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Nishigaki K. Short lifetime structures appearing in RNA and DNA. Brief Funct Genomics 2018; 18:174-181. [PMID: 30445594 DOI: 10.1093/bfgp/ely035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 09/24/2018] [Accepted: 10/02/2018] [Indexed: 11/12/2022] Open
Abstract
The structure and function of unstable single-stranded DNA (ssDNA) have not been widely examined. While numerous studies have investigated DNA as an information molecule, the different potentials of DNA, particularly those of ssDNA, remain unclear. For polypeptides, the significance of denatured structures has been established in the past two decades. Polynucleotides have chemically distinct properties from polypeptides, but their behaviours have not been thoroughly studied. In this review, three different phenomena related to unstable ssDNA are discussed: i) ssDNA cleavage of restriction enzymes; ii) single-stranded conformation polymorphism, which can be theoretically explained by single-stranded conformation dynamics; and iii) random PCR (Polymerase Chain Reaction). These features can be utilized for scientific or technical applications. Previous studies showed that the phenomena exhibited by ssDNA were correctly understood only when unstable and transient structures were taken into account. Transient structures of ssDNA may have undiscovered functions governed by very rapid processes and/or multi-diversity states because of their intrinsic natures.
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Affiliation(s)
- Koichi Nishigaki
- Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa, Japan.,Graduate School of Science and Technology, Saitama University, Shimo-okubo, Saitama City, Saitama, Japan
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2
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KARCHER SUSANJ. RECOMBINANT DNA CLONING. Mol Biol 1995. [DOI: 10.1016/b978-012397720-5.50036-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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3
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Ahuja YR, Obe G. Are rogue cells an indicator of cancer risk due to the action of bacterial restriction endonucleases? Mutat Res 1994; 310:103-12. [PMID: 7523873 DOI: 10.1016/0027-5107(94)90013-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Cytogenetic surveys in normal individuals have occasionally shown the occurrence of cells with multiple chromosome-type aberrations in some of the subjects. These cells, which are rare, have been termed as rogue cells. Rogue cells, which have been observed worldwide, have a mysterious nature. It has been suggested that they may give rise to cancer. Various mechanisms have been considered for the causation of the rouge-cell phenomenon in the past but none of them appears to be fully justified. In this paper we propose their occurrence due to the action of bacterial restriction endonucleases.
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Affiliation(s)
- Y R Ahuja
- Genetics Unit, Bhagwan Mahavir Medical Research Centre, Hyderabad, India
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4
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Obe G, Johannes C, Werthmann I, Folle GA. Chromatid-type aberrations induced by AluI in Chinese hamster ovary cells. Mutat Res 1993; 299:305-11. [PMID: 7683098 DOI: 10.1016/0165-1218(93)90107-o] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Treatment of CHO cells with AluI in the S-phase leads to chromatid-type aberrations whose frequencies are linearly correlated with dose. Treatment in the S-phase leads to fewer aberrations than treatment in the G1-phase, which is comparable to chromosomal aberration induction following X-irradiation in the G1- and S-phases. Treatment in the G1-phase leads to few chromatid-type interchanges, some of these may originate from DNA single-strand gaps induced by AluI in canonical structures of DNA and in DNA.RNA hybrids.
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Affiliation(s)
- G Obe
- Department of Genetics, Universität GH Essen, Germany
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5
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Willwand K, Kaaden OR. Capsid protein VP1 (p85) of Aleutian disease virus is a major DNA-binding protein. Virology 1988; 166:52-7. [PMID: 2842956 DOI: 10.1016/0042-6822(88)90145-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The interaction between Aleutian disease virus (ADV) DNA and proteins isolated from ADV-infected cells or ADV virions, respectively, was examined. Proteins were separated on SDS-polyacrylamide gels, transferred to nitrocellulose, and probed with 32P-labeled restriction fragments of replicative form (RF) DNA or with single-stranded virion DNA. The ADV capsid protein VP1 was found to bind the 3'-terminal BamHI fragment of RF DNA extending from map units (m.u.) 0 to 15. No binding was observed with the fragment extending from m.u. 15 to 63 and only minor amounts of label were detected with the 5'-terminal EcoRV fragment extending from m.u. 63 to 100. With the latter fragment, small amounts of label were also detected bound to higher-molecular-weight proteins of about 100,000 Da. No binding of DNA to the ADV nonstructural protein NS1 or to the ADV capsid protein VP2 was detected. Additionally, single-stranded virion DNA was found to bind to VP1.
