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Broude NE, Woodward K, Cavallo R, Cantor CR, Englert D. DNA microarrays with stem-loop DNA probes: preparation and applications. Nucleic Acids Res 2001; 29:E92. [PMID: 11574694 PMCID: PMC60252 DOI: 10.1093/nar/29.19.e92] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2001] [Revised: 07/15/2001] [Accepted: 08/01/2001] [Indexed: 11/13/2022] Open
Abstract
We have developed DNA microarrays containing stem-loop DNA probes with short single-stranded overhangs immobilized on a Packard HydroGel chip, a 3-dimensional porous gel substrate. Microarrays were fabricated by immobilizing self-complementary single-stranded oligonucleotides, which adopt a partially duplex structure upon denaturing and re-annealing. Hybridization of single-stranded DNA targets to such arrays is enhanced by contiguous stacking interactions with stem-loop probes and is highly sequence specific. Subsequent enzymatic ligation of the targets to the probes followed by stringent washing further enhances the mismatched base discrimination. We demonstrate here that these microarrays provide excellent specificity with signal-to-background ratios of from 10- to 300-fold. In a comparative study, we demonstrated that HydroGel arrays display 10-30 times higher hybridization signals than some solid surface DNA microarrays. Using Sanger sequencing reactions, we have also developed a method for preparing nested 3'-deletion sets from a target and evaluated the use of stem-loop DNA arrays for detecting p53 mutations in the deletion set. The stem-loop DNA array format is simple, robust and flexible in design, thus it is potentially useful in various DNA diagnostic tests.
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Affiliation(s)
- N E Broude
- Center for Advanced Biotechnology and Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA.
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2
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Abstract
We present data on efficient amplification of large number of DNA targets using a single-tube polymerase chain reaction (PCR). This is a further enhancement of our approach to multiplexed PCR based on PCR suppression, which allows multiple DNA amplification using only one sequence-specific primer per amplicon while the second primer is common for all targets (Broude, N.E., et al., Proc. Natl. Acad. Sci. USA 98, 206-211, 2001). The reaction conditions have been optimized for simultaneous synthesis of 30 DNA targets, mostly consisting of fragments containing single nucleotide polymorphisms (SNP). The size of the amplified fragments, derived from many different human chromosomes, varies from 100 to 600 bp. We conclude that this method has potential for highly multiplexed DNA amplification useful for SNP analyses, DNA diagnostics, and forensics.
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Affiliation(s)
- N E Broude
- Center for Advanced Biotechnology and Department of Biomedical Engineering, Boston University, MA 02215, USA.
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3
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Abstract
Double-stranded (ds) DNA is capable of the sequence-specific accommodation of an additional oligodeoxyribonucleotide strand by the peptide nucleic acid(PNA)-assisted formation of a so-called PD-loop. We demonstrate here that the PD-loop may function as an artificial primosome within linear, nonsupercoiled DNA duplexes. DNA polymerase with its strand displacement activity uses this construct to initiate the primer extension reaction at a designated dsDNA site. The primer is extended by several hundred nucleotides. The efficiency of dsDNA priming by the artificial primosome assembly is comparable to the single-stranded DNA priming used in various assays. The ability of the PD-loop structure to perform like an artificial primosome on linear dsDNA may find applications in biochemistry, molecular biology, and molecular biotechnology, as well as for DNA diagnostics. In particular, multiple labels can be incorporated into a chosen dsDNA site resulting in ultrasensitive direct quantification of specific sequences. Furthermore, nondenaturing dsDNA sequencing proceeds from the PD-loop. This approach opens the way to direct isothermal reading of the DNA sequence against a background of unrelated DNA, thereby eliminating the need for purification of the target DNA.
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Affiliation(s)
- V V Demidov
- Center for Advanced Biotechnology, Department of Biomedical Engineering, Boston University, 36 Cummington Street, Boston, MA 02215, USA.
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4
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Abstract
We have developed a strategy for multiplex PCR based on PCR suppression. PCR suppression allows DNA target amplification with only one sequence-specific primer per target and a second primer that is common for all targets. Therefore, an n-plex PCR would require only n + 1 primers. We have demonstrated uniform, efficient amplification of targeted sequences in 14-plex PCR. The high specificity of suppression PCR also provides multiplexed amplification with allele specificity. Multiplexed PCR was used to develop assays for genotyping DNA samples from cystic fibrosis-affected individuals. The new approach greatly simplifies primer design, significantly increases the PCR multiplexing level, and decreases the overall primer cost. In addition, this assay is more readily amenable to automation and is therefore suitable for high-throughput genetic diagnostics.
