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Bansal A, Kaushik S, Kukreti S. Non-canonical DNA structures: Diversity and disease association. Front Genet 2022; 13:959258. [PMID: 36134025 PMCID: PMC9483843 DOI: 10.3389/fgene.2022.959258] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/25/2022] [Indexed: 11/18/2022] Open
Abstract
A complete understanding of DNA double-helical structure discovered by James Watson and Francis Crick in 1953, unveil the importance and significance of DNA. For the last seven decades, this has been a leading light in the course of the development of modern biology and biomedical science. Apart from the predominant B-form, experimental shreds of evidence have revealed the existence of a sequence-dependent structural diversity, unusual non-canonical structures like hairpin, cruciform, Z-DNA, multistranded structures such as DNA triplex, G-quadruplex, i-motif forms, etc. The diversity in the DNA structure depends on various factors such as base sequence, ions, superhelical stress, and ligands. In response to these various factors, the polymorphism of DNA regulates various genes via different processes like replication, transcription, translation, and recombination. However, altered levels of gene expression are associated with many human genetic diseases including neurological disorders and cancer. These non-B-DNA structures are expected to play a key role in determining genetic stability, DNA damage and repair etc. The present review is a modest attempt to summarize the available literature, illustrating the occurrence of non-canonical structures at the molecular level in response to the environment and interaction with ligands and proteins. This would provide an insight to understand the biological functions of these unusual DNA structures and their recognition as potential therapeutic targets for diverse genetic diseases.
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Affiliation(s)
- Aparna Bansal
- Nucleic Acid Research Lab, Department of Chemistry, University of Delhi, Delhi, India
- Department of Chemistry, Hansraj College, University of Delhi, Delhi, India
| | - Shikha Kaushik
- Nucleic Acid Research Lab, Department of Chemistry, University of Delhi, Delhi, India
- Department of Chemistry, Rajdhani College, University of Delhi, New Delhi, India
| | - Shrikant Kukreti
- Nucleic Acid Research Lab, Department of Chemistry, University of Delhi, Delhi, India
- *Correspondence: Shrikant Kukreti,
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Khadangi F, Torkamanzehi A, Kerachian MA. Identification of missense and synonymous variants in Iranian patients suffering from autosomal dominant polycystic kidney disease. BMC Nephrol 2020; 21:408. [PMID: 32957937 PMCID: PMC7507688 DOI: 10.1186/s12882-020-02069-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 09/15/2020] [Indexed: 11/10/2022] Open
Abstract
Background Autosomal dominant polycystic kidney disease (ADPKD), the predominant type of inherited kidney disorder, occurs due to PKD1 and PKD2 gene mutations. ADPKD diagnosis is made primarily by kidney imaging. However, molecular genetic analysis is required to confirm the diagnosis. It is critical to perform a molecular genetic analysis when the imaging diagnosis is uncertain, particularly in simplex cases (i.e. a single occurrence in a family), in people with remarkably mild symptoms, or in individuals with atypical presentations. The main aim of this study is to determine the frequency of PKD1 gene mutations in Iranian patients with ADPKD diagnosis. Methods Genomic DNA was extracted from blood samples from 22 ADPKD patients, who were referred to the Qaem Hospital in Mashhad, Iran. By using appropriate primers, 16 end exons of PKD1 gene that are regional hotspots, were replicated with PCR. Then, PCR products were subjected to DNA directional Sanger sequencing. Results The DNA sequencing in the patients has shown that exons 35, 36 and 37 were non- polymorphic, and that most mutations had occurred in exons 44 and 45. In two patients, an exon-intron boundary mutation had occurred in intron 44. Most of the variants were missense and synonymous types. Conclusion In the present study, we have shown the occurrence of nine novel missense or synonymous variants in PKD1 gene. These data could contribute to an improved diagnostic and genetic counseling in clinical settings.
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Affiliation(s)
- Fatemeh Khadangi
- Department of Biology, University of Sistan and Baluchestan, Zahedan, Iran.,Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Adam Torkamanzehi
- Department of Biology, University of Sistan and Baluchestan, Zahedan, Iran
| | - Mohammad Amin Kerachian
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran. .,Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
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Gadgil RY, Romer EJ, Goodman CC, Rider SD, Damewood FJ, Barthelemy JR, Shin-Ya K, Hanenberg H, Leffak M. Replication stress at microsatellites causes DNA double-strand breaks and break-induced replication. J Biol Chem 2020; 295:15378-15397. [PMID: 32873711 DOI: 10.1074/jbc.ra120.013495] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 08/23/2020] [Indexed: 12/12/2022] Open
Abstract
Short tandemly repeated DNA sequences, termed microsatellites, are abundant in the human genome. These microsatellites exhibit length instability and susceptibility to DNA double-strand breaks (DSBs) due to their tendency to form stable non-B DNA structures. Replication-dependent microsatellite DSBs are linked to genome instability signatures in human developmental diseases and cancers. To probe the causes and consequences of microsatellite DSBs, we designed a dual-fluorescence reporter system to detect DSBs at expanded (CTG/CAG) n and polypurine/polypyrimidine (Pu/Py) mirror repeat structures alongside the c-myc replication origin integrated at a single ectopic chromosomal site. Restriction cleavage near the (CTG/CAG)100 microsatellite leads to homology-directed single-strand annealing between flanking AluY elements and reporter gene deletion that can be detected by flow cytometry. However, in the absence of restriction cleavage, endogenous and exogenous replication stressors induce DSBs at the (CTG/CAG)100 and Pu/Py microsatellites. DSBs map to a narrow region at the downstream edge of the (CTG)100 lagging-strand template. (CTG/CAG) n chromosome fragility is repeat length-dependent, whereas instability at the (Pu/Py) microsatellites depends on replication polarity. Strikingly, restriction-generated DSBs and replication-dependent DSBs are not repaired by the same mechanism. Knockdown of DNA damage response proteins increases (Rad18, polymerase (Pol) η, Pol κ) or decreases (Mus81) the sensitivity of the (CTG/CAG)100 microsatellites to replication stress. Replication stress and DSBs at the ectopic (CTG/CAG)100 microsatellite lead to break-induced replication and high-frequency mutagenesis at a flanking thymidine kinase gene. Our results show that non-B structure-prone microsatellites are susceptible to replication-dependent DSBs that cause genome instability.
