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Ngo TTM, Liu B, Wang F, Basu A, Wu C, Ha T. Dependence of nucleosome mechanical stability on DNA mismatches. eLife 2024; 13:RP95514. [PMID: 38656237 DOI: 10.7554/elife.95514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024] Open
Abstract
The organization of nucleosomes into chromatin and their accessibility are shaped by local DNA mechanics. Conversely, nucleosome positions shape genetic variations, which may originate from mismatches during replication and chemical modification of DNA. To investigate how DNA mismatches affect the mechanical stability and the exposure of nucleosomal DNA, we used an optical trap combined with single-molecule FRET and a single-molecule FRET cyclization assay. We found that a single base-pair C-C mismatch enhances DNA bendability and nucleosome mechanical stability for the 601-nucleosome positioning sequence. An increase in force required for DNA unwrapping from the histone core is observed for single base-pair C-C mismatches placed at three tested positions: at the inner turn, at the outer turn, or at the junction of the inner and outer turn of the nucleosome. The results support a model where nucleosomal DNA accessibility is reduced by mismatches, potentially explaining the preferred accumulation of single-nucleotide substitutions in the nucleosome core and serving as the source of genetic variation during evolution and cancer progression. Mechanical stability of an intact nucleosome, that is mismatch-free, is also dependent on the species as we find that yeast nucleosomes are mechanically less stable and more symmetrical in the outer turn unwrapping compared to Xenopus nucleosomes.
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Affiliation(s)
- Thuy T M Ngo
- Department of Physics, Center for Physics in Living Cells University of Illinois Urbana-Champaign, Urbana, United States
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, United States
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, Oregon Health and Science University, Portland, United States
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States
- Division of Oncological Sciences, Oregon Health and Science University, Portland, United States
| | - Bailey Liu
- Department of Biophysics, Johns Hopkins University, Baltimore, United States
| | - Feng Wang
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, United States
| | - Aakash Basu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, United States
- Department of Biosciences, Durham University, Durham, United Kingdom
| | - Carl Wu
- Department of Biology, Johns Hopkins University, Baltimore, United States
- Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, United States
| | - Taekjip Ha
- Department of Physics, Center for Physics in Living Cells University of Illinois Urbana-Champaign, Urbana, United States
- Department of Biophysics, Johns Hopkins University, Baltimore, United States
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, United States
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, United States
- Department of Pediatrics, Harvard Medical School, Boston, United States
- Howard Hughes Medical Institute, Boston, United States
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2
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Abstract
CRISPR interference is an increasingly popular method for perturbing gene expression. Guided by single-guide RNAs (sgRNAs), nuclease-deficient Cas9 proteins bind to specific DNA sequences and hinder transcription. Specificity is achieved through complementarity of the sgRNAs to the DNA. Changing complementarity by introducing single-nucleotide mismatches can be exploited to tune knockdown. Here, we present a computational pipeline to identify sgRNAs targeting specific genes in a bacterial genome, filter them, and titrate their activity by introducing mismatches. For complete details on the use and execution of this protocol, please refer to Hawkins et al. (2020).
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Affiliation(s)
- Jordi van Gestel
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - John S. Hawkins
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Horia Todor
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Carol A. Gross
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94158, USA
- California Institute of Quantitative Biology, University of California, San Francisco, San Francisco 94158, CA, USA
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3
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Kim H, Lee WJ, Oh Y, Kang SH, Hur JK, Lee H, Song W, Lim KS, Park YH, Song BS, Jin YB, Jun BH, Jung C, Lee DS, Kim SU, Lee SH. Enhancement of target specificity of CRISPR-Cas12a by using a chimeric DNA-RNA guide. Nucleic Acids Res 2020; 48:8601-8616. [PMID: 32687187 PMCID: PMC7470973 DOI: 10.1093/nar/gkaa605] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 06/14/2020] [Accepted: 07/06/2020] [Indexed: 12/24/2022] Open
Abstract
The CRISPR-Cas9 system is widely used for target-specific genome engineering. CRISPR-Cas12a (Cpf1) is one of the CRISPR effectors that controls target genes by recognizing thymine-rich protospacer adjacent motif (PAM) sequences. Cas12a has a higher sensitivity to mismatches in the guide RNA than does Cas9; therefore, off-target sequence recognition and cleavage are lower. However, it tolerates mismatches in regions distant from the PAM sequence (TTTN or TTN) in the protospacer, and off-target cleavage issues may become more problematic when Cas12a activity is improved for therapeutic purposes. Therefore, we investigated off-target cleavage by Cas12a and modified the Cas12a (cr)RNA to address the off-target cleavage issue. We developed a CRISPR-Cas12a that can induce mutations in target DNA sequences in a highly specific and effective manner by partially substituting the (cr)RNA with DNA to change the energy potential of base pairing to the target DNA. A model to explain how chimeric (cr)RNA guided CRISPR-Cas12a and SpCas9 nickase effectively work in the intracellular genome is suggested. Chimeric guide-based CRISPR- Cas12a genome editing with reduced off-target cleavage, and the resultant, increased safety has potential for therapeutic applications in incurable diseases caused by genetic mutations.
