage and chemical modification. All these activities were largely reduced in extent when analyzed on linearized plasmid DNAs. Because intramolecular triplexes (H-DNA) expose single-stranded loops, and the prokaryotic ssDNA-binding proteins g5p and g32p also protected at least the Pu-strand of the (Pu.Py) inserts from nucleolytic degradation, it seemed likely that the IF proteins take advantage of their ssDNA-binding activity in interacting with H-DNA. However, in contrast to g5p and E. coli SSB, they produced no clear band shifts with single-stranded d(GA)(20) and d(TC)(20), so that the interactions rather appear to occur via the duplex-triplex and triplex-loop junctions of H-DNA. On the other hand, the IF proteins, and also g32p, promoted the formation of intermolecular triplexes from the duplex d[A(GA)(20).(TC)(20)T] and d(GA)(20) and d(TC)(20) single strands, with preference of the Py (Pu.Py) triplex motif, substantiating an affinity of the proteins for the triplex structure as such. This triplex-stabilizing effect of IF proteins also applies to the H-DNA of (Pu.Py) insert-containing plasmids, as demonstrated by the preservation of intramolecular triplex-vimentin complexes upon linearization of their constituent supercoiled DNAs, in contrast to poor complex formation from free, linearized plasmid DNA and vimentin. Considering that (Pu.Py) sequences are found near MAR/replication origins, in upstream enhancer and promoter regions of genes, and in recombination hot spots, these results might point to roles of IF proteins in DNA replication, transcription, recombination, and repair.
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Affiliation(s)
- Guohong Li
- Max-Planck-Institut für Zellbiologie, Rosenhof, 68526 Ladenburg, Germany
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9
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Gresh N, Šponer J. Complexes of Pentahydrated Zn2+ with Guanine, Adenine, and the Guanine−Cytosine and Adenine−Thymine Base Pairs. Structures and Energies Characterized by Polarizable Molecular Mechanics and ab Initio Calculations. J Phys Chem B 1999. [DOI: 10.1021/jp9921351] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nohad Gresh
- Unité de Pharmacochimie Moléculaire et Structurale, U266 INSERM, UMR 8600 CNRS, U.F.R. des Sciences Pharmaceutiques et Biologiques, 4, avenue de l'Observatoire, 75270 Paris Cedex 06, France
| | - Jırí Šponer
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, and Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
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10
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Mäueler W, Bassili G, Epplen C, Keyl HG, Epplen JT. Protein binding to simple repetitive sequences depends on DNA secondary structure(s). Chromosome Res 1999; 7:163-6. [PMID: 10421375 DOI: 10.1023/a:1009275914130] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Simple repetitive DNA sequences are ubiquitous constituents of eukaryotic chromosomes. The properties of simple repeats generate increased interest as expansions of certain trinucleotide blocks cause human diseases. We studied protein binding and structural features of (gaa x ttc)n tracts e.g. in the polymorphic frataxin intron 1 and (gt)n(ga)m stretches from different HLA-DRB1 alleles in their original genomic environments. Electrophoretic mobility shift assays revealed that HeLa nuclear proteins bind to DNA fragments containing these simple repeat blocks. The major retarded protein/DNA complexes comprise, in both cases, zinc-dependent proteins present in nuclear extracts from different cell types. Competition experiments using various simple repeats differing in length and flanking regions demonstrate specific interactions. DNase I footprinting shows protein-binding sites located either within the repeats alone or within the repeats as well as their flanking regions, often with preference for one strand. Comparing different (gt)n(ga)m alleles, a regular pattern of footprints was not detectable in the (gt)n part indicating that the zinc-dependent protein recognizes structural rather than sequence-specific features. OsO4 and DEPC modifications followed by electrophoretic and electron microscopical analyses demonstrate that the homopurine blocks often form different types of intramolecular triple helices. A similar situation was evident using (gaa x ttc)n blocks of different lengths within frataxin intron 1 as targets. These data have functional implications for non-coding (gaa x ttc)n and (gt)n(ga)m tracts with regard to gene expression in vivo.