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Affiliation(s)
- Rujuta Yashodhan Gadgil
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - Eric J Romer
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - Caitlin C Goodman
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - S Dean Rider
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - French J Damewood
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - Joanna R Barthelemy
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - Kazuo Shin-Ya
- Biomedical Information Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Helmut Hanenberg
- Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich Heine University, Düsseldorf, Germany; Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Michael Leffak
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA.
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Lea WA, Parnell SC, Wallace DP, Calvet JP, Zelenchuk LV, Alvarez NS, Ward CJ. Human-Specific Abnormal Alternative Splicing of Wild-Type PKD1 Induces Premature Termination of Polycystin-1. J Am Soc Nephrol 2018; 29:2482-2492. [PMID: 30185468 DOI: 10.1681/asn.2018040442] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 07/06/2018] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND The major form of autosomal dominant polycystic kidney disease is caused by heterozygous mutations in PKD1, the gene that encodes polycystin-1 (PC1). Unlike PKD1 genes in the mouse and most other mammals, human PKD1 is unusual in that it contains two long polypyrimidine tracts in introns 21 and 22 (2.5 kbp and 602 bp, respectively; 97% cytosine and thymine). Although these polypyrimidine tracts have been shown to form thermodynamically stable segments of triplex DNA that can cause DNA polymerase stalling and enhance the local mutation rate, the efficiency of transcription and splicing across these cytosine- and thymine-rich introns has been unexplored. METHODS We used RT-PCR and Western blotting (using an mAb to the N terminus) to probe splicing events over exons 20-24 in the mouse and human PKD1 genes as well as Nanopore sequencing to confirm the presence of multiple splice forms. RESULTS Analysis of PC1 indicates that humans, but not mice, have a smaller than expected protein product, which we call Trunc_PC1. The findings show that Trunc_PC1 is the protein product of abnormal differential splicing across introns 21 and 22 and that 28.8%-61.5% of PKD1 transcripts terminate early. CONCLUSIONS The presence of polypyrimidine tracts decreases levels of full-length PKD1 mRNA from normal alleles. In heterozygous individuals, low levels of full-length PC1 may reduce polycystin signaling below a critical "cystogenic" threshold.
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Affiliation(s)
- Wendy A Lea
- The Jared Grantham Kidney Institute and Departments of.,Internal Medicine
| | - Stephen C Parnell
- The Jared Grantham Kidney Institute and Departments of.,Biochemistry and Molecular Biology
| | - Darren P Wallace
- The Jared Grantham Kidney Institute and Departments of.,Internal Medicine.,Molecular and Integrative Physiology, and
| | - James P Calvet
- The Jared Grantham Kidney Institute and Departments of.,Biochemistry and Molecular Biology
| | - Lesya V Zelenchuk
- The Jared Grantham Kidney Institute and Departments of.,Internal Medicine
| | - Nehemiah S Alvarez
- Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas; and.,De Novo Genomics, Kansas City, Kansas
| | - Christopher J Ward
- The Jared Grantham Kidney Institute and Departments of .,Internal Medicine.,Biochemistry and Molecular Biology
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Cordido A, Besada-Cerecedo L, García-González MA. The Genetic and Cellular Basis of Autosomal Dominant Polycystic Kidney Disease-A Primer for Clinicians. Front Pediatr 2017; 5:279. [PMID: 29326913 PMCID: PMC5741702 DOI: 10.3389/fped.2017.00279] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 12/07/2017] [Indexed: 12/14/2022] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is one of the most common genetic disorders worldwide. In recent decades, the field has undergone a revolution, starting with the identification of causal ADPKD genes, including PKD1, PKD2, and the recently identified GANAB. In addition, advances defining the genetic mechanisms, protein localization and function, and the identification of numerous pathways involved in the disease process, have contributed to a better understanding of this illness. Together, this has led to a better prognosis, diagnosis, and treatment in clinical practice. In this mini review, we summarize and discuss new insights about the molecular mechanisms underlying ADPKD, including its genetics, protein function, and cellular pathways.
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Affiliation(s)
- Adrián Cordido
- Grupo de Genética y Biología del Desarrollo de las Enfermedades Renales, Laboratorio de Nefrología (n.° 11), Instituto de Investigación Sanitaria (IDIS), Complexo Hospitalario de Santiago de Compostela (CHUS), Santiago de Compostela, Spain
| | - Lara Besada-Cerecedo
- Grupo de Genética y Biología del Desarrollo de las Enfermedades Renales, Laboratorio de Nefrología (n.° 11), Instituto de Investigación Sanitaria (IDIS), Complexo Hospitalario de Santiago de Compostela (CHUS), Santiago de Compostela, Spain
| | - Miguel A García-González
- Grupo de Genética y Biología del Desarrollo de las Enfermedades Renales, Laboratorio de Nefrología (n.° 11), Instituto de Investigación Sanitaria (IDIS), Complexo Hospitalario de Santiago de Compostela (CHUS), Santiago de Compostela, Spain
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Abstract
Repetitive genomic sequences can adopt a number of alternative DNA structures that differ from the canonical B-form duplex (i.e. non-B DNA). These non-B DNA-forming sequences have been shown to have many important biological functions related to DNA metabolic processes; for example, they may have regulatory roles in DNA transcription and replication. In addition to these regulatory functions, non-B DNA can stimulate genetic instability in the presence or absence of DNA damage, via replication-dependent and/or replication-independent pathways. This review focuses on the interactions of non-B DNA conformations with DNA repair proteins and how these interactions impact genetic instability.