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Affiliation(s)
- Hanseop Kim
- Futuristic Animal Resource & Research Center (FARRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Korea
- School of Life Sciences and Biotechnology, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu, Republic of Korea
| | - Wi-jae Lee
- Futuristic Animal Resource & Research Center (FARRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Korea
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 143-701, Republic of Korea
| | - Yeounsun Oh
- Futuristic Animal Resource & Research Center (FARRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Korea
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Seung-Hun Kang
- Futuristic Animal Resource & Research Center (FARRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Korea
- Department of Medicine, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Junho K Hur
- Department of Pathology, College of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea
- Department of Medical Genetics, College of Medicine, Hanyang University, Seoul, Republic of Korea
| | - Hyomin Lee
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea
| | - WooJeung Song
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Kyung-Seob Lim
- Futuristic Animal Resource & Research Center (FARRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Korea
| | - Young-Ho Park
- Futuristic Animal Resource & Research Center (FARRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Korea
| | - Bong-Seok Song
- Futuristic Animal Resource & Research Center (FARRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Korea
| | - Yeung Bae Jin
- National Primate Research Center (NPRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Republic of Korea
| | - Bong-Hyun Jun
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 143-701, Republic of Korea
| | - Cheulhee Jung
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Dong-Seok Lee
- School of Life Sciences and Biotechnology, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu, Republic of Korea
| | - Sun-Uk Kim
- Futuristic Animal Resource & Research Center (FARRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Korea
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Seung Hwan Lee
- National Primate Research Center (NPRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Republic of Korea
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4
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Affiliation(s)
- Maximilian Haeussler
- Genomics Institute, University of California at Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA.
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Zhao Y, Li X, Yang Y, Si S, Deng C, Wu H. A simple aptasensor for Aβ 40 oligomers based on tunable mismatched base pairs of dsDNA and graphene oxide. Biosens Bioelectron 2019; 149:111840. [PMID: 31726274 DOI: 10.1016/j.bios.2019.111840] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 10/30/2019] [Accepted: 11/01/2019] [Indexed: 12/13/2022]
Abstract
β-amyloid 1-40 oligomers (Aβ40O) is considered to be one of the important biomarkers for the diagnosis and treatment of Alzheimer's disease (AD). To explore a method with excellent performance is favorable for measuring the low concentration of Aβ40O in AD patients. Here, we developed a simple and fast method with a double stranded DNA (dsDNA)/graphene oxide (GO) based sensor, which was a fluorescent probe for a highly sensitive detection of Aβ40O down to 0.1 nM with a linear detectable range from 0.1 nM to 40 nM. The proposed sensor effectively reduced non-specific adsorption and improved the specificity of detection because of the covalent conjugation of a binding DNA (bDNA) containing Aβ40O-targeting aptamer (AptAβ) onto GO surface, as well as the optimization of the number of mismatch base pairs of dsDNA. Moreover, AD patients and healthy persons were distinguished by this present method. All advantages of this method are exactly what the clinical detection of AD biomarkers need. This novel aptasensor might pave a way towards the early diagnosis of AD.
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Affiliation(s)
- Yana Zhao
- College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, China
| | - Xin Li
- Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, 100850, China
| | - Yuan Yang
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, M5S 3G9, Canada
| | - Shihui Si
- College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, China
| | - Chunyan Deng
- College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, China.
| | - Huiyun Wu
- Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, 100850, China.
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6
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Lv J, Wu S, Wei R, Li Y, Jin J, Mu Y, Zhang Y, Kong Q, Weng X, Liu Z. The length of guide RNA and target DNA heteroduplex effects on CRISPR/Cas9 mediated genome editing efficiency in porcine cells. J Vet Sci 2019; 20:e23. [PMID: 31161741 PMCID: PMC6538514 DOI: 10.4142/jvs.2019.20.e23] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 02/27/2019] [Accepted: 03/21/2019] [Indexed: 12/25/2022] Open
Abstract
The clustered regularly interspaced short palindrome repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system is a versatile genome editing tool with high efficiency. A guide sequence of 20 nucleotides (nt) is commonly used in application of CRISPR/Cas9; however, the relationship between the length of the guide sequence and the efficiency of CRISPR/Cas9 in porcine cells is still not clear. To illustrate this issue, guide RNAs of different lengths targeting the EGFP gene were designed. Specifically, guide RNAs of 17 nt or longer were sufficient to direct the Cas9 protein to cleave target DNA sequences, while 15 nt or shorter guide RNAs had loss-of-function. Full-length guide RNAs complemented with mismatches also showed loss-of-function. When the shortened guide RNA and target DNA heteroduplex (gRNA:DNA heteroduplex) was blocked by mismatch, the CRISPR/Cas9 would be interfered with. These results suggested the length of the gRNA:DNA heteroduplex was a key factor for maintaining high efficiency of the CRISPR/Cas9 system rather than weak bonding between shortened guide RNA and Cas9 in porcine cells.
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Affiliation(s)
- Jiawei Lv
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Shuang Wu
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Renyue Wei
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Yan Li
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Junxue Jin
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Yanshuang Mu
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Yu Zhang
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Qingran Kong
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Xiaogang Weng
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Zhonghua Liu
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin 150030, China.
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Aggeli D, Karas VO, Sinnott-Armstrong NA, Varghese V, Shafer RW, Greenleaf WJ, Sherlock G. Diff-seq: A high throughput sequencing-based mismatch detection assay for DNA variant enrichment and discovery. Nucleic Acids Res 2018; 46:e42. [PMID: 29361139 PMCID: PMC5909455 DOI: 10.1093/nar/gky022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 12/15/2017] [Accepted: 01/16/2018] [Indexed: 01/15/2023] Open
Abstract
Much of the within species genetic variation is in the form of single nucleotide polymorphisms (SNPs), typically detected by whole genome sequencing (WGS) or microarray-based technologies. However, WGS produces mostly uninformative reads that perfectly match the reference, while microarrays require genome-specific reagents. We have developed Diff-seq, a sequencing-based mismatch detection assay for SNP discovery without the requirement for specialized nucleic-acid reagents. Diff-seq leverages the Surveyor endonuclease to cleave mismatched DNA molecules that are generated after cross-annealing of a complex pool of DNA fragments. Sequencing libraries enriched for Surveyor-cleaved molecules result in increased coverage at the variant sites. Diff-seq detected all mismatches present in an initial test substrate, with specific enrichment dependent on the identity and context of the variation. Application to viral sequences resulted in increased observation of variant alleles in a biologically relevant context. Diff-Seq has the potential to increase the sensitivity and efficiency of high-throughput sequencing in the detection of variation.
