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Bundey S, Hardy C, Vickers S, Kilpatrick MW, Corbett JA. Duplication of the 15q11-13 region in a patient with autism, epilepsy and ataxia. Dev Med Child Neurol 1994; 36:736-42. [PMID: 8050626 DOI: 10.1111/j.1469-8749.1994.tb11916.x] [Citation(s) in RCA: 112] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Various developmental abnormalities can give rise to the clinical syndrome of autism, and some are due to chromosomal anomalies. One syndrome has been identified in which behavioural disorder is associated with the clinical features of epilepsy and ataxia, and with the chromosomal anomaly of an extra marker chromosome containing a duplication of 15q11-13. The authors report a boy with autism, epilepsy, ataxia and an interstitial duplication of 15q, in whom molecular analysis reveals duplication of the GABRA5 and GABRB3 genes on the maternally derived chromosome.
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Hammond-Kosack MC, Kilpatrick MW, Docherty K. The human insulin gene-linked polymorphic region adopts a G-quartet structure in chromatin assembled in vitro. J Mol Endocrinol 1993; 10:121-6. [PMID: 8484861 DOI: 10.1677/jme.0.0100121] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The insulin gene-linked polymorphic region (ILPR), located 363 bp upstream of the human insulin gene, is composed of tandem repeats of the consensus sequence ACAGGGGT(G/C)(T/C)GGGG. It has previously been shown that an insulin gene fragment containing the ILPR adopts an altered DNA structure in vitro. Furthermore, oligonucleotides containing the consensus repeat sequence exhibit multiple quadriplex DNA structures. The present study was undertaken to determine whether such altered DNA structures existed within the ILPR when the insulin gene was assembled into chromatin in vitro. Chromatin assembly was achieved using histones and an extract from unfertilized eggs from Xenopus laevis. The presence of altered DNA conformations within the 5' region of the human insulin gene was investigated using the structural probe nuclease P1. Nuclease P1 recognized multiple distinct sites in the 5' flanking region of the human insulin gene in naked DNA. Most of these sites disappeared when the recombinant plasmid DNA was treated with histones and unfertilized egg extract. In the assembled DNA, the ILPR appeared as the major site of nuclease P1 hypersensitivity. Fine-mapping of the multiple reactive sites within the ILPR showed a pattern characteristic of G-quartet foldback structures similar to those that have been observed for telomeric DNA.
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Fullwood P, Jones J, Bundey S, Dudgeon J, Fielder AR, Kilpatrick MW. X linked exudative vitreoretinopathy: clinical features and genetic linkage analysis. Br J Ophthalmol 1993; 77:168-70. [PMID: 8457509 PMCID: PMC504464 DOI: 10.1136/bjo.77.3.168] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
A four generation family in which familial exudative vitreoretinopathy is inherited as an X linked condition is described. Essentially the condition is one of abnormal vascularisation and signs at birth are those of a retinopathy superficially resembling retinopathy of prematurity, retinal folds, or, in advanced cases, enophthalmos or even phthisis. Prognosis depends on the progression of the retinal changes. The family members, including seven affected males and five obligate carrier females, have been types for 20 DNA markers, and linkage analysis suggests a gene locus either at Xq21.3 or at Xp11. As the latter region includes the locus for the gene for Norrie disease, it is possible that this and X linked vitreoretinopathy are allelic. We can further speculate that the differences in severity of the clinical manifestations are dependent only upon the timing of the insult.