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Affiliation(s)
- Guliang Wang
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd. R1800, Austin, TX 78723, United States
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd. R1800, Austin, TX 78723, United States.
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Vasquez KM, Wang G. The yin and yang of repair mechanisms in DNA structure-induced genetic instability. Mutat Res 2013; 743-744:118-131. [PMID: 23219604 PMCID: PMC3661696 DOI: 10.1016/j.mrfmmm.2012.11.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 11/21/2012] [Accepted: 11/24/2012] [Indexed: 01/14/2023]
Abstract
DNA can adopt a variety of secondary structures that deviate from the canonical Watson-Crick B-DNA form. More than 10 types of non-canonical or non-B DNA secondary structures have been characterized, and the sequences that have the capacity to adopt such structures are very abundant in the human genome. Non-B DNA structures have been implicated in many important biological processes and can serve as sources of genetic instability, implicating them in disease and evolution. Non-B DNA conformations interact with a wide variety of proteins involved in replication, transcription, DNA repair, and chromatin architectural regulation. In this review, we will focus on the interactions of DNA repair proteins with non-B DNA and their roles in genetic instability, as the proteins and DNA involved in such interactions may represent plausible targets for selective therapeutic intervention.
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Affiliation(s)
- Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd. R1800, Austin, TX 78723, United States.
| | - Guliang Wang
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd. R1800, Austin, TX 78723, United States
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Abstract
Polycystic kidney diseases (PKDs) represent a large group of progressive renal disorders characterized by the development of renal cysts leading to end-stage renal disease. Enormous strides have been made in understanding the pathogenesis of PKDs and the development of new therapies. Studies of autosomal dominant and recessive polycystic kidney diseases converge on molecular mechanisms of cystogenesis, including ciliary abnormalities and intracellular calcium dysregulation, ultimately leading to increased proliferation, apoptosis and dedifferentiation. Here we review the pathobiology of PKD, highlighting recent progress in elucidating common molecular pathways of cystogenesis. We discuss available models and challenges for therapeutic discovery as well as summarize the results from preclinical experimental treatments targeting key disease-specific pathways.
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9
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Jain A, Wang G, Vasquez KM. DNA triple helices: biological consequences and therapeutic potential. Biochimie 2008; 90:1117-30. [PMID: 18331847 DOI: 10.1016/j.biochi.2008.02.011] [Citation(s) in RCA: 198] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2008] [Accepted: 02/08/2008] [Indexed: 01/25/2023]
Abstract
DNA structure is a critical element in determining its function. The DNA molecule is capable of adopting a variety of non-canonical structures, including three-stranded (i.e. triplex) structures, which will be the focus of this review. The ability to selectively modulate the activity of genes is a long-standing goal in molecular medicine. DNA triplex structures, either intermolecular triplexes formed by binding of an exogenously applied oligonucleotide to a target duplex sequence, or naturally occurring intramolecular triplexes (H-DNA) formed at endogenous mirror repeat sequences, present exploitable features that permit site-specific alteration of the genome. These structures can induce transcriptional repression and site-specific mutagenesis or recombination. Triplex-forming oligonucleotides (TFOs) can bind to duplex DNA in a sequence-specific fashion with high affinity, and can be used to direct DNA-modifying agents to selected sequences. H-DNA plays important roles in vivo and is inherently mutagenic and recombinogenic, such that elements of the H-DNA structure may be pharmacologically exploitable. In this review we discuss the biological consequences and therapeutic potential of triple helical DNA structures. We anticipate that the information provided will stimulate further investigations aimed toward improving DNA triplex-related gene targeting strategies for biotechnological and potential clinical applications.
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Affiliation(s)
- Aklank Jain
- Department of Carcinogenesis, University of Texas, M.D. Anderson Cancer Center, Science Park--Research Division, 1808 Park Road 1-C, P.O. Box 389, Smithville, TX 78957, USA
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Reed BY, McFann K, Bekheirnia MR, Reza Bekheirnia M, Nobakhthaghighi N, Nobkhthaghighi N, Masoumi A, Johnson AM, Shamshirsaz AA, Shamshiraz AA, Kelleher CL, Schrier RW. Variation in age at ESRD in autosomal dominant polycystic kidney disease. Am J Kidney Dis 2008; 51:173-83. [PMID: 18215695 PMCID: PMC2747334 DOI: 10.1053/j.ajkd.2007.10.037] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2007] [Accepted: 10/03/2007] [Indexed: 11/11/2022]
Abstract
BACKGROUND Heterogeneity manifest as more severe disease in successive generations has been attributed to genetic anticipation in patients with autosomal dominant polycystic kidney disease (ADPKD). We evaluated variation in age at end-stage renal disease (ESRD) in ADPKD families for evidence of anticipation. STUDY DESIGN Retrospective. SETTING & PARTICIPANTS 413 families with ADPKD seen at our single center between 1985 and 2004 (including 95 families with documented polycystic disease type 1 [PKD1] and 213 ADPKD families with parents born before 1930). PREDICTOR Generational status. OUTCOME Age at ESRD onset. MEASUREMENTS Time to ESRD was evaluated by using survival analysis, Cox regression, and descriptive statistics. Unstable trinucleotide repeat expansion was evaluated by means of genotyping in 6 PKD1 families. RESULTS We analyzed 413 ADPKD families (1,391 parent-offspring pairs) with known age at ESRD or last known age without ESRD (informative pairs). There was no difference in age at ESRD between parents and offspring by means of Cox regression after adjusting for correlations among family members and sex (hazard ratio, 1.019; 95% confidence interval, 0.919 to 1.13; P = 0.7). Similar analysis of PKD1 informative pairs and those with parents born before 1930 showed no differences in age at ESRD. Male ADPKD patients were 42% more likely to reach ESRD (P < 0.001), and male patients with documented PKD1 were 41% more likely to reach ESRD (P = 0.01) than female patients. LIMITATIONS Hypertension treatment unknown. CONCLUSIONS We found no evidence for anticipation of ESRD in patients with ADPKD; thus, the observed variation in age at ESRD may result from other genetic, sex, or environmental causes.