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Affiliation(s)
- W Mäueler
- Molecular Human Genetics, Ruhr-University, Bochum, Germany
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11
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Palecek E, Brázdová M, Cernocká H, Vlk D, Brázda V, Vojtesek B. Effect of transition metals on binding of p53 protein to supercoiled DNA and to consensus sequence in DNA fragments. Oncogene 1999; 18:3617-25. [PMID: 10380883 DOI: 10.1038/sj.onc.1202710] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Recently we have shown that wild-type human p53 protein binds preferentially to supercoiled (sc) DNA in vitro in both the presence and absence of the p53 consensus sequence (p53CON). This binding produces a ladder of retarded bands on an agarose gel. Using immunoblotting with the antibody DO-1, we show that the bands obtained correspond to ethidium-stained DNA, suggesting that each band of the ladder contains a DNA-p53 complex. The intensity and the number of these hands are decreased by physiological concentrations of zinc ions. At higher zinc concentrations, binding of p53 to scDNA is completely inhibited. The binding of additional zinc ions to p53 appears much weaker than the binding of the intrinsic zinc ion in the DNA binding site of the core domain. In contrast to previously published data suggesting that 100 microM zinc ions do not influence p53 binding to p53CON in a DNA oligonucleotide, we show that 5-20 microM zinc efficiently inhibits binding of p53 to p53CON in DNA fragments. We also show that relatively low concentrations of dithiothreitol but not of 2-mercaptoethanol decrease the concentration of free zinc ions, thereby preventing their inhibitory effect on binding of p53 to DNA. Nickel and cobalt ions inhibit binding of p53 to scDNA and to its consensus sequence in linear DNA fragments less efficiently than zinc; cobalt ions are least efficient, requiring >100 microM Co2+ for full inhibition of p53 binding. Modulation of binding of p53 to DNA by physiological concentrations of zinc might represent a novel pathway that regulates p53 activity in vivo.
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Affiliation(s)
- E Palecek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno
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12
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Mäueler W, Bassili G, Arnold R, Renkawitz R, Epplen JT. The (gt)n(ga)m containing intron 2 of HLA-DRB alleles binds a zinc-dependent protein and forms non B-DNA structures. Gene 1999; 226:9-23. [PMID: 9889299 DOI: 10.1016/s0378-1119(98)00573-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We studied protein binding and structural features of perfect and imperfect composite (gt)n(ga)m blocks from different HLA-DRB1 alleles in their original genomic and artificial environments. The major retarded protein/DNA complex of the genomic (gt)n(ga)m fragments comprises a zinc-dependent protein present in nuclear extracts from different cell types. The protein binding is characterized by moderate affinities independent of the polymorphic form of the physiological microsatellite allele. The binding affinity depends on the 5' and 3' adjacent single copy parts. DNase I footprinting of genome-derived fragments revealed that the 5' adjacent sequence and the (gt)n repeat are preferentially protected on the (gt)n(ga)m strand. Comparing three alleles, a regular pattern of footprints was not detectable in the (gt)n part, indicating that the zinc-dependent protein recognizes structural rather than sequence-specific features in this region. Chemical probing resulted in a pattern characteristic for Z-DNA in the (gt)n tract of the fragments. However, EMSA experiments using the Z-DNA specific monoclonal antibody mABZ-22 did not prove the presence of Z-DNA. As demonstrated by chemical modifications of the different (ga)m targets, only one of three (gt)n(ga)m fragments formed intramolecular triplexes of the type H-y3 and H-y5. DNase I footprinting revealed only weak protection, if any, in the homopurine tract. Rather, the (tc)m strands are hypersensitive for DNase I. This is probably due to structural conversions into intramolecular *H-triplexes after binding of HIZP.
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Affiliation(s)
- W Mäueler
- Molekulare Humangenetik, Ruhr-Universität, 44801, Bochum, Germany
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13
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14
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Kejnovsky E, Kypr J. Millimolar concentrations of zinc and other metal cations cause sedimentation of DNA. Nucleic Acids Res 1998; 26:5295-9. [PMID: 9826751 PMCID: PMC148012 DOI: 10.1093/nar/26.23.5295] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
We demonstrate that DNA sediments in the presence of millimolar concentrations of zinc or related metal cations and that EDTA entirely dissolves the sediment. The sedimentation is promoted by alkaline pH but the pH dependence is abolished by submillimolar concentrations of phosphate anions. We suspect that the metal cations generate sedimenting particles of insoluble hydroxides or phosphates for which DNA has a strong affinity. The events involved in DNA-metal phosphate co-sedimentation are similar to the processes that enable calcium phosphate-assisted transfection. Hence, work with even submillimolar concentrations of zinc and most other metal cations, which many DNA-binding proteins need for their activities, requires care to avoid the sedimentation of DNA. Literature reporting about zinc effects on DNA is discussed from the point of view of the present results.