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Affiliation(s)
- K Willwand
- Institute of Virology, Hannover Veterinary School, Federal Republic of Germany
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6
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Hofer B, Müller D, Köster H. Escherichia coli RNA polymerase binding to a DNA terminus prevents formation of a closed promoter complex. BIOCHIMICA ET BIOPHYSICA ACTA 1987; 910:254-60. [PMID: 3315004 DOI: 10.1016/0167-4781(87)90118-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A 302 bp DNA fragment and a 113 bp subfragment of the former, both containing the fd gene VIII promoter (P VIII), were found to exhibit temperature-dependent differential behaviour in RNA chain initiation from P VIII. At 37 degrees C no significant differences were observed, while at 17 degrees C chain initiation was strongly suppressed only with the 113 bp fragment. This phenomenon depended on the presence of the (blunt) DNA terminus upstream from P VIII (position -70). Footprinting revealed that at 17 degrees C RNA polymerase was bound to this DNA fragment in a different mode. Contacts were observed only upstream from position -25. On the contrary, at 37 degrees C only the promoter complex footprint was visible. These results indicate that at 17 degrees C formation of the non-initiating complex is more favourable than formation of the promoter complex (which is closed at 17 degrees C; Hofer, B., Müller, D. and Köster, H. (1985) Nucleic Acids Res. 13, 5995-6013) and that formation of both complexes is mutually exclusive. No footprints of RNA polymerase were observed at other DNA termini. This indicates a sequence-specificity for the interaction at the terminus of the 113 bp fragment. The footprint pattern, together with features of the DNA sequence, suggests that the contacts involved in this interaction are similar to those promoter contacts formed upstream from position -20 and that DNA without a -10 region can be specifically recognized by RNA polymerase.
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Affiliation(s)
- B Hofer
- Institut für Organische Chemie und Biochemie der Universität Hamburg, F.R.G
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7
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Svaren J, Inagami S, Lovegren E, Chalkley R. DNA denatures upon drying after ethanol precipitation. Nucleic Acids Res 1987; 15:8739-54. [PMID: 3684571 PMCID: PMC306402 DOI: 10.1093/nar/15.21.8739] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
We have observed that ethanol precipitation and subsequent drying of small (less than 400 bp) radiolabelled DNA fragments is able to induce a transition to a form that migrates aberrantly on acrylamide gels. This unusual form has increased sensitivity to S1 nuclease, decreased sensitivity to restriction enzymes, and a concentration dependence for the reversion to the duplex form. Apparently, DNA denatures upon dehydration so that redissolving at low dilution will allow the collapse of DNA fragments into single-stranded hairpin structures. These structures are stable enough at low dilution to prevent complete reannealing of single stranded species. These single stranded species show strong binding to unidentified proteins present in nuclear extracts. This may give rise to misleading interpretations of mobility shift assays, especially if the single-stranded conformers have a similar mobility to the duplex fragment, which can occur in fragments that are 50-100 bp long. Evidence is presented that DNA, in general, denatures upon dehydration, but that hindrances to rotation in the solid state may prevent long fragments from dissociating.
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Affiliation(s)
- J Svaren
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232
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Greaves DR, Borst P. Trypanosoma brucei variant-specific glycoprotein gene chromatin is sensitive to single-strand-specific endonuclease digestion. J Mol Biol 1987; 197:471-83. [PMID: 2831370 DOI: 10.1016/0022-2836(87)90559-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Active variant surface glycoprotein (VSG) gene chromatin is preferentially digested by the restriction enzyme HinfI in nuclei of bloodstream variants of Trypanosoma brucei. HinfI sensitivity of VSG gene chromatin is not observed in nuclei of relapse variants in which the VSG gene has been inactivated in situ. Active VSG gene chromatin is preferentially degraded by the single-strand-specific endonucleases S1 and Bal31. This sensitivity is not the result of pre-existing single-strand breaks or a detectably altered nucleosomal organization. Trypanosome nuclei in which the run-on transcription of VSG genes has been specifically shut down have been used to show that Hinfl and Bal31 sensitivity is not dependent upon continued transcription of the VSG gene. The presence of single-stranded DNA regions within VSG gene chromatin is consistent with a model in which VSG genes are activated by increased torsional stress.