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Affiliation(s)
- N E Broude
- Center for Advanced Biotechnology and Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA.
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5
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Broude NE, Demidov VV, Kuhn H, Gorenstein J, Pulyaeva H, Volkovitsky P, Drukier AK, Frank-Kamenetskii MD. PNA openers as a tool for direct quantification of specific targets in duplex DNA. J Biomol Struct Dyn 1999; 17:237-44. [PMID: 10563573 DOI: 10.1080/07391102.1999.10508356] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
We report a new approach for target quantification directly within DNA duplex. Our assay is based on the formation of a new biomolecular structure, the PD-loop. The approach takes advantage of a selective hybridization of a probe to double-stranded DNA (dsDNA), which is locally opened by a pair of bis-PNA oligomers. To optimize the technique, several experimental formats are tested with the use of PNA and oligonucleotide probes. The highest sensitivity is achieved when the hybridized probe is extended and multiply labeled with 125I-dCTP by DNA polymerase via strand displacement in the presence of single-strand binding (SSB) protein. In this case, the PNA-assisted probe hybridization combined with the method of multiphoton detection (MPD) allows to monitor sub-attomolar amounts of the HIV-1 target on the background of unrelated DNA at sub-nCi level of radioactivity. The developed robust methodology is highly discriminative to single mutations, thus being of practical use for DNA analysis.
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Affiliation(s)
- N E Broude
- Center for Advanced Biotechnology, Department of Biomedical Engineering, Boston University, MA 02215, USA.
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6
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Abstract
We previously described a targeted genomic differential display method (TGDD: Broude NE, Chandra A, Smith CL. Differential display of genomic subsets containing specific interspersed repeats. Proc. Natl. Acad. Sci. USA 1997;94:4548-53). In that method, presently characterized as method I, targeting was accomplished by capturing DNA fragments containing specific a sequence by hybridization with complementary single-stranded DNA. The captured fragments were amplified by PCR. Here, we describe method II where targeting is accomplished by PCR using primers specific to the target sequence. Method II takes advantage of PCR suppression to eliminate fragments not containing the target sequence (Siebert PDA, Chenchik A, Kellogg DE, Lukyanov KA and Lukyanov SA. An improved PCR method for walking in uncloned genomic DNA. Nucleic Acids Res 1995;23:1087-1088). Targeting focuses analysis on and around interesting areas and additionally serves to reduce the complexity of the amplified subset. These approaches are useful to amplify genome subsets containing a variety of targets including various conserved sequences coding for cis-acting elements or protein motifs.
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Affiliation(s)
- N E Broude
- Center for Advanced Biotechnology, Boston University, MA 02215, USA
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7
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Lavrentieva I, Broude NE, Lebedev Y, Gottesman II, Lukyanov SA, Smith CL, Sverdlov ED. High polymorphism level of genomic sequences flanking insertion sites of human endogenous retroviral long terminal repeats. FEBS Lett 1999; 443:341-7. [PMID: 10025960 DOI: 10.1016/s0014-5793(99)00004-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The polymorphism at the multitude of loci adjacent to human endogenous retrovirus long terminal repeats (LTRs) was analyzed by a technique for whole genome differential display based on the PCR suppression effect that provides selective amplification and display of genomic sequences flanking interspersed repeated elements. This strategy is simple, target-specific, requires a small amount of DNA and provides reproducible and highly informative data. The average frequency of polymorphism observed in the vicinity of the LTR insertion sites was found to be about 12%. The high incidence of polymorphism within the LTR flanks together with the frequent location of LTRs near genes makes the LTR loci a useful source of polymorphic markers for gene mapping.
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Affiliation(s)
- I Lavrentieva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow
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8
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Oliveira RP, Broude NE, Macedo AM, Cantor CR, Smith CL, Pena SD. Probing the genetic population structure of Trypanosoma cruzi with polymorphic microsatellites. Proc Natl Acad Sci U S A 1998; 95:3776-80. [PMID: 9520443 PMCID: PMC19913 DOI: 10.1073/pnas.95.7.3776] [Citation(s) in RCA: 131] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
We describe here the identification of eight polymorphic microsatellite loci with (CA)n repeats in the Trypanosoma cruzi genome based on the affinity capture of fragments using biotinylated (CA)12 attached to streptavidin-coated magnetic beads. The presence of two peaks in PCR amplification products from individual clones confirmed that T. cruzi is diploid. Hardy-Weinberg and linkage disequilibrium analyses suggested that sexual reproduction is rare or absent and that the population structure is clonal. Several strains, especially those isolated from nonhuman sources, showed more than two alleles in many loci demonstrating that they were multiclonal. The phylogenetic analysis of T. cruzi based on microsatellites revealed a great genetic distance among strains, although the strain dispersion profile in the Wagner network was in general agreement with the species dimorphism found by PCR amplification of the divergent region of the rRNA 24Salpha gene.