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Affiliation(s)
- E Kejnovsky
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-61265 Brno, Czech Republic
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15
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Xu G, Goodridge AG. A CT repeat in the promoter of the chicken malic enzyme gene is essential for function at an alternative transcription start site. Arch Biochem Biophys 1998; 358:83-91. [PMID: 9750168 DOI: 10.1006/abbi.1998.0852] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
CT repeats are abundant in eukaryotic genomes and have been implicated in a number of biological events. The promoter of the chicken malic enzyme gene contains a long polypyrimidine/polypurine tract that includes seven tandem CTs. This CT repeat region together with 14 immediately downstream nucleotides functions as an active alternative promoter when linked to a reporter gene and may direct transcription initiation at a cluster of minor sites in the endogenous gene [G. Xu and A. G. Goodridge (1996) J. Biol. Chem. 271, 16008-16019]. In the sequence required for promoter activity, -105 to -83 bp, there are two purines; only the A at -83 bp influences promoter activity. Mutation of different four-nucleotide stretches of the CT repeats to purines decreased promoter activity as a function of the increase in GC content. Increasing the number of CT repeats by changing pyrimidines downstream of (CT)7 to CTs increased promoter activity. These sequences and other regions showed moderate sensitivity to S1 nuclease in supercoiled plasmids, suggesting the presence of non-B-DNA structures. Increasing the length of the CT repeats should increase the propensity to adopt non-B-DNA structures such as triplexes. Constructs with 10, 15, or 22 repeats had increased expression relative to wild type. Thus, the ability of CT repeats to form non-B-DNA structures may be functionally important.
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Affiliation(s)
- G Xu
- Department of Biochemistry, University of Iowa, Iowa City, Iowa, 52242, USA
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16
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Ortiz-Lombardía M, Jiménez-García E, García-Bassets I, Azorín F. The interaction of zinc(II) ions with antiparallel-stranded d(GA)n DNA homoduplexes. J Biomol Struct Dyn 1998; 16:243-51. [PMID: 9833664 DOI: 10.1080/07391102.1998.10508243] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
In the presence of specific metal-ions (namely zinc but also cadmium, cobalt and manganese), d(GA x TC)n DNA sequences can form non-B-DNA conformations. At low metal-ion concentration they form [GA(GA x TC)] intramolecular triplexes but, upon increasing the metal concentration, the formation of (GA x GA) intramolecular hairpins is detected. In this paper we address the question of the specific effects of zinc on the structure of the d(GA x TC)n sequences. In the presence of zinc, the DMS-reactivity of the (GA x GA) hairpins is strongly reduced suggesting a direct interaction of the metal-ion with the N7-group of the guanines. This effect is specific for antiparallel-stranded d(GA)n homoduplexes. No such strong decrease in DMS-reactivity is observed in B-DNA duplexes or in d(GGA)n and d(GGGA)n homoduplexes. In addition, the thermal stability of antiparallel-stranded d(GA)n homoduplexes increases in the presence of zinc. On the contrary, the melting temperature of similar B-DNA molecules decreases upon increasing the zinc concentration. Altogether, these result indicate that zinc plays an specific role on the stabilization of the (GA x GA) intramolecular hairpins.
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Affiliation(s)
- M Ortiz-Lombardía
- Departament de Biologia Molecular i Cellular, Centre d'Investigació i Desenvolupament, Barcelona, Spain
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17
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Jiménez-García E, Vaquero A, Espinás ML, Soliva R, Orozco M, Bernués J, Azorín F. The GAGA factor of Drosophila binds triple-stranded DNA. J Biol Chem 1998; 273:24640-8. [PMID: 9733760 DOI: 10.1074/jbc.273.38.24640] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Drosophila GAGA factor binds specifically to simple repeating d(GA.TC)n DNA sequences. These sequences are known to be capable of forming triple-stranded DNA as well as other non-B-DNA conformations. Here, it is shown that GAGA binds to a d[CT(GA.TC)]22 intermolecular triplex with similar specificity and affinity as to a regular double-stranded B-form d(GA.TC)22 sequence. The interaction of GAGA with triplex DNA cannot, however, stimulate transcription in vitro. The affinity of GAGA for triplexes of the purine motif, such as a d[AG(GA.TC)]22 intermolecular triplex, is significantly lower. The DNA binding domain of GAGA is sufficient for efficient binding to triplex DNA. Based on the reported solution structure of the complex of GAGA-DNA binding domain with double-stranded DNA, a model for its interaction with triplex DNA is proposed in which most of the protein-DNA contacts observed in duplex DNA are maintained, especially those occurring through the minor groove. The higher negative charge of the triplex is likely to have also an important contribution to both the specificity and affinity of the interaction.