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Affiliation(s)
- Dimitra Aggeli
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Vlad O Karas
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Vici Varghese
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Robert W Shafer
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Gavin Sherlock
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
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Kimsey IJ, Szymanski ES, Zahurancik WJ, Shakya A, Xue Y, Chu CC, Sathyamoorthy B, Suo Z, Al-Hashimi HM. Dynamic basis for dG•dT misincorporation via tautomerization and ionization. Nature 2018; 554:195-201. [PMID: 29420478 PMCID: PMC5808992 DOI: 10.1038/nature25487] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 12/21/2017] [Indexed: 12/22/2022]
Abstract
Tautomeric and anionic Watson-Crick-like mismatches have important roles in replication and translation errors through mechanisms that are not fully understood. Here, using NMR relaxation dispersion, we resolve a sequence-dependent kinetic network connecting G•T/U wobbles with three distinct Watson-Crick mismatches: two rapidly exchanging tautomeric species (Genol•T/UG•Tenol/Uenol; population less than 0.4%) and one anionic species (G•T-/U-; population around 0.001% at neutral pH). The sequence-dependent tautomerization or ionization step was inserted into a minimal kinetic mechanism for correct incorporation during replication after the initial binding of the nucleotide, leading to accurate predictions of the probability of dG•dT misincorporation across different polymerases and pH conditions and for a chemically modified nucleotide, and providing mechanisms for sequence-dependent misincorporation. Our results indicate that the energetic penalty for tautomerization and/or ionization accounts for an approximately 10-2 to 10-3-fold discrimination against misincorporation, which proceeds primarily via tautomeric dGenol•dT and dG•dTenol, with contributions from anionic dG•dT- dominant at pH 8.4 and above or for some mutagenic nucleotides.
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Affiliation(s)
- Isaac J Kimsey
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Eric S Szymanski
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Walter J Zahurancik
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, USA
| | - Anisha Shakya
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Yi Xue
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Chia-Chieh Chu
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
| | | | - Zucai Suo
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, USA
| | - Hashim M Al-Hashimi
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
- Department of Chemistry, Duke University, Durham, North Carolina 27710, USA
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Shpitz B, Klein E, Malinger P, Osmolovsky G, Gochberg S, Bomstein Y, Bernheim J. Altered Expression of the Dna Mismatch Repair Proteins Hmlh1 and Hmsh2 in Cutaneous Dysplastic Nevi and Malignant Melanoma. Int J Biol Markers 2018; 20:65-8. [PMID: 15832775 DOI: 10.1177/172460080502000110] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 11/16/2022]
Abstract
Molecular alterations in the mismatch repair system suggest that this mechanism may be important in the evolution of cutaneous melanoma. Our current study evaluated the expression of two mismatch repair proteins, hMLH1 and hMSH2, in dysplastic nevi (DN) and cutaneous melanoma (CM). Immunohistochemical staining of these proteins was performed on 55 CM and 30 DN specimens. The staining results were divided into three groups: negative, partially positive and strongly positive. Normal adjacent skin cells served as an internal control for positive immunostaining. Altered immunoreactivity of one of the proteins was found in four (13.4%) DN and seven (12.7%) CM. Lack of staining for hMLH1 was observed in two (6.7%) cases of DN and five (9.1%) cases of CM; staining for hMSH2 was absent in two (6.7%) of the DN and two (3.6%) of the CM specimens. Partially positive staining was found in 33.3% and 53.3% for hMLH1 and hMSH2, respectively, in DN, and in 54.5% and 69.1%, respectively, in CMM. Our study shows that complete or partial loss of MMR protein expression occurs in a subset of both DN and CM and may represent a distinct pathway in the development of some DN and CM.
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Affiliation(s)
- B Shpitz
- Department of Surgery, Laboratory of Oncogenetics, Sapir Medical Center, Meir General Hospital, Kfar Sava, Israel.
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Samans B, Chalhoub B, Snowdon RJ. Surviving a Genome Collision: Genomic Signatures of Allopolyploidization in the Recent Crop Species Brassica napus. Plant Genome 2017; 10. [PMID: 29293818 DOI: 10.3835/plantgenome2017.02.0013] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Polyploidization has played a major role in crop plant evolution, leading to advantageous traits that have been selected by humans. Here, we describe restructuring patterns in the genome of L., a recent allopolyploid species. Widespread segmental deletions, duplications, and homeologous chromosome exchanges were identified in diverse genome sequences from 32 natural and 20 synthetic accessions, indicating that homeologous exchanges are a major driver of postpolyploidization genome diversification. Breakpoints of genomic rearrangements are rich in microsatellite sequences that are known to interact with the meiotic recombination machinery. In both synthetic and natural , a subgenome bias was observed toward exchanges replacing larger chromosome segments from the C-subgenome by their smaller, homeologous A-subgenome segments, driving postpolyploidization genome size reduction. Selection in natural favored segmental deletions involving genes associated with immunity, reproduction, and adaptation. Deletions affecting mismatch repair system genes, which are assumed to control homeologous recombination, were also found to be under selection. Structural exchanges between homeologous subgenomes appear to be a major source of novel genetic diversity in de novo allopolyploids. Documenting the consequences of genomic collision by genomic resequencing gives insights into the adaptive processes accompanying allopolyploidization.