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Affiliation(s)
- Berenice Y Reed
- Department of Medicine, Division of Renal Diseases and Hypertension, American Indian and Alaska Native Program, University of Colorado at Denver and Health Sciences Center, Denver, CO 80262, USA.
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Bacolla A, Collins JR, Gold B, Chuzhanova N, Yi M, Stephens RM, Stefanov S, Olsh A, Jakupciak JP, Dean M, Lempicki RA, Cooper DN, Wells RD. Long homopurine*homopyrimidine sequences are characteristic of genes expressed in brain and the pseudoautosomal region. Nucleic Acids Res 2006; 34:2663-75. [PMID: 16714445 PMCID: PMC1464109 DOI: 10.1093/nar/gkl354] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2006] [Revised: 03/13/2006] [Accepted: 04/20/2006] [Indexed: 01/20/2023] Open
Abstract
Homo(purine*pyrimidine) sequences (R*Y tracts) with mirror repeat symmetries form stable triplexes that block replication and transcription and promote genetic rearrangements. A systematic search was conducted to map the location of the longest R*Y tracts in the human genome in order to assess their potential function(s). The 814 R*Y tracts with > or =250 uninterrupted base pairs were preferentially clustered in the pseudoautosomal region of the sex chromosomes and located in the introns of 228 annotated genes whose protein products were associated with functions at the cell membrane. These genes were highly expressed in the brain and particularly in genes associated with susceptibility to mental disorders, such as schizophrenia. The set of 1957 genes harboring the 2886 R*Y tracts with > or =100 uninterrupted base pairs was additionally enriched in proteins associated with phosphorylation, signal transduction, development and morphogenesis. Comparisons of the > or =250 bp R*Y tracts in the mouse and chimpanzee genomes indicated that these sequences have mutated faster than the surrounding regions and are longer in humans than in chimpanzees. These results support a role for long R*Y tracts in promoting recombination and genome diversity during evolution through destabilization of chromosomal DNA, thereby inducing repair and mutation.
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Affiliation(s)
- Albino Bacolla
- Institute of Biosciences and Technology, Center for Genome Research, Texas A&M University System Health Science Center, Texas Medical Center2121 West Holcombe Blvd, Houston, TX 77030, USA
- Advanced Biomedical Computing Center, NCI-FrederickFrederick, MD 21702, USA
- Laboratory of Genomic Diversity, NCI-FrederickFrederick, MD 21702, USA
- Biostatistics and Bioinformatics Unit, Cardiff UniversityCardiff CF14 4XN, UK
- Institute of Medical Genetics, Cardiff UniversityHeath Park, Cardiff CF14 4XN, UK
- National Institute of Standards and Technology, DNA Technologies Group, Biotechnology DivisionGaithersburg, MD 20899, USA
- Laboratory of Immunopathogenesis and Bioinformatics, SAIC-Frederick, Inc.Frederick, MD 21702, USA
| | - Jack R. Collins
- Advanced Biomedical Computing Center, NCI-FrederickFrederick, MD 21702, USA
| | - Bert Gold
- Laboratory of Genomic Diversity, NCI-FrederickFrederick, MD 21702, USA
| | - Nadia Chuzhanova
- Biostatistics and Bioinformatics Unit, Cardiff UniversityCardiff CF14 4XN, UK
- Institute of Medical Genetics, Cardiff UniversityHeath Park, Cardiff CF14 4XN, UK
| | - Ming Yi
- Advanced Biomedical Computing Center, NCI-FrederickFrederick, MD 21702, USA
| | - Robert M. Stephens
- Advanced Biomedical Computing Center, NCI-FrederickFrederick, MD 21702, USA
| | - Stefan Stefanov
- Laboratory of Genomic Diversity, NCI-FrederickFrederick, MD 21702, USA
| | - Adam Olsh
- Laboratory of Genomic Diversity, NCI-FrederickFrederick, MD 21702, USA
| | - John P. Jakupciak
- National Institute of Standards and Technology, DNA Technologies Group, Biotechnology DivisionGaithersburg, MD 20899, USA
| | - Michael Dean
- Laboratory of Genomic Diversity, NCI-FrederickFrederick, MD 21702, USA
| | - Richard A. Lempicki
- Laboratory of Immunopathogenesis and Bioinformatics, SAIC-Frederick, Inc.Frederick, MD 21702, USA
| | - David N. Cooper
- Institute of Medical Genetics, Cardiff UniversityHeath Park, Cardiff CF14 4XN, UK
| | - Robert D. Wells
- To whom correspondence should be addressed. Tel: +1 713 677 7651; Fax: +1 713 677 7689;
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12
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Vouk K, Strmecki L, Stekrova J, Reiterova J, Bidovec M, Hudler P, Kenig A, Jereb S, Zupanic-Pajnic I, Balazic J, Haarpaintner G, Leskovar B, Adamlje A, Skoflic A, Dovc R, Hojs R, Komel R. PKD1 and PKD2 mutations in Slovenian families with autosomal dominant polycystic kidney disease. BMC MEDICAL GENETICS 2006; 7:6. [PMID: 16430766 PMCID: PMC1434729 DOI: 10.1186/1471-2350-7-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2005] [Accepted: 01/23/2006] [Indexed: 11/13/2022]
Abstract
Background Autosomal dominant polycystic kidney disease (ADPKD) is a genetically heterogeneous disorder caused by mutations in at least two different loci. Prior to performing mutation screening, if DNA samples of sufficient number of family members are available, it is worthwhile to assign the gene involved in disease progression by the genetic linkage analysis. Methods We collected samples from 36 Slovene ADPKD families and performed linkage analysis in 16 of them. Linkage was assessed by the use of microsatellite polymorphic markers, four in the case of PKD1 (KG8, AC2.5, CW3 and CW2) and five for PKD2 (D4S1534, D4S2929, D4S1542, D4S1563 and D4S423). Partial PKD1 mutation screening was undertaken by analysing exons 23 and 31–46 and PKD2 . Results Lod scores indicated linkage to PKD1 in six families and to PKD2 in two families. One family was linked to none and in seven families linkage to both genes was possible. Partial PKD1 mutation screening was performed in 33 patients (including 20 patients from the families where linkage analysis could not be performed). We analysed PKD2 in 2 patients where lod scores indicated linkage to PKD2 and in 7 families where linkage to both genes was possible. We detected six mutations and eight polymorphisms in PKD1 and one mutation and three polymorphisms in PKD2. Conclusion In our study group of ADPKD patients we detected seven mutations: three frameshift, one missense, two nonsense and one putative splicing mutation. Three have been described previously and 4 are novel. Three newly described framesfift mutations in PKD1 seem to be associated with more severe clinical course of ADPKD. Previously described nonsense mutation in PKD2 seems to be associated with cysts in liver and milder clinical course.