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Affiliation(s)
- E Jiménez-García
- Departament de Biologia Molecular i Cellular, Centre d'Investigació i Desenvolupament, CSIC, Jordi Girona Salgado 18-26, 08034 Barcelona, Spain
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18
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Mäueler W, Kyas A, Keyl HG, Epplen JT. A genome-derived (gaa.ttc)24 trinucleotide block binds nuclear protein(s) specifically and forms triple helices. Gene 1998; 215:389-403. [PMID: 9714838 DOI: 10.1016/s0378-1119(98)00266-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The properties of simple trinucleotide repeats generate increased interest as expansions of certain trinucleotide blocks cause human diseases. Here, we studied protein binding and structural features of a perfect (gaa.ttc)24 tract in its original genomic environment. Electrophoretic mobility shift assays revealed that HeLa nuclear proteins bind to the DNA fragment containing the (gaa.ttc)24 block. Competition experiments using simple (gt.ac)n repeats differing in length and flanking regions showed no cross-reactivity with the major retarded band. For the specific (gaa. ttc)n/protein complex, a binding constant of 9.3x10-9 mol/l was determined. DNase I footprinting revealed protein binding sites located exclusively within the repeat with a preference for the (gaa)24 strand. OsO4 and DEPC modifications followed by electrophoretic and electron microscopical analyses showed that the (gaa.ttc)24 block forms different types of intramolecular triple helices: Under superhelical stress, different H-DNA isomers are evident, whereas exclusively H-Y forms were detected in the relaxed state. Together, these data have functional implications for genomic (gaa.ttc)n tracts.
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Affiliation(s)
- W Mäueler
- Department of Molecular Human Genetics, Ruhr University, 44780, Bochum, Germany
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Nishikawa N, Kanda N, Oishi M, Kiyama R. Enrichment of oligo(dG).oligo(dC)-containing fragments from human genomic DNA by Mg 2+-dependent triplex affinity capture. Nucleic Acids Res 1997; 25:1701-8. [PMID: 9108150 PMCID: PMC146659 DOI: 10.1093/nar/25.9.1701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Oligo(dG).oligo(dC)- or short poly(dG).poly(dC)-containing fragments were enriched and cloned by means of Mg2+-dependent triplex affinity capture and subsequent cloning procedures. A library constructed after three cycles of enrichment showed that approximately 80% of the clones in the supercoiled form formed a complex with labeled oligonucleotide (dG)34. However, while the rest of the clones retained the ability to form a complex (type I clones), 90.9% failed to form a complex when they were linearized. This group of DNA was abundant in the genomic DNA, although it showed only approximately 3-fold enrichment by one cycle of affinity capture. This group was further classified into two species (types II and III) based on complex formation ability after phenol extraction. Type II clones retained the complex formation ability after treatment, while the human telomere [(TTAGGG)n] and telomere-like [(TGGAA)n] or [(TGGAG)n] sequences belonging to type III clones did not. Serial deletion experiments and the binding assays using oligonucleotides confirmed that the repetitive units containing T(G)nT ( n = 3-5) tracts or (G)n-motifs (n >/= 3) were the sites of complex formation for type II and III clones. On the other hand, type I clones contained poly(dG).poly(dC) tracts at least 10 nt long, and DNase I-footprinting analysis indicated that these tracts were the sites of complex formation.
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Affiliation(s)
- N Nishikawa
- Institute of Molecular and Cellular Biosciences, University of Tokyo, Yayoi, Bunkyo-ku, Tokyo 113, Japan
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20
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Xu G, Goodridge AG. Characterization of a polypyrimidine/polypurine tract in the promoter of the gene for chicken malic enzyme. J Biol Chem 1996; 271:16008-19. [PMID: 8663263 DOI: 10.1074/jbc.271.27.16008] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Starvation inhibits and refeeding stimulates transcription of the malic enzyme gene in chick liver. DNA between -320 and +72 base pairs (bp) is DNase I-hypersensitive in hepatic nuclei from fed but not starved chicks (Ma, X. J., and Goodridge, A. G. (1992) Nucleic Acids Res. 20, 4997-5002). A polypyrimidine/polypurine (PPY/PPU) tract lies within the DNase I-hypersensitive region. In hepatocytes transiently transfected with plasmids containing triiodothyronine response elements and a minimal promoter from the malic enzyme gene linked to the chloramphenicol acetyltransferase gene, deletion of the PPY/PPU tract inhibited chloramphenicol acetyltransferase activity by about 90% with or without triiodothyronine. Fine mapping of S1 nuclease-sensitive sites suggests that the PPY/PPU tract can assume different isoforms of non-B-DNA, some of which may be triplex structures. The PPY/PPU tract contains specific binding sites for single- and double-stranded DNA binding proteins and, with 8 bp 3' of the tract, can function as a promoter. A (CT)7 repeat binds single-stranded DNA-binding protein and is essential for promoter activity. Two C-rich elements bind single-stranded DNA-binding proteins and may mediate inhibition of promoter function. The single- and double-stranded DNA-binding proteins that interact with the PPY/PPU tract may regulate transcription of the malic enzyme gene.