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Kamola PJ, Nakano Y, Takahashi T, Wilson PA, Ui-Tei K. The siRNA Non-seed Region and Its Target Sequences Are Auxiliary Determinants of Off-Target Effects. PLoS Comput Biol 2015; 11:e1004656. [PMID: 26657993 PMCID: PMC4676691 DOI: 10.1371/journal.pcbi.1004656] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 11/16/2015] [Indexed: 01/06/2023] Open
Abstract
RNA interference (RNAi) is a powerful tool for post-transcriptional gene silencing. However, the siRNA guide strand may bind unintended off-target transcripts via partial sequence complementarity by a mechanism closely mirroring micro RNA (miRNA) silencing. To better understand these off-target effects, we investigated the correlation between sequence features within various subsections of siRNA guide strands, and its corresponding target sequences, with off-target activities. Our results confirm previous reports that strength of base-pairing in the siRNA seed region is the primary factor determining the efficiency of off-target silencing. However, the degree of downregulation of off-target transcripts with shared seed sequence is not necessarily similar, suggesting that there are additional auxiliary factors that influence the silencing potential. Here, we demonstrate that both the melting temperature (Tm) in a subsection of siRNA non-seed region, and the GC contents of its corresponding target sequences, are negatively correlated with the efficiency of off-target effect. Analysis of experimentally validated miRNA targets demonstrated a similar trend, indicating a putative conserved mechanistic feature of seed region-dependent targeting mechanism. These observations may prove useful as parameters for off-target prediction algorithms and improve siRNA ‘specificity’ design rules. Small interfering RNAs (siRNAs) are double stranded RNA molecules designed to perfectly match the sequence of a target gene and silence its expression. The function is exerted through the RNA interference (RNAi) pathway and has revolutionised biological research due to its ease-of-use and high potency. While siRNAs were initially believed to be highly specific, they have subsequently been observed to interact with other, unintended messenger RNAs. However, the mechanistic details of this process remain poorly understood, and there is a paucity of strategies and guidelines directed toward mitigating this issue. To address this potential safety liability, we performed a comprehensive analysis of sequence characteristics of siRNA duplexes and their target regions. Results from luciferase-reporter assays and global expression data confirmed previous observations that the siRNA seed region is the primary determinant for off-target gene recognition and binding. Furthermore, our analysis revealed the important contribution of siRNA non-seed region, and its corresponding target sequences, to the potency of off-target knockdown. Similar results were observed in an equivalent evaluation of the miRNA-targeting mechanism, suggesting that the correlating features arise through an evolutionary conserved mechanistic factor.
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Affiliation(s)
- Piotr J. Kamola
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- Safety Assessment, GlaxoSmithKline R&D, Ware, Hertfordshire, United Kingdom
- Computational Biology, GlaxoSmithKline R&D, Stevenage, Hertfordshire, United Kingdom
- Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Harwell Science and Innovation Campus, United Kingdom
| | - Yuko Nakano
- Department of Biological Sciences, University of Tokyo, Bunkyo, Tokyo, Japan
| | - Tomoko Takahashi
- Department of Biological Sciences, University of Tokyo, Bunkyo, Tokyo, Japan
| | - Paul A. Wilson
- Computational Biology, GlaxoSmithKline R&D, Stevenage, Hertfordshire, United Kingdom
| | - Kumiko Ui-Tei
- Department of Biological Sciences, University of Tokyo, Bunkyo, Tokyo, Japan
- Department of Computational Biology and Medical Sciences, University of Tokyo, Kashiwa, Chiba, Japan
- * E-mail:
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Heyn B, Pogodalla N, Brakmann S. The double mutation L109M and R448M of HIV-1 reverse transcriptase decreases fidelity of DNA synthesis by promoting mismatch elongation. Biol Chem 2015; 396:1315-23. [PMID: 26351907 DOI: 10.1515/hsz-2015-0115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 07/20/2015] [Indexed: 11/15/2022]
Abstract
Changes of Leu109 and Arg448 of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) have as yet not been associated with altered fitness. However, in a recent study, we described that the simultaneous substitution of L109 and R448 by methionine leads to an error-producing polymerase phenotype that is not observed for the isolated substitutions. The double mutant increased the error rate of DNA-dependent DNA synthesis 3.1-fold as compared to the wildtype enzyme and showed a mutational spectrum with a fraction of 28% frameshift mutations and 48% transitions. We show here that weaker binding of DNA:DNA primer-templates as indicated by an increased dissociation rate constant (koff) could account for the higher frameshift error rate. Furthermore, we were able to explain the prevalence of transition mutations with the finding that HIV-1 RT variant L109M/R448M preferred misincorporation of C opposite A and elongation of C:A mismatches.