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Affiliation(s)
- Katja Vouk
- Medical Centre for Molecular Biology, Institute of Biochemistry, Faculty of Medicine, Vrazov trg 2, 1000 Ljubljana, Slovenia
| | - Lana Strmecki
- Medical Centre for Molecular Biology, Institute of Biochemistry, Faculty of Medicine, Vrazov trg 2, 1000 Ljubljana, Slovenia
| | - Jitka Stekrova
- Department of Medical Genetics and Department of Nephrology,1Faculty of Medicine, Charles University, Albertov 2, 12800 Prague 2, Czech Republic
| | - Jana Reiterova
- Department of Medical Genetics and Department of Nephrology,1Faculty of Medicine, Charles University, Albertov 2, 12800 Prague 2, Czech Republic
| | - Matjaz Bidovec
- Children's Hospital Ljubljana, Clinic for Paediatric Nephrology and Radiology Unit, Vrazov trg 1, 1000 Ljubljana, Slovenia
| | - Petra Hudler
- Medical Centre for Molecular Biology, Institute of Biochemistry, Faculty of Medicine, Vrazov trg 2, 1000 Ljubljana, Slovenia
| | - Anton Kenig
- Children's Hospital Ljubljana, Clinic for Paediatric Nephrology and Radiology Unit, Vrazov trg 1, 1000 Ljubljana, Slovenia
| | - Simona Jereb
- Children's Hospital Ljubljana, Clinic for Paediatric Nephrology and Radiology Unit, Vrazov trg 1, 1000 Ljubljana, Slovenia
| | - Irena Zupanic-Pajnic
- Institute of Forensic Medicine, Faculty of Medicine, Korytkova 2, 1000 Ljubljana, Slovenia
| | - Joze Balazic
- Institute of Forensic Medicine, Faculty of Medicine, Korytkova 2, 1000 Ljubljana, Slovenia
| | - Guido Haarpaintner
- Medical Centre for Molecular Biology, Institute of Biochemistry, Faculty of Medicine, Vrazov trg 2, 1000 Ljubljana, Slovenia
| | - Bostjan Leskovar
- Trbovlje General Hospital, Dialysis Department, Rudarska 7, Trbovlje, Slovenia
| | - Anton Adamlje
- Trbovlje General Hospital, Dialysis Department, Rudarska 7, Trbovlje, Slovenia
| | - Antun Skoflic
- Celje General Hospital, Nephrology Department and Dialysis Centre, Oblakova 5, 3000 Celje, Slovenia
| | - Reina Dovc
- Celje General Hospital, Nephrology Department and Dialysis Centre, Oblakova 5, 3000 Celje, Slovenia
| | - Radovan Hojs
- Maribor General Hospital, Clinical Department for Internal Medicine, Nephrology Department, 2000 Maribor, Slovenia
| | - Radovan Komel
- Medical Centre for Molecular Biology, Institute of Biochemistry, Faculty of Medicine, Vrazov trg 2, 1000 Ljubljana, Slovenia
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13
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Bacolla A, Jaworski A, Larson JE, Jakupciak JP, Chuzhanova N, Abeysinghe SS, O'Connell CD, Cooper DN, Wells RD. Breakpoints of gross deletions coincide with non-B DNA conformations. Proc Natl Acad Sci U S A 2004; 101:14162-7. [PMID: 15377784 PMCID: PMC521098 DOI: 10.1073/pnas.0405974101] [Citation(s) in RCA: 159] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2004] [Indexed: 01/15/2023] Open
Abstract
Genomic rearrangements are a frequent source of instability, but the mechanisms involved are poorly understood. A 2.5-kbp poly(purine.pyrimidine) sequence from the human PKD1 gene, known to form non-B DNA structures, induced long deletions and other instabilities in plasmids that were mediated by mismatch repair and, in some cases, transcription. The breakpoints occurred at predicted non-B DNA structures. Distance measurements also indicated a significant proximity of alternating purine-pyrimidine and oligo(purine.pyrimidine) tracts to breakpoint junctions in 222 gross deletions and translocations, respectively, involved in human diseases. In 11 deletions analyzed, breakpoints were explicable by non-B DNA structure formation. We conclude that alternative DNA conformations trigger genomic rearrangements through recombination-repair activities.