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Hammond-Kosack MC, Kilpatrick MW, Docherty K. Analysis of DNA structure in the human insulin gene-linked polymorphic region in vivo. J Mol Endocrinol 1992; 9:221-5. [PMID: 1476609 DOI: 10.1677/jme.0.0090221] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
An altered DNA structure exists within the hypervariable region located 360 bp upstream of the human insulin gene. The aim of the present study was to determine whether this structure exists in the insulin gene in vivo, and whether its presence is related to the expression of the insulin gene. However, since there were no clonal human beta-cell lines available for such studies, the human insulin gene was transfected into a rat insulinoma-derived beta-cell line and several human insulin-expressing clones were selected. One such cell line was treated in vivo with the DNA structural probe bromoacetaldehyde and the chromosomal DNA was extracted. Following digestion with TaqI and subsequent digestion with S1-nuclease to cleave at the bromoacetaldehyde-reactive sites, the DNA was subjected to agarose gel electrophoresis, and insulin gene fragments were detected by Southern blot analysis. Bromoacetaldehyde generated subfragments of 2500, 1700 and 800 bp in the human insulin gene isolated from the rat beta-cell line, while the human insulin gene in the non-expressing HeLa cell line was unreactive to bromoacetaldehyde. These results suggest that an altered structure might exist in the insulin gene-linked polymorphic region of the human insulin gene in vivo, and that this structure may play a role in the expression of the insulin gene.
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Glass IA, Del Mastro RG, Lanyon WG, Raeburn JA, Kilpatrick MW, Webb TP, Connor JM. Tightly linked polymorphic markers for fragile X syndrome and prenatal cytogenetic diagnostic experience. AMERICAN JOURNAL OF MEDICAL GENETICS 1992; 43:1050-6. [PMID: 1415337 DOI: 10.1002/ajmg.1320430632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Linkage analysis using the polymorphic loci DXS369, DXS296, DXS297 and DXS306 was carried out on a cohort of 17 families segregating for fragile X syndrome. The observed recombination fractions at: DXS369 (Zmax = 3.02; theta = 0.06), DXS297 (Zmax = 2.92; theta = 0.0), DXS296 (Zmax = 3.82; theta = 0.0), DXA306 (Zmax = 4.55; theta = 0.05) confirm that these loci are tightly linked to FRAXA. Our experience in the cytogenetic analysis of 58 at risk pregnancies by chorionic villus or fetal blood sample examination documents a false negative rate in obligate carrier male pregnancies for CVS of 11% and for FBS of 3%.
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Abstract
The Gorlin (naevoid-basal-cell-carcinoma) syndrome is an autosomal dominant disorder characterised by multiple naevoid basal-cell carcinomas, recurrent odontogenic keratocysts, skeletal anomalies, intracranial calcification, and developmental malformations. Characterisation of the gene that causes the syndrome may improve our understanding of the pathogenesis of other basal-cell carcinomas. By linkage analysis, we have shown that the gene is located on chromosome 9q22.3-q31; the most likely position is between DNA markers D9S12 and D9S53. Location of the gene for Gorlin syndrome offers the possibility that DNA markers can be used in risk estimation and presymptomatic identification of patients for surveillance.
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Hammond-Kosack MC, Dobrinski B, Lurz R, Docherty K, Kilpatrick MW. The human insulin gene linked polymorphic region exhibits an altered DNA structure. Nucleic Acids Res 1992; 20:231-6. [PMID: 1741248 PMCID: PMC310359 DOI: 10.1093/nar/20.2.231] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Regulation of transcription of the human insulin gene appears to involve a series of DNA sequences in the 5' region. Hypersensitivity to DNA structural probes has previously been demonstrated in regulatory regions of cloned genomic DNA fragments, and been correlated with gene activity. To investigate the structure of the DNA in the human insulin gene, bromoacetaldehyde and S1 nuclease were reacted with a supercoiled plasmid containing a 5kb genomic insulin fragment. Both probes revealed the human insulin gene linked polymorphic region (ILPR), a region (-363) upstream of the transcriptional start site which contains multiple repeats of a 14-15mer oligonucleotide with the consensus sequence ACAGGGGT(G/C)(T/C)GGGG, as the major hypersensitive site. Fine mapping and electron microscopic analysis both show a very different behaviour of the two DNA strands in the region of the ILPR and suggest the G-rich strand may be adopting a highly structured conformation with the complementary strand remaining largely single stranded.