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Chen TW, Gan RC, Chang YF, Liao WC, Wu TH, Lee CC, Huang PJ, Lee CY, Chen YYM, Chiu CH, Tang P. Is the whole greater than the sum of its parts? De novo assembly strategies for bacterial genomes based on paired-end sequencing. BMC Genomics 2015; 16:648. [PMID: 26315384 PMCID: PMC4552406 DOI: 10.1186/s12864-015-1859-8] [Citation(s) in RCA: 8] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 08/18/2015] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Whole genome sequence construction is becoming increasingly feasible because of advances in next generation sequencing (NGS), including increasing throughput and read length. By simply overlapping paired-end reads, we can obtain longer reads with higher accuracy, which can facilitate the assembly process. However, the influences of different library sizes and assembly methods on paired-end sequencing-based de novo assembly remain poorly understood. RESULTS We used 250 bp Illumina Miseq paired-end reads of different library sizes generated from genomic DNA from Escherichia coli DH1 and Streptococcus parasanguinis FW213 to compare the assembly results of different library sizes and assembly approaches. Our data indicate that overlapping paired-end reads can increase read accuracy but sometimes cause insertion or deletions. Regarding genome assembly, merged reads only outcompete original paired-end reads when coverage depth is low, and larger libraries tend to yield better assembly results. These results imply that distance information is the most critical factor during assembly. Our results also indicate that when depth is sufficiently high, assembly from subsets can sometimes produce better results. CONCLUSIONS In summary, this study provides systematic evaluations of de novo assembly from paired end sequencing data. Among the assembly strategies, we find that overlapping paired-end reads is not always beneficial for bacteria genome assembly and should be avoided or used with caution especially for genomes containing high fraction of repetitive sequences. Because increasing numbers of projects aim at bacteria genome sequencing, our study provides valuable suggestions for the field of genomic sequence construction.
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Affiliation(s)
- Ting-Wen Chen
- Bioinformatics Core Laboratory, Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.
| | - Ruei-Chi Gan
- Bioinformatics Core Laboratory, Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.
| | - Yi-Feng Chang
- Bioinformatics Core Laboratory, Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan.
| | - Wei-Chao Liao
- Bioinformatics Core Laboratory, Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.
| | | | - Chi-Ching Lee
- Bioinformatics Core Laboratory, Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.
| | - Po-Jung Huang
- Bioinformatics Core Laboratory, Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.
| | - Cheng-Yang Lee
- Bioinformatics Core Laboratory, Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.
| | - Yi-Ywan M Chen
- Department of Microbiology and Immunology, Chang Gung University, Taoyuan, Taiwan.
- Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan.
| | - Cheng-Hsun Chiu
- Molecular Infectious Diseases Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan.
| | - Petrus Tang
- Bioinformatics Core Laboratory, Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.
- Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan.
- Molecular Infectious Diseases Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan.
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14
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Abstract
Bending with high curvature is one of the major mechanical properties of double-stranded DNA (dsDNA) that is essential for its biological functions. The emergence of a kink arising from local melting in the middle of dsDNA has been suggested as a mechanism of releasing the energy cost of bending. Herein, we report that strong bending induces two types of short dsDNA deformations, induced by two types of local melting, namely, a kink in the middle and forks at the ends, which we demonstrate using D-shaped DNA nanostructures. The two types of deformed dsDNA structures dynamically interconvert on a millisecond timescale. The transition from a fork to a kink is dominated by entropic contribution (anti-Arrhenius behavior), while the transition from a kink to a fork is dominated by enthalpic contributions. The presence of mismatches in dsDNA accelerates kink formation, and the transition from a kink to a fork is removed when the mismatch size is three base pairs.
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Affiliation(s)
- Cheolhee Kim
- Department of Physics, Pohang University of Science and Technology, Pohang 790-784 (Republic of Korea)
| | - O-chul Lee
- Department of Physics, Pohang University of Science and Technology, Pohang 790-784 (Republic of Korea)
| | - Jae-Yeol Kim
- Department of Physics, Pohang University of Science and Technology, Pohang 790-784 (Republic of Korea)
| | - Wokyung Sung
- Department of Physics, Pohang University of Science and Technology, Pohang 790-784 (Republic of Korea)
- IBS Center for Self-assembly and Complexity, Pohang 790-784 (Republic of Korea)
| | - Nam Ki Lee
- Department of Physics, Pohang University of Science and Technology, Pohang 790-784 (Republic of Korea).
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15
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Khan N, Kolimi N, Rathinavelan T. Twisting right to left: A…A mismatch in a CAG trinucleotide repeat overexpansion provokes left-handed Z-DNA conformation. PLoS Comput Biol 2015; 11:e1004162. [PMID: 25876062 PMCID: PMC4395422 DOI: 10.1371/journal.pcbi.1004162] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 01/28/2015] [Indexed: 12/02/2022] Open
Abstract
Conformational polymorphism of DNA is a major causative factor behind several incurable trinucleotide repeat expansion disorders that arise from overexpansion of trinucleotide repeats located in coding/non-coding regions of specific genes. Hairpin DNA structures that are formed due to overexpansion of CAG repeat lead to Huntington’s disorder and spinocerebellar ataxias. Nonetheless, DNA hairpin stem structure that generally embraces B-form with canonical base pairs is poorly understood in the context of periodic noncanonical A…A mismatch as found in CAG repeat overexpansion. Molecular dynamics simulations on DNA hairpin stems containing A…A mismatches in a CAG repeat overexpansion show that A…A dictates local Z-form irrespective of starting glycosyl conformation, in sharp contrast to canonical DNA duplex. Transition from B-to-Z is due to the mechanistic effect that originates from its pronounced nonisostericity with flanking canonical base pairs facilitated by base extrusion, backbone and/or base flipping. Based on these structural insights we envisage that such an unusual DNA structure of the CAG hairpin stem may have a role in disease pathogenesis. As this is the first study that delineates the influence of a single A…A mismatch in reversing DNA helicity, it would further have an impact on understanding DNA mismatch repair. When a set of 3 nucleotides in a DNA sequence repeats beyond a certain number, it leads to incurable neurological or neuromuscular disorders. Such DNA sequences tend to form unusual DNA structures comprising of base pairing schemes different from the canonical A…T/G…C base pairs. Influence of such unusual base pairing on the overall 3-dimensional structure of DNA and its impact on the pathogenesis of disorder is not well understood. CAG repeat overexpansion that leads to Huntington’s disorder and several spinocerebellar ataxias forms noncanonical A…A base pair in between canonical C…G and G…C base pairs. However, no detailed structural information is available on the influence of an A…A mismatch on a DNA structure under any sequence context. Here, we have shown for the first time that A…A base pairing in a CAG repeat provokes the formation of left-handed Z-DNA due to the pronounced structural dissimilarity of A…A base pair with G…C base pair, leading to periodic B-Z junction. Thus, these results suggest that formation of periodic B-Z junction may be one of the molecular bases for CAG repeat instability.