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Affiliation(s)
- Albino Bacolla
- Institute of Biosciences and Technology, Center for Genome Research, Texas A&M University System Health Science Center, Texas Medical Center, 2121 Holcombe Boulevard, Houston, TX 77030, USA
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14
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Patel HP, Lu L, Blaszak RT, Bissler JJ. PKD1 intron 21: triplex DNA formation and effect on replication. Nucleic Acids Res 2004; 32:1460-8. [PMID: 14990751 PMCID: PMC390299 DOI: 10.1093/nar/gkh312] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Although autosomal dominant polycystic kidney disease is transmitted in an autosomal dominant fashion, there is evidence that the pathophysiology of cystogenesis involves a second hit somatic mutation superimposed upon the inherited germline mutation within the renal tubule cells. The polypurine.polypyrimidine (Pu.Py) tract of PKD1 intron 21 may play a role in promoting somatic mutations. To better characterize this tract and to evaluate its potential to participate in mutagenesis, we investigated the thermodynamics of intramolecular triplex formation by 15 Pu.Py mirror repeat tracts from PKD1 intron 21 by 2D gel electrophoresis. We demonstrate that intramolecular triplexes form with modest superhelical tensions for all the tracts examined. Primer extension studies demonstrated significant polymerase arrest within the Pu.Py tracts in one direction of replication only. We found correlation between polymerization arrest and both the potential length of the triplex and superhelical tension of intramolecular triplex formation. The presence of a Pu.Py tract also led to a replication blockade and double-strand breakage using an SV40 in vitro replication assay with HeLa cell extracts. During DNA replication, the G-rich template of the PKD1 Pu.Py tracts may form a triplex structure with the nascent strand, thereby blocking replication and potentially leading to recombination and mutation.
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Affiliation(s)
- Hiren P Patel
- Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229-3039, USA
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15
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Rossetti S, Strmecki L, Gamble V, Burton S, Sneddon V, Peral B, Roy S, Bakkaloglu A, Komel R, Winearls CG, Harris PC. Mutation analysis of the entire PKD1 gene: genetic and diagnostic implications. Am J Hum Genet 2001; 68:46-63. [PMID: 11115377 PMCID: PMC1234934 DOI: 10.1086/316939] [Citation(s) in RCA: 170] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2000] [Accepted: 11/09/2000] [Indexed: 01/16/2023] Open
Abstract
Mutation screening of the major autosomal dominant polycystic kidney disease (ADPKD) locus, PKD1, has proved difficult because of the large transcript and complex reiterated gene region. We have developed methods, employing long polymerase chain reaction (PCR) and specific reverse transcription-PCR, to amplify all of the PKD1 coding area. The gene was screened for mutations in 131 unrelated patients with ADPKD, using the protein-truncation test and direct sequencing. Mutations were identified in 57 families, and, including 24 previously characterized changes from this cohort, a detection rate of 52.3% was achieved in 155 families. Mutations were found in all areas of the gene, from exons 1 to 46, with no clear hotspot identified. There was no significant difference in mutation frequency between the single-copy and duplicated areas, but mutations were more than twice as frequent in the 3' half of the gene, compared with the 5' half. The majority of changes were predicted to truncate the protein through nonsense mutations (32%), insertions or deletions (29.6%), or splicing changes (6.2%), although the figures were biased by the methods employed, and, in sequenced areas, approximately 50% of all mutations were missense or in-frame. Studies elsewhere have suggested that gene conversion may be a significant cause of mutation at PKD1, but only 3 of 69 different mutations matched PKD1-like HG sequence. A relatively high rate of new PKD1 mutation was calculated, 1.8x10-5 mutations per generation, consistent with the many different mutations identified (69 in 81 pedigrees) and suggesting significant selection against mutant alleles. The mutation detection rate, in this study, of >50% is comparable to that achieved for other large multiexon genes and shows the feasibility of genetic diagnosis in this disorder.
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Affiliation(s)
- Sandro Rossetti
- Division of Nephrology, Mayo Clinic, Rochester, MN; Institute of Molecular Medicine, John Radcliffe Hospital, and Oxford Renal Unit, The Oxford Radcliffe Hospital, Oxford, United Kingdom; Instituto de Investigaciones Biomedicas Alberto Sols, CSIC-UAM, Madrid; Institute of Child Health, London; Department of Pediatric Nephrology, Hacettepe University, Ankara, Turkey; and Medical Centre for Molecular Biology, Institute of Biochemistry, Ljubljana, Slovenia
| | - Lana Strmecki
- Division of Nephrology, Mayo Clinic, Rochester, MN; Institute of Molecular Medicine, John Radcliffe Hospital, and Oxford Renal Unit, The Oxford Radcliffe Hospital, Oxford, United Kingdom; Instituto de Investigaciones Biomedicas Alberto Sols, CSIC-UAM, Madrid; Institute of Child Health, London; Department of Pediatric Nephrology, Hacettepe University, Ankara, Turkey; and Medical Centre for Molecular Biology, Institute of Biochemistry, Ljubljana, Slovenia
| | - Vicki Gamble
- Division of Nephrology, Mayo Clinic, Rochester, MN; Institute of Molecular Medicine, John Radcliffe Hospital, and Oxford Renal Unit, The Oxford Radcliffe Hospital, Oxford, United Kingdom; Instituto de Investigaciones Biomedicas Alberto Sols, CSIC-UAM, Madrid; Institute of Child Health, London; Department of Pediatric Nephrology, Hacettepe University, Ankara, Turkey; and Medical Centre for Molecular Biology, Institute of Biochemistry, Ljubljana, Slovenia