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Affiliation(s)
- R P Oliveira
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901 Brazil
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9
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Cantor CR, Sano T, Broude NE, Smith CL. Instrumentation in molecular biomedical diagnostics: an overview. Genet Anal 1997; 14:31-6. [PMID: 9349936 DOI: 10.1016/s1050-3862(97)00006-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- C R Cantor
- Center for Advanced Biotechnology, Boston University, MA 02215, USA.
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10
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Abstract
A genomic differential display method was developed that analyzes many restriction fragment length polymorphisms simultaneously. Interspersed repeat sequences were used to reduce DNA sample complexity and to target genomic subsets of interest. This work focused on trinucleotide repeats because of their importance in human inherited diseases. Immobilized repeat-containing oligonucleotides were used to capture genomic DNA fragments containing sequences complementary to the oligonucleotide. Captured fragments were amplified by PCR and fluorescently labeled using primers complementary to the repeat sequence and/or to the known sequences ligated to the ends of the restriction fragments. The labeled PCR fragments were displayed by size on a high-resolution automated fluorescent DNA sequencing instrument. Although there was a conservation in the overall pattern of displayed genome subsets, many clear and reproducible differences were detected when genomes from different individuals were compared. Fewer differences were detected within, than between, monozygotic twin pair genomes. In control experiments, the method distinguished between Huntington disease alleles with normal and expanded CAG repeat lengths.
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Affiliation(s)
- N E Broude
- Department of Biomedical Engineering, Boston University, 36 Cummington Street, Boston, MA 02215, USA
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11
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Fu DJ, Broude NE, Köster H, Smith CL, Cantor CR. Efficient preparation of short DNA sequence ladders potentially suitable for MALDI-TOF DNA sequencing. Genet Anal 1996; 12:137-42. [PMID: 8673738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Duplex probes with five-base single-stranded overhangs were developed for positional sequencing by hybridization [Broude et al., Proc Natl Acad Sci USA 91:3072-3076, 1994]. The partially duplex probes can be employed to capture single-stranded oligonucleotide targets and form primer-template complexes. Recently we showed that partially duplex probes can prime Sanger sequencing reactions on immobilized, but non-ligated long single-stranded targets (approximately 500 nucleotide) [Fu et al., Proc Natl Acad Sci, in press]. Here immobilized, non-ligated partially duplex probes were used to capture and sequence short single-stranded targets. This strategy is capable of rapidly preparing large numbers of samples for future mass spectrometric DNA sequencing.
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Affiliation(s)
- D J Fu
- Sequenom, Inc., Boston, MA 02210, USA
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12
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Fu DJ, Broude NE, Köster H, Smith CL, Cantor CR. A DNA sequencing strategy that requires only five bases of known terminal sequence for priming. Proc Natl Acad Sci U S A 1995; 92:10162-6. [PMID: 7479746 PMCID: PMC40756 DOI: 10.1073/pnas.92.22.10162] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
We have previously reported an enhanced version of sequencing by hybridization (SBH), termed positional SBH (PSBH). PSBH uses partially duplex probes containing single-stranded 3' overhangs, instead of simple single-stranded probes. Stacking interactions between the duplex probe and a single-stranded target allow us to reduce the probe sizes required to 5-base single-stranded overhangs. Here we demonstrate the use of PSBH to capture relatively long single-stranded DNA targets and perform standard solid-state Sanger sequencing on these primer-template complexes without ligation. Our results indicate that only 5 bases of known terminal sequence are required for priming. In addition, the partially duplex probes have the ability to capture their specific target from a mixture of five single-stranded targets with different 3'-terminal sequences. This indicates the potential utility of the PSBH approach to sequence mixtures of DNA targets without prior purification.