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Affiliation(s)
- Noorain Khan
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana State, India
| | - Narendar Kolimi
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana State, India
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16
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Duan R, Wang B, Hong F, Zhang T, Jia Y, Huang J, Hakeem A, Liu N, Lou X, Xia F. Real-time monitoring of enzyme-free strand displacement cascades by colorimetric assays. Nanoscale 2015; 7:5719-25. [PMID: 25744386 DOI: 10.1039/c5nr00697j] [Citation(s) in RCA: 16] [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] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The enzyme-free toehold-mediated strand displacement reaction has shown potential for building programmable DNA circuits, biosensors, molecular machines and chemical reaction networks. Here we report a simple colorimetric method using gold nanoparticles as signal generators for the real-time detection of the product of the strand displacement cascade. During the process the assembled gold nanoparticles can be separated, resulting in a color change of the solution. This assay can also be applied in complex mixtures, fetal bovine serum, and to detect single-base mismatches. These results suggest that this method could be of general utility to monitor more complex enzyme-free strand displacement reaction-based programmable systems or for further low-cost diagnostic applications.
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Affiliation(s)
- Ruixue Duan
- Key Laboratory for Large-Format Battery Materials and Systems, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, China.
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17
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Ng KS, Lam SL. NMR proton chemical shift prediction of C·C mismatches in B-DNA. J Magn Reson 2015; 252:87-93. [PMID: 25681800 DOI: 10.1016/j.jmr.2015.01.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 01/09/2015] [Accepted: 01/11/2015] [Indexed: 05/15/2023]
Abstract
Accurate prediction of DNA chemical shifts facilitates resonance assignment and allows recognition of different conformational features. Based on the nearest neighbor model and base pair replacement approach, we have determined a set of triplet chemical shift values and correction factors for predicting the proton chemical shifts of B-DNA containing an internal C·C mismatch. Our results provide a reliable chemical shift prediction with an accuracy of 0.07 ppm for non-labile protons and 0.09 ppm for labile protons. In addition, we have also shown that the correction factors for C·C mismatches can be used interchangeably with those for T·T mismatches. As a result, we have generalized a set of correction factors for predicting the flanking residue chemical shifts of pyrimidine·pyrimidine mismatches.
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Affiliation(s)
- Kui Sang Ng
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
| | - Sik Lok Lam
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
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18
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Guarné A, Charbonnier JB. Insights from a decade of biophysical studies on MutL: Roles in strand discrimination and mismatch removal. Prog Biophys Mol Biol 2015; 117:149-156. [PMID: 25701376 DOI: 10.1016/j.pbiomolbio.2015.02.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Revised: 01/31/2015] [Accepted: 02/09/2015] [Indexed: 11/18/2022]
Abstract
DNA mismatch repair (MMR) is a conserved pathway that safeguards genome integrity by correcting replication errors. The coordinated actions of two proteins (MutS and MutL) initiate the mismatch repair response and defects in the genes encoding for these proteins have been linked to sporadic and hereditary cancers. The basic steps to repair a mismatch include recognizing the mismatch, discriminating the newly synthesized from the parental strand, removing and re-synthesizing the erroneous strand. Although the DNA mismatch repair pathway has been extensively studied over the last four decades, the strand discrimination mechanism has remained elusive in most organisms. Work over the last decade has brought significant progress onto this step of the pathway, in turn ascribing new and critical roles to the MutL protein. In this review, we describe biochemical, biophysical and structural analyses that have clarified how MutL aids at discriminating the newly synthesized strand from its template and marking it for removal.
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Affiliation(s)
- Alba Guarné
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.
| | - Jean-Baptiste Charbonnier
- CEA, IBITECS, Laboratoire de Biologie Structurale et Radiobiologie, CE-Saclay, F-91191 Gif sur Yvette, France; CNRS, URA 2096, F-91191 Gif sur Yvette, France.
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19
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Hirao I, Kimoto M. [Expansion of the genetic alphabet of DNA toward xenobiology]. Seikagaku 2015; 87:101-111. [PMID: 26571562] [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: 06/05/2023]
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20
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Guan Z, Liu J, Bai W, Lv Z, Jiang X, Yang S, Chen A, Lv G. Label-free and sensitive fluorescent detection of sequence-specific single-strand DNA based on S1 nuclease cleavage effects. PLoS One 2014; 9:e108401. [PMID: 25285445 PMCID: PMC4186753 DOI: 10.1371/journal.pone.0108401] [Citation(s) in RCA: 5] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Accepted: 08/27/2014] [Indexed: 11/18/2022] Open
Abstract
The ability to detect sequence-specific single-strand DNA (ssDNA) in complex, contaminant-ridden samples, using a fluorescent method directly without a DNA extraction and PCR step could simplify the detection of pathogens in the field and in the clinic. Here, we have demonstrated a simple label-free sensing strategy to detect ssDNA by employing its complementary ssDNA, S1 nuclease and nucleic acid fluorescent dyes. Upon clearing away redundant complementary ssDNA and possibly mismatched double strand DNA by using S1 nuclease, the fluorescent signal-to-noise ratio could be increased dramatically. It enabled the method to be adaptable to three different types of DNA fluorescent dyes and the ability to detect target ssDNA in complex, multicomponent samples, like tissue homogenate. The method can distinguish a two-base mismatch from avian influenza A (H1N1) virus. Also, it can detect the appearance of 50 pM target ssDNA in 0.5 µg · mL(-1) Lambda DNA, and 50 nM target ssDNA in 5 µg · mL(-1) Lambda DNA or in tissue homogenate. It is facile and cost-effective, and could be easily extended to detect other ssDNA with many common nucleic acid fluorescent dyes.