| | - Sarah Burton
- Division of Nephrology, Mayo Clinic, Rochester, MN; Institute of Molecular Medicine, John Radcliffe Hospital, and Oxford Renal Unit, The Oxford Radcliffe Hospital, Oxford, United Kingdom; Instituto de Investigaciones Biomedicas Alberto Sols, CSIC-UAM, Madrid; Institute of Child Health, London; Department of Pediatric Nephrology, Hacettepe University, Ankara, Turkey; and Medical Centre for Molecular Biology, Institute of Biochemistry, Ljubljana, Slovenia
| | - Vicky Sneddon
- Division of Nephrology, Mayo Clinic, Rochester, MN; Institute of Molecular Medicine, John Radcliffe Hospital, and Oxford Renal Unit, The Oxford Radcliffe Hospital, Oxford, United Kingdom; Instituto de Investigaciones Biomedicas Alberto Sols, CSIC-UAM, Madrid; Institute of Child Health, London; Department of Pediatric Nephrology, Hacettepe University, Ankara, Turkey; and Medical Centre for Molecular Biology, Institute of Biochemistry, Ljubljana, Slovenia
| | - Belén Peral
- Division of Nephrology, Mayo Clinic, Rochester, MN; Institute of Molecular Medicine, John Radcliffe Hospital, and Oxford Renal Unit, The Oxford Radcliffe Hospital, Oxford, United Kingdom; Instituto de Investigaciones Biomedicas Alberto Sols, CSIC-UAM, Madrid; Institute of Child Health, London; Department of Pediatric Nephrology, Hacettepe University, Ankara, Turkey; and Medical Centre for Molecular Biology, Institute of Biochemistry, Ljubljana, Slovenia
| | - Sushmita Roy
- Division of Nephrology, Mayo Clinic, Rochester, MN; Institute of Molecular Medicine, John Radcliffe Hospital, and Oxford Renal Unit, The Oxford Radcliffe Hospital, Oxford, United Kingdom; Instituto de Investigaciones Biomedicas Alberto Sols, CSIC-UAM, Madrid; Institute of Child Health, London; Department of Pediatric Nephrology, Hacettepe University, Ankara, Turkey; and Medical Centre for Molecular Biology, Institute of Biochemistry, Ljubljana, Slovenia
| | - Aysin Bakkaloglu
- Division of Nephrology, Mayo Clinic, Rochester, MN; Institute of Molecular Medicine, John Radcliffe Hospital, and Oxford Renal Unit, The Oxford Radcliffe Hospital, Oxford, United Kingdom; Instituto de Investigaciones Biomedicas Alberto Sols, CSIC-UAM, Madrid; Institute of Child Health, London; Department of Pediatric Nephrology, Hacettepe University, Ankara, Turkey; and Medical Centre for Molecular Biology, Institute of Biochemistry, Ljubljana, Slovenia
| | - Radovan Komel
- Division of Nephrology, Mayo Clinic, Rochester, MN; Institute of Molecular Medicine, John Radcliffe Hospital, and Oxford Renal Unit, The Oxford Radcliffe Hospital, Oxford, United Kingdom; Instituto de Investigaciones Biomedicas Alberto Sols, CSIC-UAM, Madrid; Institute of Child Health, London; Department of Pediatric Nephrology, Hacettepe University, Ankara, Turkey; and Medical Centre for Molecular Biology, Institute of Biochemistry, Ljubljana, Slovenia
| | - Christopher G. Winearls
- Division of Nephrology, Mayo Clinic, Rochester, MN; Institute of Molecular Medicine, John Radcliffe Hospital, and Oxford Renal Unit, The Oxford Radcliffe Hospital, Oxford, United Kingdom; Instituto de Investigaciones Biomedicas Alberto Sols, CSIC-UAM, Madrid; Institute of Child Health, London; Department of Pediatric Nephrology, Hacettepe University, Ankara, Turkey; and Medical Centre for Molecular Biology, Institute of Biochemistry, Ljubljana, Slovenia
| | - Peter C. Harris
- Division of Nephrology, Mayo Clinic, Rochester, MN; Institute of Molecular Medicine, John Radcliffe Hospital, and Oxford Renal Unit, The Oxford Radcliffe Hospital, Oxford, United Kingdom; Instituto de Investigaciones Biomedicas Alberto Sols, CSIC-UAM, Madrid; Institute of Child Health, London; Department of Pediatric Nephrology, Hacettepe University, Ankara, Turkey; and Medical Centre for Molecular Biology, Institute of Biochemistry, Ljubljana, Slovenia
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16
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Watnick T, Phakdeekitcharoen B, Johnson A, Gandolph M, Wang M, Briefel G, Klinger KW, Kimberling W, Gabow P, Germino GG. Mutation detection of PKD1 identifies a novel mutation common to three families with aneurysms and/or very-early-onset disease. Am J Hum Genet 1999; 65:1561-71. [PMID: 10577909 PMCID: PMC1288366 DOI: 10.1086/302657] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/1999] [Accepted: 10/01/1999] [Indexed: 11/03/2022] Open
Abstract
It is known that several of the most severe complications of autosomal-dominant polycystic kidney disease, such as intracranial aneurysms, cluster in families. There have been no studies reported to date, however, that have attempted to correlate severely affected pedigrees with a particular genotype. Until recently, in fact, mutation detection for most of the PKD1 gene was virtually impossible because of the presence of several highly homologous loci also located on chromosome 16. In this report we describe a cluster of 4 bp in exon 15 that are unique to PKD1. Forward and reverse PKD1-specific primers were designed in this location to amplify regions of the gene from exons 11-21 by use of long-range PCR. The two templates described were used to analyze 35 pedigrees selected for study because they included individuals with either intracranial aneurysms and/or very-early-onset disease. We identified eight novel truncating mutations, two missense mutations not found in a panel of controls, and several informative polymorphisms. Many of the polymorphisms were also present in the homologous loci, supporting the idea that they may serve as a reservoir for genetic variability in the PKD1 gene. Surprisingly, we found that three independently ascertained pedigrees had an identical 2-bp deletion in exon 15. This raises the possibility that particular genotypes may be associated with more-severe disease.