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Affiliation(s)
- D J Fu
- Sequenom, Inc., Boston, MA 02210, USA
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13
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Abstract
An enhanced version of DNA sequencing by hybridization (SBH), termed positional SBH (PSBH), has been developed. PSBH uses duplex probes containing single-stranded 3' overhangs, instead of simple single-stranded probes. Stacking interactions between the duplex probe and a single-stranded target should provide enhanced stringency in distinguishing perfectly matched 3' sequences. A second enhancement is the use of enzyme-catalyzed steps, instead of pure physical hybridization. The feasibility of this scheme has been investigated using biotinylated duplex probes containing single-stranded 5-base 3' overhangs, immobilized on streptavidin-coated magnetic beads. Ligation of a single-stranded target, hybridized to the single-stranded region of the duplex probes, provided enhanced discrimination of perfectly matched targets from those containing mismatches. In distinction to the serious complications caused by base composition effects in ordinary SBH, there was little effect of base composition in PSBH. The hardest mismatch to discriminate was the one furthest from the phosphodiester bond formed by ligation. However, mismatches in this position were efficiently discriminated by 3' extension of the duplex probe using a template-dependent DNA polymerase. These results demonstrate that PSBH offers considerable promise to facilitate actual implementations of SBH.
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Affiliation(s)
- N E Broude
- Center for Advanced Biotechnology, Boston University, MA 02215
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14
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Sverdlov ED, Broude NE, Monastyrskaya GS. Ion-transporting ATPases: reverse genetics and direct logic. Mol Gen Mikrobiol Virusol 1993:3-9. [PMID: 8289845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- E D Sverdlov
- Shemyakin Institute of Biorganic Chemistry, Russian Academy of Sciences, Moscow
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15
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Akopyanz NS, Broude NE, Bekman EP, Marzen EO, Sverdlov ED. Tissue-specific expression of Na,K-ATPase beta-subunit. Does beta 2 expression correlate with tumorigenesis? FEBS Lett 1991; 289:8-10. [PMID: 1654277 DOI: 10.1016/0014-5793(91)80896-b] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We have found a substantial decrease in the level of Na,K-ATPase beta 2-subunit mRNA in xenografts of human renal, lung hepatocellular carcinomas in nude mice as compared with corresponding normal tissues, as well as in the neuroblastoma cell line as compared with the neuron primary cell culture. The level of beta 1 mRNA is decreased in kidney and lung tumor cells, but is unchanged in hepatocellular carcinoma. In the neuroblastoma cell line the level of beta 1 subunit mRNA was found to be higher then in neuron primary cell culture. The level of alpha 1 mRNA in investigated tumors was the same as in normal tissues. These results may give evidence of the involvement of beta 2-subunit in the process of tumorigenesis as was shown for some other adhesion molecules.
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Affiliation(s)
- N S Akopyanz
- Shemyakin Institute of Bioorganic Chemistry, USSR Academy of Sciences, Moscow
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16
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Modyanov NN, Petrukhin KE, Sverdlov VE, Grishin AV, Orlova MY, Kostina MB, Makarevich OI, Broude NE, Monastyrskaya GS, Sverdlov ED. The family of human Na,K-ATPase genes. ATP1AL1 gene is transcriptionally competent and probably encodes the related ion transport ATPase. FEBS Lett 1991; 278:91-4. [PMID: 1847115 DOI: 10.1016/0014-5793(91)80091-g] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The multigene family of human Na,K-ATPase is composed of 5 alpha-subunit genes, 3 of which were shown to encode the functionally active alpha 1, alpha 2 and alpha 3 isoforms of the catalytic subunits. This report describes the isolation, mapping and partial sequencing of the fourth gene (ATP1AL1) that was demonstrated here to be functionally active and expressed in human brain and kidney. Limited DNA sequencing of the ATP1AL1 exons allowed one to suggest that the gene probably encodes a new ion transport ATPase rather than an isoform of the Na,K-ATPase or the closely related H,K-ATPase.
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Affiliation(s)
- N N Modyanov
- Shemyakin Institute of Bioorganic Chemistry, USSR Academy of Sciences, Moscow
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17
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Ushkaryov YuA, Monastyrskaya GS, Broude NE, Nikiforova NN, Bessarab DA, Orlova MYu, Petrukhin KE, Modyanov NN, Sverdlov ED. Human Na+,K+-ATPase genes. Beta-subunit gene family contains at least one gene and one pseudogene. FEBS Lett 1989; 257:439-42. [PMID: 2555225 DOI: 10.1016/0014-5793(89)81591-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The existence of a chromosome gene family containing at least one gene and one pseudogene was shown for the Na+,K+-ATPase beta-subunit. A partial structure of the beta 1-gene was determined, the coding part of which was completely homologous to cDNA of the Na+,K+-ATPase beta I-subunit from HeLa cells. The region encoding the putative protein transmembrane domain was shown to be bordered by two introns. The structure of a pseudogene (beta psi) was determined. This pseudogene is processed and contains multiple stop codons. Its homology to the beta I-subunit cDNA from HeLa cells is about 88%.