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Kainulainen K, Steinmann B, Collins F, Dietz HC, Francomano CA, Child A, Kilpatrick MW, Brock DJ, Keston M, Pyeritz RE. Marfan syndrome: no evidence for heterogeneity in different populations, and more precise mapping of the gene. Am J Hum Genet 1991; 49:662-7. [PMID: 1882844 PMCID: PMC1683142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Marfan syndrome is a dominantly inherited connective tissue disorder with manifestations in the cardiovascular, ocular, and skeletal systems. The diagnosis is hampered by both high variability in the phenotypic expression and late manifestation of symptoms. The cause of Marfan syndrome remains unknown, but our group has recently reported the genetic linkage of Marfan syndrome to a polymorphic marker on chromosome 15. To analyze the possible heterogeneity behind Marfan syndrome, we have performed linkage analyses for four chromosome 15 markers in 17 families from five different populations: Scottish, English, Swiss, American, and Finnish. By combining the linkage data of all the studied families into a LINKMAP analysis we obtained a maximal LOD score of 11.2, which maps the Marfan syndrome locus between D15S25 and D15S45 on the long arm of chromosome 15. The data reveal no evidence for genetic heterogeneity behind Marfan syndrome and provide us with a more precise location of both the Marfan syndrome locus and flanking markers. This information will provide the basis for the DNA diagnostics of Marfan syndrome in the future.
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Abstract
A family with 11 normal boys has been typed with DNA probes spanning the whole of the X-chromosome to observe directly the recombination events in 11 meioses from one female. This has (a) identified apparent recombination hot-spots on the X-chromosome; (b) shown the positions and numbers of cross-overs that have occurred in the p and q arms; (c) not shown any cross-overs in the centromeric region and (d) enabled the calculation of the genetic length of the X-chromosome.
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Del Mastro RG, Bundey S, Kilpatrick MW. Adrenoleucodystrophy: a molecular genetic study in five families. J Med Genet 1990; 27:670-5. [PMID: 2277380 PMCID: PMC1017255 DOI: 10.1136/jmg.27.11.670] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A genetic study has been performed on five adrenoleucodystrophy families using DNA probes from Xq28. Members of each family had previously been tested for carrier status using the biochemical assay for very long chain fatty acids (VLCFAs), but several persons at risk had equivocal results. DNA analysis with four DNA probes St14-1 (DXS52), DX13 (DXS15), MN12 (DXS33), and hs7 showed no crossovers between them and the disease locus in persons who were clinically affected or had high levels of VLCFA or both. Thus, the genotypes provided by the DNA probes could be used for accurate carrier detection and prenatal diagnosis could be offered. Of the 17 at risk females with VLCFA levels in the normal (1 SD) range, five were defined as carriers and 12 were considered not to be.
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36
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Blanton SH, Sarfarazi M, Eiberg H, de Groote J, Farndon PA, Kilpatrick MW, Child AH, Pope FM, Peltonen L, Francomano CA. An exclusion map of Marfan syndrome. J Med Genet 1990; 27:73-7. [PMID: 2319588 PMCID: PMC1016923 DOI: 10.1136/jmg.27.2.73] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The combined genetic data between the Marfan syndrome and 75 informative loci on 18 autosomes were used to construct an exclusion map for this disorder. Data are also presented for a further two unmapped markers. The most likely location of the Marfan syndrome gene is highlighted and all the unexcluded areas of the genome are displayed in a graphical form. This exclusion map shows that almost 75% of the genome has been excluded as a likely location for the Marfan syndrome gene in the majority of the families studied. Apart from chromosomes 8, 13, 21, and 22, for which no data were available, other regions not excluded yet include 5p, 6p, 9p, 10p, 12p, 15, 17p, 18, and 20p. Future linkage analysis using markers located in the highlighted regions should facilitate the identification of the site of the Marfan syndrome gene.