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Affiliation(s)
- Zheng Guan
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences; Key Laboratory of Agro-food Quality and Safety, Ministry of Agriculture, Beijing, China
- Institute of Materia Medica, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jinchuan Liu
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences; Key Laboratory of Agro-food Quality and Safety, Ministry of Agriculture, Beijing, China
| | - Wenhui Bai
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences; Key Laboratory of Agro-food Quality and Safety, Ministry of Agriculture, Beijing, China
| | - Zhenzhen Lv
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences; Key Laboratory of Agro-food Quality and Safety, Ministry of Agriculture, Beijing, China
| | - Xiaoling Jiang
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences; Key Laboratory of Agro-food Quality and Safety, Ministry of Agriculture, Beijing, China
| | - Shuming Yang
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences; Key Laboratory of Agro-food Quality and Safety, Ministry of Agriculture, Beijing, China
| | - Ailiang Chen
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences; Key Laboratory of Agro-food Quality and Safety, Ministry of Agriculture, Beijing, China
- * E-mail: (AC); (GL)
| | - Guiyuan Lv
- Institute of Materia Medica, Zhejiang Chinese Medical University, Hangzhou, China
- * E-mail: (AC); (GL)
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21
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Alfsnes K, Raynaud X, Tønjum T, Ambur OH. Mathematical and live meningococcal models for simple sequence repeat dynamics - coherent predictions and observations. PLoS One 2014; 9:e101637. [PMID: 24999629 PMCID: PMC4085013 DOI: 10.1371/journal.pone.0101637] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 06/10/2014] [Indexed: 11/18/2022] Open
Abstract
Evolvability by means of simple sequence repeat (SSR) instability is a feature under the constant influence of opposing selective pressures to expand and compress the repeat tract and is mechanistically influenced by factors that affect genetic instability. In addition to direct selection for protein expression and structural integrity, other factors that influence tract length evolution were studied. The genetic instability of SSRs that switch the expression of antibiotic resistance ON and OFF was modelled mathematically and monitored in a panel of live meningococcal strains. The mathematical model showed that the SSR length of a theoretical locus in an evolving population may be shaped by direct selection of expression status (ON or OFF), tract length dependent (α) and tract length independent factors (β). According to the model an increase in α drives the evolution towards shorter tracts. An increase in β drives the evolution towards a normal distribution of tract lengths given that an upper and a lower limit are set. Insertion and deletion biases were shown to skew allelic distributions in both directions. The meningococcal SSR model was tested in vivo by monitoring the frequency of spectinomycin resistance OFF→ON switching in a designed locus. The instability of a comprehensive panel of the homopolymeric SSRs, constituted of a range of 5-13 guanine nucleotides, was monitored in wildtype and mismatch repair deficient backgrounds. Both the repeat length itself and mismatch repair deficiency were shown to influence the genetic instability of the homopolymeric tracts. A possible insertion bias was observed in tracts ≤G10. Finally, an inverse correlation between the number of tract-encoded amino acids and growth in the presence of ON-selection illustrated a limitation to SSR expansion in an essential gene associated with the designed model locus and the protein function mediating antibiotic resistance.
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Affiliation(s)
- Kristian Alfsnes
- Department of Microbiology, University of Oslo, Oslo, Norway
- Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway
| | - Xavier Raynaud
- Department of Mathematics, University of Oslo, Oslo, Norway
| | - Tone Tønjum
- Department of Microbiology, University of Oslo, Oslo, Norway
- Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway
| | - Ole Herman Ambur
- Department of Microbiology, University of Oslo, Oslo, Norway
- Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
- * E-mail:
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22
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Lu N, Gao A, Dai P, Song S, Fan C, Wang Y, Li T. CMOS-compatible silicon nanowire field-effect transistors for ultrasensitive and label-free microRNAs sensing. Small 2014; 10:2022-8. [PMID: 24574202 DOI: 10.1002/smll.201302990] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2013] [Revised: 09/19/2013] [Indexed: 05/24/2023]
Abstract
MicroRNAs (miRNAs) have been regarded as promising biomarkers for the diagnosis and prognosis of early-stage cancer as their expression levels are associated with different types of human cancers. However, it is a challenge to produce low-cost miRNA sensors, as well as retain a high sensitivity, both of which are essential factors that must be considered in fabricating nanoscale biosensors and in future biomedical applications. To address such challenges, we develop a complementary metal oxide semiconductor (CMOS)-compatible SiNW-FET biosensor fabricated by an anisotropic wet etching technology with self-limitation which provides a much lower manufacturing cost and an ultrahigh sensitivity. This nanosensor shows a rapid (< 1 minute) detection of miR-21 and miR-205, with a low limit of detection (LOD) of 1 zeptomole (ca. 600 copies), as well as an excellent discrimination for single-nucleotide mismatched sequences of tumor-associated miRNAs. To investigate its applicability in real settings, we have detected miRNAs in total RNA extracted from lung cancer cells as well as human serum samples using the nanosensors, which demonstrates their potential use in identifying clinical samples for early diagnosis of cancer.