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Affiliation(s)
- Ushkaryov YuA
- Shemyakin Institute of Bioorganic Chemistry, USSR Academy of Sciences, Moscow
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18
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Abstract
Complete primary structures of both subunits of Na+,K+-ATPase from various sources have been established by a combination of the methods for molecular cloning and protein chemistry. The gene family homologous to the alpha-subunit cDNA of animal Na+,K+-ATPases has been found in the human genome. Some genes of this family encode the known isoforms (alpha I and alpha II) of the Na+,K+-ATPase catalytic subunit. The proteins coded by other genes can be either new isoforms of the Na+,K+-ATPase catalytic subunit or other ion-transporting ATPases. Expression of the genes of this family proceeds in a tissue-specific manner and changes during the postnatal development and neoplastic transformation. The complete exon-intron structure of one of the genes of this family has been established. This gene codes for the form of the catalytic subunit, the existence of which has been unknown. Apparently, all the genes of the discovered family have a similar intron-exon structure. There is certain correlation between the gene structure and the proposed domain arrangement of the alpha-subunit. The results obtained have become the basis for the experiments which prove the existence of the earlier unknown alpha III isoform of the Na+,K+-ATPase catalytic subunit and have made possible the study of its function.
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Affiliation(s)
- N E Broude
- Sheyakin Institute of Bioorganic Chemistry, USSR Academy of Sciences, Moscow
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19
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Sverdlov ED, Bessarab DA, Malyshev IV, Petrukhin KE, Smirnov YuV, Ushkaryov YuA, Monastyrskaya GS, Broude NE, Modyanov NN. Family of human Na+,K+-ATPase genes. Structure of the putative regulatory region of the alpha+-gene. FEBS Lett 1989; 244:481-3. [PMID: 2537767 DOI: 10.1016/0014-5793(89)80588-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The primary structure of the putative regulatory region of a gene of the Na+,K+-ATPase multigene family in the human genome has been determined. This region includes the first exon with all of the untranslatable sequence of mRNA and a dozen nucleotides, coding for the first four amino acids of the hypothetic precursor of the alpha+-subunit. The entire region comprises over 1400 bp. The possible role of specific nucleotide blocks within this region in comparison with other genes is discussed.
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Affiliation(s)
- E D Sverdlov
- Shemyakin Institute of Bioorganic Chemistry, USSR Academy of Sciences, Moscow
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20
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Sverdlov ED, Akopyanz NS, Petrukhin KE, Broude NE, Monastyrskaya GS, Modyanov NN. Na+,K+-ATPase: tissue-specific expression of genes coding for alpha-subunit in diverse human tissues. FEBS Lett 1988; 239:65-8. [PMID: 2846349 DOI: 10.1016/0014-5793(88)80546-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The expression of genes coding for alpha and alpha III isoforms of Na+,K+-ATPase alpha-subunit has been studied in human kidney, brain, thyroid and liver cells. The expression was shown to be subjected to a tissue-specific control and also depended on the developmental stage. The tissue-specific expression of genes coding for different isoforms of the catalytic subunit of Na+,K+-ATPase perhaps may be attributed to various functions of proteins belonging to this family.
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Affiliation(s)
- E D Sverdlov
- Shemyakin Institute of Bioorganic Chemistry, USSR Academy of Sciences, Moscow
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21
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Khlebodarova TM, Karasik GI, Lapteva SE, Matveeva NM, Serov OL, Sverdlov ED, Broude NE, Modyanov NN, Monastyrskaya GS. Chromosomal localization of the gene coding for the beta-subunit of Na+,K+-ATPase in the American mink (Mustela vison). FEBS Lett 1988; 236:240-2. [PMID: 2841166 DOI: 10.1016/0014-5793(88)80322-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The BATP gene coding for the beta-subunit of Na+,K+-ATPase has been localized on chromosome 13 of the American mink (Mustela vison) using mink-Chinese hamster somatic cell hybrids and pig cDNA clones as probes. The AATP gene for the alpha-subunit of Na+,K+-ATPase is on mink chromosome 2 [(1987) FEBS Lett. 217, 42-44]. Consequently, the AATP and BATP genes for the Na+,K+-ATPase occupy separate mink chromosomes.