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Affiliation(s)
- D R Greaves
- Division of Molecular Biology, Netherlands Cancer Institute, Antoni van Leeuwenhoekhuis, Amsterdam
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9
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Reckmann B, Krauss G. The cleavage of single-stranded DNA by the isoschizomeric restriction endonuclease HhaI and CfoI. BIOCHIMICA ET BIOPHYSICA ACTA 1987; 908:90-6. [PMID: 3026483 DOI: 10.1016/0167-4781(87)90025-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The cleavage of single-stranded (ss) M13mp8(+) DNA by the isoschizomeric restriction endonucleases HhaI and CfoI has been investigated. The two enzymes differ considerably in their ability to cleave ssDNA. HhaI cleaves ssDNA about two orders of magnitude faster than does CfoI, although both enzymes show the same activity when assayed on double-stranded DNA. From the cleavage of oligonucleotides and of M13mp8(+) DNA fragments it is concluded that cleavage of ssDNA occurs via transiently formed double-stranded hairpin structures. A rough correlation exists between the stability of the secondary structures and the cleavage efficiency.
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10
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Nishigaki K, Kaneko Y, Wakuda H, Husimi Y, Tanaka T. Type II restriction endonucleases cleave single-stranded DNAs in general. Nucleic Acids Res 1985; 13:5747-60. [PMID: 2994012 PMCID: PMC321909 DOI: 10.1093/nar/13.16.5747] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Restriction endonucleases (13 out of 18 species used for the test) were certified to cleave single-stranded(ss)DNA. Such enzymes as AvaII, HaeII, DdeI, AluI, Sau3AI, AccII,TthHB8I and HapII were newly reported to cleave ssDNA. A model to account for the cleavage of ssDNA by restriction enzymes was proposed with supportive data. The essential part of the model was that restriction enzymes preferentially cleave transiently formed secondary structures (called canonical structures) in ssDNA composed of two recognition sequences with two fold rotational symmetry. This means that a restriction enzyme can cleave ssDNAs in general so far as the DNAs have the sequences of restriction sites for the enzyme, and that the rate of cleavage depends on the stabilities of canonical structures.
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11
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Hofer B, Müller D, Köster H. The pathway of E. coli RNA polymerase-promoter complex formation as visualized by footprinting. Nucleic Acids Res 1985; 13:5995-6013. [PMID: 3898021 PMCID: PMC321928 DOI: 10.1093/nar/13.16.5995] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The pathway of E. coli RNA polymerase-promoter complex formation was probed by characterization of low temperature intermediates at the major coat protein promoter of phage fd DMA. Three different complexes could be distinguished. One of them represents the active 'open' complex, the other two have to be regarded as 'closed'. The promoter contacts of the lower temperature complexes were totally comprised within the contacts of the higher temperature complexes. Increase in temperature led to extension of contacts into the downstream direction, while the upstream border of the complexes remained virtually unchanged. Only in the 'open' complex contacts were extended beyond the start site of transcription.
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12
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Been MD, Champoux JJ. Breakage of single-stranded DNA by eukaryotic type 1 topoisomerase occurs only at regions with the potential for base-pairing. J Mol Biol 1984; 180:515-31. [PMID: 6098684 DOI: 10.1016/0022-2836(84)90025-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Eukaryotic type 1 DNA topoisomerases break single-stranded DNA at specific sites. A preferred site for rat liver topoisomerase breakage in single-stranded phi X174 DNA was located within a region of the DNA with the potential for duplex formation. To investigate the relationship between sites of breakage in duplex and single-stranded DNA, a restriction fragment containing sequences from the transcriptional regulatory and enhancer region of the simian virus 40 genome was used as a substrate for topoisomerase. While different patterns of breakage in the native and denatured forms of the DNA were observed, some sites of breakage were common to both forms. The break sites in the denatured DNA were a subset of the break sites in the duplex DNA and were located in regions which had the potential for intrastrand base-pairing due to distal complementary sequences. A series of single-stranded fragments were generated with the distal complementary sequences deleted and these fragments were used as substrates for topoisomerase breakage. The lack of detectable breakage at a site when the complementary sequence was deleted, suggests that topoisomerase acts at duplex regions in the single-stranded DNA and that it is not active on regions of single-stranded DNA that are not base-paired.