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Higgins NP, Collier DA, Kilpatrick MW, Krause HM. Supercoiling and integration host factor change the DNA conformation and alter the flow of convergent transcription in phage Mu. J Biol Chem 1989; 264:3035-42. [PMID: 2644278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Transcription of bacteriophage Mu is modulated by its repressor, by negative supercoiling, and by the Escherichia coli protein integration host factor (IHF). Two converging Mu promoters regulate lytic and lysogenic development. The influence of IHF on these convergent promoters depended on the DNA conformation. When Mu operator DNA changed from the relaxed to the negative supercoiled form, IHF changed from a stimulatory factor to an inhibitor of the repressor promoter, and the ratio of the lytic transcript relative to the repressor transcript increased by 40-fold. Flexibility in Mu operator DNA was demonstrated by an unusual supercoil-induced DNA conformation, which was detectable by chemical modification with bromoacetaldehyde or digestion with P1 nuclease. IHF binding adjacent to this site induced dramatic bending of Mu DNA. A topological model we call a superloop is proposed to explain the effect of IHF on Mu transcription in vitro and on the lytic-lysogeny decision of the virus grown in IHF and gyrase mutants.
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38
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Kilpatrick MW, Torri A, Kang DS, Engler JA, Wells RD. Unusual DNA structures in the adenovirus genome. J Biol Chem 1986; 261:11350-4. [PMID: 3015967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
More than 80% (approximately 29 kilobase pairs) of the adenovirus serotype 2 genome was surveyed for the presence of unusual DNA conformations. Seven recombinant DNAs containing the largest HindIII fragments of AD2 DNA were analyzed for the presence of negative supercoil-dependent S1 nuclease-sensitive sites. Four plasmids each contained a specific site of S1 nuclease sensitivity whereas the other three showed no reaction. Further investigation was focused on a plasmid containing one of the positively reacting fragments (fragment C) which contained the major late promoter at coordinate 16.4 on the genome; three serotypes (Ad2, Ad7, Ad12) were studied. Fine mapping studies revealed the S1-sensitive sites to be a small region (approximately 6 base pairs) located at the TATA box of the major late promoter in all three cases. Other determinations (supercoil relaxation, T7 gene 3 product sensitivity, bromoacetaldehyde reactivity, anomalous gel mobility, the influence of negative superhelical density on nuclease sensitivity) led to the conclusion that the B-helix deformation was not due to a previously recognized DNA conformation (left-handed Z-DNA, cruciform, bent DNA), but may be accounted for by the homopurine X homopyrimidine nature of this region.
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McLean MJ, Blaho JA, Kilpatrick MW, Wells RD. Consecutive A X T pairs can adopt a left-handed DNA structure. Proc Natl Acad Sci U S A 1986; 83:5884-8. [PMID: 3016726 PMCID: PMC386401 DOI: 10.1073/pnas.83.16.5884] [Citation(s) in RCA: 86] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The capacity of six sequences with different numbers and orientations of A.T pairs flanked by alternating C.G pairs to adopt left-handed structures was evaluated in recombinant plasmids. A series of synthetic oligodeoxynucleotides were cloned into the BamHI site of pRW790, a small plasmid (approximately 2 kilobases) prepared especially for conformational studies of this type. Supercoil relaxation studies by two-dimensional gel electrophoresis on topoisomers of each plasmid revealed the energetics and structures of the left-handed helices. Also, the presence of supercoil-induced altered DNA conformations within the inserts of topoisomer populations of the plasmids was detected by reaction with S1 nuclease followed by restriction mapping of the cleavage sites. We conclude that consecutive T.A base pairs, whether alternating (TATA) or contiguous (TTTT), can adopt a left-handed conformation (presumably Z) when flanked by reasonably short runs of alternating (C-G)n (n = 3-5). Thus, these results substantially broaden the range of DNA sequences that can adopt left-handed Z conformations.