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Affiliation(s)
- T M Khlebodarova
- Institute of Cytology and Genetics, USSR Academy of Sciences, Siberian Department, Novosibirsk
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22
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Abstract
The phenomenon of transformation of E. coli cells under electric treatment has been studied. The cells of strains MH 1, HB 101 and DH 1 after EDTA treatment in an isotonic medium were transformed with DNA pBR322 by applying a single exponential pulse (E = 10 kV/cm, T = 1.5 ms) to the suspension. The maximum transformation efficiency obtained was 4 X 10(6) colonies/micrograms DNA. The maximum transformation frequency was 0.4% at a DNA concentration of 15 micrograms/ml.
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Affiliation(s)
- E S Cymbalyuk
- A.N. Frumkin Institute of Electrochemistry, USSR Academy of Sciences, Moscow
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23
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Affiliation(s)
- K E Petrukhin
- M.M. Shemyakin Institute of Bioorganic Chemistry, USSR Academy of Sciences, Moscow
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24
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Ovchinnikov YuA, Monastyrskaya GS, Broude NE, Ushkaryov YuA, Melkov AM, Smirnov YuV, Malyshev IV, Allikmets RL, Kostina MB, Dulubova IE. Family of human Na+, K+-ATPase genes. Structure of the gene for the catalytic subunit (alpha III-form) and its relationship with structural features of the protein. FEBS Lett 1988; 233:87-94. [PMID: 2838329 DOI: 10.1016/0014-5793(88)81361-9] [Citation(s) in RCA: 63] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The primary structure of a gene of the Na+, K+-ATPase multigenic family in the human genome has been determined. The gene corresponds to a hypothetical alpha III-form of the enzyme catalytic subunit. The gene comprises over 25,000 bp, and its protein coding region includes 23 exons and 22 introns. Possible correlation between structural features of the protein and location of introns in the gene are discussed.
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Affiliation(s)
- Ovchinnikov YuA
- Shemyakin Institute of Bioorganic Chemistry, USSR Academy of Sciences, Moscow
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25
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Sverdlov ED, Petrukhin KE, Akop'iants NS, Broude NE, Monastyrskaia GS. [Differential expression of 2 genes of the Na+,K+-AtPase subunit in normal and tumor tissues in humans]. Dokl Akad Nauk SSSR 1988; 298:236-9. [PMID: 2834164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Sverdlov VE, Broude NE, Monastyrskaia GS, Sverdlov ED, Grishin AV. [DNA from various mammalian organs gives different restriction fragments during hybridization with cDNA for Na+,K+-ATPase alpha- and beta-subunits]. Dokl Akad Nauk SSSR 1987; 296:236-8. [PMID: 2824158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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27
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Sverdlov ED, Broude NE, Sverdlov VE, Monastyrskaya GS, Grishin AV, Petrukhin KE, Akopyanz NS, Modyanov NN, Ovchinnikov YuA. Family of Na+,K+-ATPase genes. Intra-individual tissue-specific restriction fragment length polymorphism. FEBS Lett 1987; 221:129-33. [PMID: 2887455 DOI: 10.1016/0014-5793(87)80366-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Intra-individual tissue-specific restriction fragment length polymorphism (RFLP) has been demonstrated in DNA isolated from different mammalian tissues using cDNAs of alpha- and beta-subunits of Na+,K+-ATPase as hybridization probes. We propose that the RFLPs could result from gene rearrangements in the gene loci for the alpha- and beta-subunits of Na+,K+-ATPase. The changes in restriction patterns have been shown to occur during embryonic development and tumor formation. In addition, the tissue specificity of the expression of different genes of the family of Na+,K+-ATPase genes and their low expression in tumor cells have been demonstrated.
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Sverdlov ED, Monastyrskaya GS, Broude NE, Ushkaryov YuA, Allikmets RL, Melkov AM, Smirnov YuV, Malyshev IV, Dulobova IE, Petrukhin KE. The family of human Na+,K+-ATPase genes. No less than five genes and/or pseudogenes related to the alpha-subunit. FEBS Lett 1987; 217:275-8. [PMID: 3036582 DOI: 10.1016/0014-5793(87)80677-4] [Citation(s) in RCA: 72] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Five different nucleotide sequences have been found in the human genome homologous to the gene of the alpha-subunit of Na+,K+-ATPase. A comparative analysis of the primary structure of these genes in the region 749-1328 (in coordinates of cDNA from the pig alpha-subunit) is presented.