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Affiliation(s)
- Terry Watnick
- Johns Hopkins
University School of Medicine, Division of Nephrology, and
Johns Hopkins-Bayview Hospital, Division of
Nephrology, Baltimore; University of Colorado Health Sciences
Center, Polycystic Kidney Disease Research Group, Denver;
Department of Genetics, Center for Hereditary and
Communication Disorders, Boys Town National Research Hospital, Omaha;
Genzyme Corporation, Framingham,
MA
| | - Bunyong Phakdeekitcharoen
- Johns Hopkins
University School of Medicine, Division of Nephrology, and
Johns Hopkins-Bayview Hospital, Division of
Nephrology, Baltimore; University of Colorado Health Sciences
Center, Polycystic Kidney Disease Research Group, Denver;
Department of Genetics, Center for Hereditary and
Communication Disorders, Boys Town National Research Hospital, Omaha;
Genzyme Corporation, Framingham,
MA
| | - Ann Johnson
- Johns Hopkins
University School of Medicine, Division of Nephrology, and
Johns Hopkins-Bayview Hospital, Division of
Nephrology, Baltimore; University of Colorado Health Sciences
Center, Polycystic Kidney Disease Research Group, Denver;
Department of Genetics, Center for Hereditary and
Communication Disorders, Boys Town National Research Hospital, Omaha;
Genzyme Corporation, Framingham,
MA
| | - Michael Gandolph
- Johns Hopkins
University School of Medicine, Division of Nephrology, and
Johns Hopkins-Bayview Hospital, Division of
Nephrology, Baltimore; University of Colorado Health Sciences
Center, Polycystic Kidney Disease Research Group, Denver;
Department of Genetics, Center for Hereditary and
Communication Disorders, Boys Town National Research Hospital, Omaha;
Genzyme Corporation, Framingham,
MA
| | - Mei Wang
- Johns Hopkins
University School of Medicine, Division of Nephrology, and
Johns Hopkins-Bayview Hospital, Division of
Nephrology, Baltimore; University of Colorado Health Sciences
Center, Polycystic Kidney Disease Research Group, Denver;
Department of Genetics, Center for Hereditary and
Communication Disorders, Boys Town National Research Hospital, Omaha;
Genzyme Corporation, Framingham,
MA
| | - Gary Briefel
- Johns Hopkins
University School of Medicine, Division of Nephrology, and
Johns Hopkins-Bayview Hospital, Division of
Nephrology, Baltimore; University of Colorado Health Sciences
Center, Polycystic Kidney Disease Research Group, Denver;
Department of Genetics, Center for Hereditary and
Communication Disorders, Boys Town National Research Hospital, Omaha;
Genzyme Corporation, Framingham,
MA
| | - Katherine W. Klinger
- Johns Hopkins
University School of Medicine, Division of Nephrology, and
Johns Hopkins-Bayview Hospital, Division of
Nephrology, Baltimore; University of Colorado Health Sciences
Center, Polycystic Kidney Disease Research Group, Denver;
Department of Genetics, Center for Hereditary and
Communication Disorders, Boys Town National Research Hospital, Omaha;
Genzyme Corporation, Framingham,
MA
| | - William Kimberling
- Johns Hopkins
University School of Medicine, Division of Nephrology, and
Johns Hopkins-Bayview Hospital, Division of
Nephrology, Baltimore; University of Colorado Health Sciences
Center, Polycystic Kidney Disease Research Group, Denver;
Department of Genetics, Center for Hereditary and
Communication Disorders, Boys Town National Research Hospital, Omaha;
Genzyme Corporation, Framingham,
MA
| | - Patricia Gabow
- Johns Hopkins
University School of Medicine, Division of Nephrology, and
Johns Hopkins-Bayview Hospital, Division of
Nephrology, Baltimore; University of Colorado Health Sciences
Center, Polycystic Kidney Disease Research Group, Denver;
Department of Genetics, Center for Hereditary and
Communication Disorders, Boys Town National Research Hospital, Omaha;
Genzyme Corporation, Framingham,
MA
| | - Gregory G. Germino
- Johns Hopkins
University School of Medicine, Division of Nephrology, and
Johns Hopkins-Bayview Hospital, Division of
Nephrology, Baltimore; University of Colorado Health Sciences
Center, Polycystic Kidney Disease Research Group, Denver;
Department of Genetics, Center for Hereditary and
Communication Disorders, Boys Town National Research Hospital, Omaha;
Genzyme Corporation, Framingham,
MA
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17
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Potaman VN, Bissler JJ. Overcoming a barrier for DNA polymerization in triplex-forming sequences. Nucleic Acids Res 1999; 27:e5. [PMID: 10454624 PMCID: PMC148516 DOI: 10.1093/nar/27.15.e5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Folded structures in the DNA template, such as hairpins and multi-stranded structures, often serve as pause and arrest sites for DNA polymerases. DNA polymerization is particularly difficult on mirror-repeated homopurine.homopyrimidine templates where triple-stranded (triplex) structures may form between the nascent and folded template strands. In order to use a linear PCR amplification approach for the structural analysis of DNA in mirror-repeated sequences we modified a conventional protocol. The barrier for DNA synthesis can be eliminated using an oligonucleotide that hybridizes with the template to prevent its folding and is subsequently displaced by the progressing polymerase. The described approach is potentially useful for sequencing and analysis of chemical adducts and point mutations in a variety of sequences prone to the formation of folded structures, such as long hairpins and quadruplexes.
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Affiliation(s)
- V N Potaman
- Institute of Biosciences and Technology, The Texas A&M University System Health Science Center, 2121 West Holcombe Boulevard, Houston, TX 77030, USA.
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