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40
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Teo I, Sedgwick B, Kilpatrick MW, McCarthy TV, Lindahl T. The intracellular signal for induction of resistance to alkylating agents in E. coli. Cell 1986; 45:315-24. [PMID: 3009022 DOI: 10.1016/0092-8674(86)90396-x] [Citation(s) in RCA: 167] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The E. coli ada gene positively controls its own expression and that of other genes (alkA, alkB, aidB) involved in repair of DNA alkylation damage. The cloned ada and alkA genes and purified Ada protein have been used in cell-free systems to identify the inducing signal. Self-methylation of the Ada protein by transfer of a methyl group from a phosphotriester in alkylated DNA to a cysteine residue in the protein converts it to an activator of transcription. The covalently modified Ada protein binds specifically to promoter regions containing the sequence d(AAANNAAAGCGCA) immediately upstream of the RNA polymerase binding sites. This is apparently the first example of conversion of a regulatory gene product to a transcriptional activator by a posttranslational modification event.
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41
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Zacharias W, Larson JE, Kilpatrick MW, Wells RD. HhaI methylase and restriction endonuclease as probes for B to Z DNA conformational changes in d(GCGC) sequences. Nucleic Acids Res 1984; 12:7677-92. [PMID: 6093048 PMCID: PMC320193 DOI: 10.1093/nar/12.20.7677] [Citation(s) in RCA: 64] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The capacity of the modification methylase (MHhaI) and restriction endonuclease (HhaI) form Haemophilus haemolyticus to methylate and cleave, respectively, recognition sites which are in right-handed B or left-handed Z structures was determined in vitro. Plasmids containing tracts of (dC-dG) as well as numerous individual d(GCGC) sites distributed around the vector were studied. Negative supercoiling was used to convert the (dC-dG) tracts (approximately 30 bp in length) from a right-handed to a left-handed conformation. (Methyl-3H)-SAM was used to localize and quantitate modified d(GCGC) recognition sites, whereas cleavage by HhaI was used to detect unmethylated sites. In the left-handed Z-form, the (dC-dG) blocks were not methylated by MHhaI and not cleaved by HhaI. A two-dimensional gel analysis of a family of 33 topoisomers treated with MHhaI revealed that the lack of methylation in the (dC-dG) blocks was directly correlated to the supercoil-induced B to Z transition in these segments. These results are significant with respect to enzyme-DNA interactions in general and provide the basis for using HhaI and MHhaI as probes for different DNA structures and conformational transitions under physiological conditions.
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Kilpatrick MW, Klysik J, Singleton CK, Zarling DA, Jovin TM, Hanau LH, Erlanger BF, Wells RD. Intervening sequences in human fetal globin genes adopt left-handed Z helices. J Biol Chem 1984; 259:7268-74. [PMID: 6202693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The large intervening sequences ( IVS2 ) of three human fetal globin genes contain tracts of alternating purine-pyrimidine sequences approximately 40-60 base pairs in length which adopt left-handed Z DNA helices under the influence of negative supercoiling. The amount of negative supercoiling (approximately 0.045) required for the right- to left-handed transitions is within the physiological range. The structural aberrations between the right- and left-handed helices were mapped by sequencing the S1 nuclease cleavage sites. Two-dimensional gel electrophoretic analyses of the supercoil-induced relaxation served to characterize the type and length of left-handed structure. Furthermore, binding studies with several types of antibodies confirmed the presence of left-handed helices. Since these simple sequences appear to be hotspots for recombination and gene conversion, unusual DNA conformations may participate in genetic expression.