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Matveeva NM, Khlebodarova TM, Karasik GI, Rubtsov NB, Serov OL, Sverdlov ED, Broude NE, Modyanov NN, Monastyrskaya GS. Chromosomal localization of the gene coding for alpha-subunit of Na+,K+-ATPase in the American mink (Mustela vison). FEBS Lett 1987; 217:42-4. [PMID: 3036574 DOI: 10.1016/0014-5793(87)81238-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The gene coding for the alpha-subunit of Na+,K+-ATPase has been localized on chromosome 2 of the American mink (Mustela vison) using the somatic cell hybrids mink-Chinese hamster and pig cDNA clones as hybridization probes.
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Monastyrskaya GS, Broude NE, Allikmets RL, Melkov AM, Malyshev IV, Dulubova IE, Petrukhin KE. The family of human Na+,K+-ATPase genes. A partial nucleotide sequence related to the alpha-subunit. FEBS Lett 1987; 213:73-80. [PMID: 3030810 DOI: 10.1016/0014-5793(87)81467-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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31
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Broude NE, Monastyrskaia GS, Petrukhin KE, Grishin AV, Kiiatkin NI. [Primary structure of the beta-subunit of Na+,K+-ATPase from the swine kidney. II. Reverse transcription, cloning of mRNA, complete nucleotide sequence corresponding to the structural region of the gene]. Bioorg Khim 1987; 13:14-9. [PMID: 2436627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
mRNA coding for beta-subunit of Na+, K+-ATPase from pig kidney is about 24-25S as deduced from the hybridization pattern of poly (A)+-RNA with two synthetic oligonucleotides structurally corresponding to two peptides isolated from the tryptic hydrolyzate of beta-subunit. Cloning of cDNA allowed to determine the complete structure of the gene and to deduce the amino acid sequence of beta-subunit of Na+, K+-ATPase. The beta-subunit contains 302 amino acid residues and the protein is not processed at the N-nor at the C-terminus.
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Monastyrskaia GS, Broude NE, Melkov AM, Smirnov IV, Malyshev IV, Ahsenyan SG, Salomatina IS, Svehdlov VE, Grishin AV, Petrukhin KE, Modyanov NN. [Primary structure of the alpha-subunit of Na+,K+-ATPase from the swine kidney. III. Complete nucleotide sequence corresponding to the structural region of the gene]. Bioorg Khim 1987; 13:20-6. [PMID: 3032208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The nucleotide sequence of the cDNA, containing coding region of the alpha-subunit of the pig kidney Na+, K+-ATPase, was determined. The region contains 3063 b.p. coding for 1021 amino acid residues. In the course of processing, five amino acid residues are cleaved to yield the mature Na+, K+-ATPase alpha-subunit containing 1016 amino acid residues.
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Modyanov NN, Broude NE, Petrukhin KE, Grishin AV, Arzamazova NM, Aldanova NA, Monastyrskaya GS, Sverdlov ED. Pig kidney Na+,K+-ATPase. Primary structure and spatial organization. FEBS Lett 1986; 201:237-45. [PMID: 2423371 DOI: 10.1016/0014-5793(86)80616-0] [Citation(s) in RCA: 191] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
cDNAs complementary to pig kidney mRNAs coding for alpha- and beta-subunits of Na+,K+-ATPase were cloned and sequenced. Selective tryptic hydrolysis of the alpha-subunit within the membrane-bound enzyme and tryptic hydrolysis of the immobilized isolated beta-subunit were also performed. The mature alpha- and beta-subunits contain 1016 and 302 amino acid residues, respectively. Structural data on the peptides from extramembrane regions of the alpha-subunit and on glycopeptides of the beta-subunit underlie a model for the transmembrane arrangement of Na+,K+-ATPase polypeptide chains.
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34
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Petrukhin KE, Grishin AV, Arsenian SG, Broude NE, Grinkevich VA. [Problems associated with the use of highly degenerated oligonucleotide probes. Identification of mRNA and cDNA clones corresponding to the gene for the alpha subunit of Na+,K+-ATPase]. Bioorg Khim 1985; 11:1636-41. [PMID: 3002392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Oligonucleotides deduced from the amino acid sequence of a hexapeptide Lys-Asp-Phe-Ala-Glu-Asn were synthesized and used as probes to screen a pig kidney cDNA library for a specific DNA sequence coding for the alpha-subunit of Na+, K+-ATPase. It was shown that the mixed oligoprobe, consisting of 64 heptadecamers, could be only suitable for mRNA blot analysis. To identify the clones with specific cDNA inserts, mixed oligoprobes were fractionated by HPLC technique. For the same purpose a new set of oligonucleotides, synthesized as four groups of 16 different heptadecamers each, was used.