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Affiliation(s)
- G Xu
- Department of Biochemistry, University of Iowa, Iowa City, Iowa 52240, USA
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21
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Pecinka P, Huertas D, Azorín F, Palecek E. Intramolecular TAT triplex in (dA)58.(dT)58. influence of ions. J Biomol Struct Dyn 1995; 13:29-46. [PMID: 8527029 DOI: 10.1080/07391102.1995.10508819] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Supercoil-stabilized intramolecular triplexes have been described under various conditions in different polypurine.polypyrimidine sequences such as (dG)n.(dC)n and mixed sequences including d(GA)n.d(CT)n while information about the triplexes in (dA)n.(dT)n is scarce. Using osmium tetroxide complexes and diethyl pyrocarbonate as structural probes, we show a pyrimidine.purine.pyrimidine (TAT) triplex in (dA)58.(dT)58 sequence in a supercoiled plasmid pE19. Strong modification of approximately six central thymines and approximately six T's at the 3'-end of the (dT)58 stretch as well as the DEPC modification of the 5'-half of the (dA)58 strand suggested the prevalence of the H-y3 triplex conformer. At native superhelix density, optimum conditions for the triplex formation were close to 1 mM MgCl2, pH 8.5. At room temperature and MgCl2 concentrations below 0.5 and above 5 mM, almost no triplex was formed. It is suggested that the absence of the triplex at higher MgCl2 concentrations is due to the stabilization of the duplex by Mg2+ ions which prevents the duplex opening necessary for the triplex formation. At higher temperatures, favorable for duplex opening (e.g. 55 degrees C), the TAT triplex is formed even in the presence of 10 mM MgCl2. Among Ca2+, Sr2+, Ba2+, Cd2+, Zn2+ and Ni2+, only Ca2+ and Sr2+ yielded a modification pattern similar to that obtained with Mg2+; the modification pattern produced in the presence of Sr2+ was, however, much less intense. In the presence of 1 mM MgCl2, a decrease in pH from 8.5 to 7.7 resulted in a strong decrease of the triplex content. At highly negative superhelix density, the conditions for triplex formation were less stringent, and the triplex was observed even in the absence of MgCl2.
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Affiliation(s)
- P Pecinka
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
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Nishikawa N, Oishi M, Kiyama R. Construction of a human genomic library of clones containing poly(dG-dA).poly(dT-dC) tracts by Mg(2+)-dependent triplex affinity capture. DNA polymorphism associated with the tracts. J Biol Chem 1995; 270:9258-64. [PMID: 7721845 DOI: 10.1074/jbc.270.16.9258] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Microsatellite DNA is a useful tool for detecting DNA polymorphisms among species or individuals, especially those among closely related individuals. We constructed a library of clones that contained poly(dG-dA).poly(dT-dC) tracts from human genomic DNA by Mg(2+)-dependent triplex DNA formation. Examination of triplex DNA formation in the presence of various metal ions Mg2+, Mn2+, or Zn2+ revealed that the procedure worked best in the presence of Mg2+. Affinity enrichment was performed with AluI-digested chromosomal DNA mixed with biotinylated (dG-dA)17 in the presence of Mg2+. A library constructed after three cycles of affinity enrichment showed that over 80% of the clones contained at least one poly(dG-dA).poly(dT-dC) tract. Most of them contained a perfect (dG-dA)n repeat 30-84 base pairs in length, while some contained variants such as (dC-dT)10-(dC)-(dC-dT)9. Using the clones from the library as a probe, we detected DNA polymorphisms associated with the repeat length of the tracts in the Japanese population. We also detected a microsatellite instability among the tracts in a cancer tissue sample.