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Kilpatrick MW, Klysik J, Singleton CK, Zarling DA, Jovin TM, Hanau LH, Erlanger BF, Wells RD. Intervening sequences in human fetal globin genes adopt left-handed Z helices. J Biol Chem 1984. [DOI: 10.1016/s0021-9258(17)39867-8] [Citation(s) in RCA: 72] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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44
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Singleton CK, Kilpatrick MW, Wells RD. S1 nuclease recognizes DNA conformational junctions between left-handed helical (dT-dG n. dC-dA)n and contiguous right-handed sequences. J Biol Chem 1984; 259:1963-7. [PMID: 6319416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The ability of negative supercoiling to induce a left-handed helix in the recombinant plasmid pRW777, which contains a tract of 64 base pairs of almost perfect (dT-dG) . (dC-dA) from the mouse kappa immunoglobin gene, was studied. S1 nuclease recognizes and cleaves within the junction region which must exist adjacent to the (dT-dG)n . (dC-dA)n tract when in a left-handed state. The cleavage pattern indicates conformational flexibility and structural differences between the two existing junctions. The 64-base pair alternating copolymer undergoes the supercoil-induced formation of a left-handed state over the superhelical density range of -0.04 to -0.06, indicating that (dT-dG)n . (dC-dA) sequences form a left-handed helix less readily than (dC-dG)n . (dC-dG)n sequences of equivalent length. However, these supercoil densities are within the range found in vivo. Supercoil relaxation and antibody binding studies confirmed that the (dT-dG)n . (dC-dA)n tract in supercoiled pRW777 was in a left-handed helix.
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Singleton CK, Kilpatrick MW, Wells RD. S1 nuclease recognizes DNA conformational junctions between left-handed helical (dT-dG n. dC-dA)n and contiguous right-handed sequences. J Biol Chem 1984. [DOI: 10.1016/s0021-9258(17)43501-0] [Citation(s) in RCA: 77] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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46
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O'Connor T, Kilpatrick MW, Klysik J, Larson JE, Martin JC, Singleton CK, Stirdivant SM, Zacharias W, Wells RD. Left-handed Z-DNA helices in polymers, restriction fragments, and recombinant plasmids. J Biomol Struct Dyn 1983; 1:999-1009. [PMID: 6101088 DOI: 10.1080/07391102.1983.10507498] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Studies on DNA polymers, restriction fragments, and recombinant plasmids have revealed the following: A) A family of left-handed DNA conformations exists for (dC-dG)n.(dC-dG)n. The observation of a particular conformation is dependent on the salt, the salt concentration and dehydrating agent. B) In sodium acetate solutions, (dC-dG)n.(dC-dG)n forms left-handed, psi(+)-condensed structures as detected by Raman spectroscopy and circular dichroism. C) (dT-dG)n.(dC-dA)n undergoes a right-to-left-handed transition only when reacted with AAF and at high salt concentrations. D) Transitions observed for polymer DNAs also are observed for restriction fragments containing both (dC-dG).(dC-dG) and (dT-dG).(dC-dA) sequences, but the transitions in the fragments generally require higher salt concentrations than observed for the polymers. E) Studies with recombinant plasmids containing (dC-dG) sequences from 10 to 58 bp in length demonstrate that left-handed Z-DNA segments can exist contiguous to B-DNA segments. F) Negative supercoil density (sigma less than or equal to -0.072) is sufficient to convert the (dC-dG) regions in those plasmids into left-handed structures under physiological ionic conditions (200 mM NaCl). G) The favorable free energy contribution of methylation in stabilizing the Z form in fragments and plasmids is approximately offset by the unfavorable free energy contributions of the B/Z junctions. H) Sl and BAL 31 nucleases recognize aberrant structural features at the confluence of the B and Z regions. I) Detailed mapping of Sl nuclease cleavage on supercoiled plasmids shows that the nuclease sensitive regions extend over at least five to ten bp. J) Even though the (dT-dG)n.(dC-dA)n polymer requires base modification and high salt conditions to undergo the R----L transition, supercoiling (sigma less than or equal to -0.07) can supply enough energy to allow a plasmid containing the intervening sequence of a human fetal globin gene with (dT-dG).(dC-dA) sequences to undergo a R----L transition.