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Petrukhin KE, Broude NE, Arsenian SG, Grishin AV, Dzhandzhurgazian KN. [Primary structure of the alpha subunit of Na+,K+-ATPase. II. Isolation, reverse transcription and cloning of messenger RNA]. Bioorg Khim 1985; 11:1607-13. [PMID: 2417606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Messenger RNA, coding for the alpha-subunit of the Na+, K+-ATPase, was isolated from outer medulla of pig kidney. Within 25S-26S region the mRNA yields a band of specific hybridization with three oligonucleotide probes synthesized according to data on structures of three peptides isolated from the tryptic hydrolysate of the protein. Translation of the enriched poly(A+)-fraction of RNA in Xenopus laevis oocytes followed by the immunochemical identification of the products confirmed the presence of RNA coding for the desired protein. This RNA preparation was used for synthesis and cloning of double stranded cDNA.
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Broude NE, Kussova KS, Medvedeva NI, Budowsky EI. Proteins of the 30-S subunit of Escherichia coli ribosomes which interact directly with natural mRNA. Eur J Biochem 1983; 132:139-45. [PMID: 6341057 DOI: 10.1111/j.1432-1033.1983.tb07338.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Ultraviolet irradiation (254 nm) of the complexes of MS2 phage RNA (mRNA) and the 30-S subunits of Escherichia coli ribosomes prepared at 0 degrees C and 37 degrees C in the presence and absence of initiation factor 3 (IF-3) causes cross-linking of mRNA with proteins S3, S4, S5, S7, S9, S18 and IF-3. Hence, these proteins interact directly with mRNA within the complex 30-S-subunit . mRNA. Addition of IF-3 results in an increase of the rate of complex formation and decrease of its dissociation rate. The addition of IF-3 changes the relative amounts of cross-linked proteins (mainly S3, S4 and S18). Decreasing the temperature from 37 degrees C to 0 degrees C not only decelerates the complex formation rate but also changes the relative amount of cross-linked proteins, indicating the influence of the conditions on the structure of the complex.
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Turchinsky MF, Broude NE, Kussova KS, Abduraschidova GG, Muchamedganova EV, Schatsky IN, Bystrova TF, Budowsky EI. Polynucleotide-protein interactions in the translation system. Detection of contacts between some ribosomal split proteins and 16-S RNA in 30-S subunits of Escherichia coli ribosomes. Eur J Biochem 1978; 90:83-8. [PMID: 361396 DOI: 10.1111/j.1432-1033.1978.tb12577.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Direct contacts between 16-S RNA and split proteins S2, S3, S5, S14 and S21 inside the 30-S subunit of Escherichia coli ribosomes were evidenced by the formation of ultraviolet-induced (lambda = 254 nm) RNA-protein cross-links. 30-S subunits were reassembled from core particles and a mixture of split proteins containing in each case a single 125I-labelled protein. All the proteins tested are cross-linked as a result of a single-hit process; proteins S3 and S21 were cross-linked at the highest rate.
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38
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Sverdlov ED, Gus'kova LI, Broude NE, Budovskiĭ EI. [A chemical approach to the stacking interaction study. I. Stacking interactions in cytidine-containing olignoucleotides]. Mol Biol 1974; 8:944-8. [PMID: 4469596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Broude NE, Budovskii EI, Venkstern TV, Shershneva LP. Modification of yeast tRNA1 Val with glyoxal. Mol Biol 1974; 7:733-40. [PMID: 4599328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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40
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Broude NE, Budowsky EI. The reaction of glyoxal with nucleic acid components. V. Denaturation of DNA under the action of glyoxal. Biochim Biophys Acta 1973; 294:378-84. [PMID: 4705992 DOI: 10.1016/0005-2787(73)90092-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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41
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Broude NE, Budowsky EI. The reaction of glyoxal with nucleic acid components. 3. Kinetics of the reaction with monomers. Biochim Biophys Acta 1971; 254:380-8. [PMID: 5137601 DOI: 10.1016/0005-2787(71)90868-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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42
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Mazurenko NN, Broude NE, Budowsky EI. Reaction of glyoxal with nucleic acid components. IV. Reduction of guanine-glyoxal adduct with sodium borohydride. Biochim Biophys Acta 1971; 254:389-92. [PMID: 5137602 DOI: 10.1016/0005-2787(71)90869-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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