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13
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Analysis of DNA structural patterns and sequence organization at the larval cuticle locus in Drosophila melanogaster. Mol Cell Biol 1984. [PMID: 6227807 DOI: 10.1128/mcb.3.10.1724] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We examined the pattern of DNA organization at the larval cuticle gene complex 44D of Drosophila melanogaster, using micrococcal nuclease and the 1,10-phenanthroline-cuprous complex. The initial cleavage patterns obtained with both reagents exhibited "gaps" at the positions of each of the genes examined, as well as at a pseudogene sequence contained within the complex. An additional gap for which no gene exists was observed for both patterns. The cleavage pattern obtained with micrococcal nuclease was unaltered, at a level of resolution of +/- 50 base pairs, in a mutant containing a transposable element. Analysis of the sequence data from this 5.5-kilobase gene cluster indicated that the sequence per se, and not the general base composition, is a dominant factor in determining the patterns observed.
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14
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Eissenberg JC, Elgin SC. Analysis of DNA structural patterns and sequence organization at the larval cuticle locus in Drosophila melanogaster. Mol Cell Biol 1983; 3:1724-9. [PMID: 6227807 PMCID: PMC370033 DOI: 10.1128/mcb.3.10.1724-1729.1983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
We examined the pattern of DNA organization at the larval cuticle gene complex 44D of Drosophila melanogaster, using micrococcal nuclease and the 1,10-phenanthroline-cuprous complex. The initial cleavage patterns obtained with both reagents exhibited "gaps" at the positions of each of the genes examined, as well as at a pseudogene sequence contained within the complex. An additional gap for which no gene exists was observed for both patterns. The cleavage pattern obtained with micrococcal nuclease was unaltered, at a level of resolution of +/- 50 base pairs, in a mutant containing a transposable element. Analysis of the sequence data from this 5.5-kilobase gene cluster indicated that the sequence per se, and not the general base composition, is a dominant factor in determining the patterns observed.
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Harrington CA, Chikaraishi DM. Identification and sequence of the initiation site for rat 45S ribosomal RNA synthesis. Nucleic Acids Res 1983; 11:3317-32. [PMID: 6304628 PMCID: PMC325965 DOI: 10.1093/nar/11.10.3317] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The transcription initiation site for rat 45S precursor ribosomal RNA synthesis was determined by nuclease protection mapping with two single-strand endonucleases. S1 and mung bean, and one single-strand exonuclease, ExoVII. These experiments were performed with end-labeled ribosomal DNA from double-stranded pBR322 recombinants and from single-stranded M13 recombinants. Results from experiments using both kinds of DNA and all three enzymes showed that the 5' end of 45S RNA mapped to a unique site 125 bases upstream from the Hind III site in the ribosomal DNA gene. The DNA surrounding this site (designated +1) was sequenced from -281 to +641. The entire sequence of this region shows extensive homology to the comparable region of mouse. This includes three stretches of T residues in the non-coding strand between +300 and +630. Two sets of direct repeats adjacent to these T-rich regions are observed. Comparison of the mouse and human ribosomal DNA transcription initiation sites with the rat sequence reported in this paper demonstrates a conserved sequence at +2 to +16, CTGACACGCTGTCCT. This suggests that this region may be important for the initiation of transcription on mammalian ribosomal DNAs.
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Cartwright IL, Elgin SC. Analysis of chromatin structure and DNA sequence organization: use of the 1,10-phenanthroline-cuprous complex. Nucleic Acids Res 1982; 10:5835-52. [PMID: 6292854 PMCID: PMC320934 DOI: 10.1093/nar/10.19.5835] [Citation(s) in RCA: 71] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Limited treatment of Drosophila nuclei with the 1,10-phenanthroline-cuprous complex leads to rapid production of nucleosomal ladders indistinguishable from those obtained by micrococcal nuclease digestion. An investigation of the preferential sites of cleavage of protein-free DNA at locus 67B1 surprisingly indicated that both reagents recognized very similar features. Thus, a virtually identical pattern of preferential cleavages was generated over a 12 kb fragment encoding four transcripts at this locus. The distribution of cleavage sites was highly non-random, with major sites falling in the spacers between the genes. Both reagents cleaved certain chromatin-specific sites near the 5' ends of the genes. However, an analysis of preferential cleavages at the sequence level did not reveal the same close correspondence. We suggest that both reagents can recognize some localized secondary structural features of the DNA and that the particular distribution of sequences present at this locus results in a distinctive pattern of cleavage sites that delineates gene and spacer segments.
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