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Kilpatrick MW, Wei CF, Gray HB, Wells RD. BAL 31 nuclease as a probe in concentrated salt for the B-Z DNA junction. Nucleic Acids Res 1983; 11:3811-22. [PMID: 6304643 PMCID: PMC326004 DOI: 10.1093/nar/11.11.3811] [Citation(s) in RCA: 65] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The BAL 31 nuclease, an extracellular nuclease from A. espejiana, specifically recognizes and cleaves the salt induced conformational junction between B and Z-DNA. Short segments of (dC-dG) left-handed Z-helix, comprising approximately 1% of the total DNA, are specifically detected within two different recombinant plasmids. The BAL 31 enzyme is highly resistant to inactivation by the presence of high concentrations of a variety of electrolytes that stabilize left-handed helices, is active at physiological pH, and can be used to probe both linear and circular DNAs. Additionally, the nuclease cleaves left-handed (dC-dG)n only very poorly, if at all. Thus, the BAL 31 nuclease can be utilized as a probe for helical junctions and consequently for segments of left-handed DNA that might exist within predominantly right-handed naturally occurring genomes.
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48
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Wells RD, Brennan R, Chapman KA, Goodman TC, Hart PA, Hillen W, Kellogg DR, Kilpatrick MW, Klein RD, Klysik J, Lambert PF, Larson JE, Miglietta JJ, Neuendorf SK, O'Connor TR, Singleton CK, Stirdivant SM, Veneziale CM, Wartell RM, Zacharias W. Left-handed DNA helices, supercoiling, and the B-Z junction. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 1983; 47 Pt 1:77-84. [PMID: 6345066 DOI: 10.1101/sqb.1983.047.01.010] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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49
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Walker RT, Chelton ET, Kilpatrick MW, Rogers MJ, Simmons J. The nucleotide sequence of the 5S rRNA from Spiroplasma species BC3 and Mycoplasma mycoides sp. capri PG3. Nucleic Acids Res 1982; 10:6363-7. [PMID: 6757862 PMCID: PMC326925 DOI: 10.1093/nar/10.20.6363] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Using in vitro labelling techniques, the complete nucleotide sequence of the 5S ribosomal RNAs isolated from the honeybee pathogen, Spiroplasma species BC3 and Mycoplasma mycoides sp. capri PG3, have been determined. The latter shows only 3 differences from the reported sequence of M. capricolum 5S rRNA, indicating that these two species are very closely related. The Spiroplasma sequence is also 107 nucleotides long and a comparative analysis of the sequence confirms that this Spiroplasma species is closely related to the Mycoplasma species and that they and the Gram-positive eubacteria have descended from a common ancestor and in the process the cell wall-less organisms have lost a large percentage of their genome.
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Kilpatrick MW, Walker RT. The nucleotide sequence of the tRNAMMet from the archaebacterium Thermoplasma acidophilum. Nucleic Acids Res 1981; 9:4387-90. [PMID: 6913864 PMCID: PMC327441 DOI: 10.1093/nar/9.17.4387] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Using in vitro labelling techniques, a tRNAMMet from Thermoplasma acidophilum, a member of the Archaebacteriae, has been shown to have the sequence: pGCCGGG Gs4UGGCUCANCUGGAGGAGC m2(2)GCCGGACmUCAUt6AAUCCGGAGGUCUCGGG psi psi CmGAUCCCCGAUCCCGGCACCAOH. Despite the small genome size of this non-parasitic organism, eight modified nucleosides are present, one of which is typically eubacterial, one of which is typically eukaryotic and some of which appear to be unique to the archaebacteria. There is no close sequence homology between this tRNA and that of any other methionine tRNA so far sequenced (less than 70%) but it has almost 90% homology with the nucleotide sequence proposed by Eigen and Oswatitsch for the ancestral quasi-species.
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