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Affiliation(s)
- N Nishikawa
- Institute of Molecular and Cellular Biosciences, University of Tokyo, Japan
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McDonald CD, Hollingsworth MA, Maher LJ. Enzymatic and chemical probing of an S1 nuclease-sensitive site upstream from the human CFTR gene. Gene X 1994; 150:267-74. [PMID: 7529740 DOI: 10.1016/0378-1119(94)90436-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Similar purine/pyrimidine mirror repeat (PMR) DNA sequences have been identified in the 5'-flanking regions of the human cystic fibrosis transmembrane conductance regulator (hCFTR) and mucin (hMUC1) genes, and supercoiled (but not linearized) plasmids containing these promoter regions were previously shown to be sensitive to digestion by S1 nuclease. The PMR element derived from the hCFTR promoter region is now sub-cloned and characterized at nucleotide resolution with respect to its reactivity toward nucleases S1 and P1, and toward the chemical probes dimethyl sulfate, chloroacetaldehyde, diethylpyrocarbonate and osmium tetroxide. These probes confirm the presence, at pH 4.5 (but not at pH 7.1), of a non-B-DNA structure. This non-B-DNA structure is distinct from H-DNA, because enzymatic and chemical probing detect single-stranded character in the absence of a stable intramolecular triple helix or extruded purine strand.
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Affiliation(s)
- C D McDonald
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha 68198-6805
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Mäueler W, Kyas A, Bröcker F, Epplen JT. Altered electrophoretic behavior of DNA due to short-time UV-B irradiation. Electrophoresis 1994; 15:1499-505. [PMID: 7720686 DOI: 10.1002/elps.11501501214] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
UV-B irradiation is often inevitable for visualization of DNA fragments after ethidium bromide staining. Three different simple-repeat-containing, double-stranded genomic DNA fragments were analyzed for UV-B (312 nm) damage using different gel electrophoretic systems. The effects of UV-B light were obvious after 5 min (31.5 kJ/m2) of irradiation in native polyacrylamide gel electrophoresis (PAGE). Standard single-strand conformation analyses revealed no alterations while a modification did. Sodium dodecyl sulfate (SDS)-PAGE was found to be highly sensitive with regard to the detection of damages and their time/dosage dependency. In addition, SDS-PAGE analysis pointed to different events occurring during UV-B irradiation. Alterations in DNA conformation were detected in every single strand analyzed after 1 min (6.3 kJ/m2) of UV-B exposure. Gel retardation analyses revealed significant changes of protein binding to target DNAs after 2 min of irradiation--possibly stemming from structural modifications and/or originating from binding sites for proteins involved in DNA repair.
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Affiliation(s)
- W Mäueler
- Molecular Human Genetics, Ruhr University, Bochum, Germany
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26
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Mäueler W, Frank G, Muller M, Epplen JT. A complex composed of at least two HeLa nuclear proteins protects preferentially one DNA strand of the simple (gt)n(ga)m containing region of intron 2 in HLA-DRB genes. J Cell Biochem 1994; 56:74-85. [PMID: 7806593 DOI: 10.1002/jcb.240560112] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Electrophoretic mobility shift assays reveal that HeLa nuclear proteins bind fast and with measurable affinity to target DNAs containing mixed simple repetitive (gt)n(ga)m stretches. Preincubation of the proteins at elevated temperature prevents the formation of the major DNA/protein complex in favour of several distinct assemblies. A similar pattern of retarded bands was observed employing higher salt concentrations in the binding reaction. Thus conformational changes of different proteins appear to influence the complex rather than alternating DNA structures. Separation of the total nuclear extract into a water soluble and an insoluble protein fraction leads to a complete loss of target DNA binding capability of the fractions. The binding capacity is restored by combining the two fractions suggesting that at least two protein components are necessary to form a complex with the target sequence. The proteins can be differentiated into heat sensitive, water soluble and temperature stable, water insoluble, respectively. Furthermore, specifically binding polypeptides are not detectable by Southwestern analyses, probably because the essential components are separated during electrophoresis. DNase I footprint analyses yield four different protein binding regions only on the (gt)n(ga)m harbouring strand. The footprints cover larger portions of the mixed simple repeat in addition to a portion 5' of the (gt)n part. Hence at least two nuclear protein components of unknown biological function have to be present simultaneously to protect preferentially the (gt)n(ga)m-containing strand of intron 2 in HLA-DRB genes.
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Affiliation(s)
- W Mäueler
- Molekulare Humangenetik, Ruhr-Universität, Bochum, Germany
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