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Affiliation(s)
- Na Lu
- State Key Laboratories of Transducer, Technology & Science and Technology on Micro-system Laboratory, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 200050, Shanghai, China
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23
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Li M, Zhang Q, Liu L, Lu W, Wei H, Li RW, Lu S. Expression of the mismatch repair gene hMLH1 is enhanced in non-small cell lung cancer with EGFR mutations. PLoS One 2013; 8:e78500. [PMID: 24205245 PMCID: PMC3812034 DOI: 10.1371/journal.pone.0078500] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 09/13/2013] [Indexed: 11/19/2022] Open
Abstract
Mismatch repair (MMR) plays a pivotal role in keeping the genome stable. MMR dysfunction can lead to carcinogenesis by gene mutation accumulation. HMSH2 and hMLH1 are two key components of MMR. High or low expression of them often mark the status of MMR function. Mutations (EGFR, KRAS, etc) are common in non-small cell lung cancer (NSCLC). However, it is not clear what role MMR plays in NSCLC gene mutations. The expression of MMR proteins hMSH2 and hMLH1, and the proliferation markers PCNA and Ki67 were measured by immunohistochemistry in 181 NSCLCs. EGFR and KRAS mutations were identified by high resolution melting analysis. Stronger hMLH1 expression correlated to a higher frequency of EGFR mutations in exon 19 and 21 (p<0.0005). Overexpression of hMLH1 and the adenocarcinoma subtype were both independent factors that related to EGFR mutations in NSCLCs (p=0.013 and p<0.0005). The expression of hMLH1, hMSH2 and PCNA increased, while Ki67 expression significantly decreased (p=0.030) in NSCLCs with EGFR mutations. Overexpression of hMLH1 could be a new molecular marker to predict the response to EGFR-TKIs in NSCLCs. Furthermore, EGFR mutations might be an early event of NSCLC that occur before MMR dysfunction.
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Affiliation(s)
- Mei Li
- Central Laboratory, The Second Hospital of Dalian Medical University, Dalian, PR China
| | - Qiuping Zhang
- Department of Pathology, The First Hospital of Dalian Medical University, Dalian, PR China
| | - Lina Liu
- Department of Internal Medicine, The First Hospital of Dalian Medical University, Dalian, PR China
| | - Weipeng Lu
- Central Laboratory, The Second Hospital of Dalian Medical University, Dalian, PR China
| | - Hong Wei
- Central Laboratory, The Second Hospital of Dalian Medical University, Dalian, PR China
| | - Rachel W. Li
- The Medical School, The Australian Medical University, Canberra, Australia
| | - Shen Lu
- Central Laboratory, The Second Hospital of Dalian Medical University, Dalian, PR China
- * E-mail:
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24
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Milanović R, Stanec S, Stanec M, Korusić A, Husedzinović I, Razumović JJ. Expression of genes responsible for the repair of mispaired bases of the DNA (MLH1) in invasive ductal breast carcinoma. Coll Antropol 2013; 37:929-935. [PMID: 24308239] [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: 06/02/2023]
Abstract
Breast cancer is a heterogeneous group of diseases determined and distinguished by cellular type, gene expression and clinical signs and symptoms. Identification of histological and biological markers is of great value in predicting the progression of tumor growth and anticipating the expected response to various treatment options. Due to a high degree of cell proliferation in breast tumors and high genetic instability of these tumors, as a consequence of defective DNA repair mechanisms, chemotherapy as a treatment option often renders very successful results. During our scientific research we wanted to determine the involvement of the genetic polymorphisms of DNA mismatch repair system (MLH1 gene) and the subsequent development of breast carcinoma. This study included 108 patients who were surgically treated for invasive breast cancer at the Department of Plastic, Reconstructive and Aesthetic Surgery, University Hospital "Dubrava". The expression of the MLH1 gene was determined by immunohistochemical methods. The results showed that 82.9% of tumor cells expressed the MLH1 gene. Analysis of survival rate for patients with invasive ductal breast cancer showed a statistically significant (p = 0.043) correlation with the expression of MLH1 genes. The overall five year survival rate of our patients was 78.7%. These results indicate that there is a possible involvement of MLH1 gene in the progression and development of breast cancer.
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Affiliation(s)
- Rudolf Milanović
- University of Zagreb, University Hospital "Dubrava", Department for Plastic, Reconstructive and Aesthetic Surgery, Zagreb, Croatia.
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25
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Ledeker BM, De Long SK. The effect of multiple primer-template mismatches on quantitative PCR accuracy and development of a multi-primer set assay for accurate quantification of pcrA gene sequence variants. J Microbiol Methods 2013; 94:224-31. [PMID: 23806694 DOI: 10.1016/j.mimet.2013.06.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 06/14/2013] [Accepted: 06/15/2013] [Indexed: 11/19/2022]
Abstract
Quantitative PCR (qPCR) is a critical tool for quantifying the abundance of specific organisms and the level or expression of target genes in medically and environmentally relevant systems. However, often the power of this tool has been limited because primer-template mismatches, due to sequence variations of targeted genes, can lead to inaccuracies in measured gene quantities, detection failures, and spurious conclusions. Currently available primer design guidelines for qPCR were developed for pure culture applications, and available primer design strategies for mixed cultures were developed for detection rather than accurate quantification. Furthermore, past studies examining the impact of mismatches have focused only on single mismatches while instances of multiple mismatches are common. There are currently no appropriate solutions to overcome the challenges posed by sequence variations. Here, we report results that provide a comprehensive, quantitative understanding of the impact of multiple primer-template mismatches on qPCR accuracy and demonstrate a multi-primer set approach to accurately quantify a model gene pcrA (encoding perchlorate reductase) that has substantial sequence variation. Results showed that for multiple mismatches (up to 3 mismatches) in primer regions where mismatches were previously considered tolerable (middle and 5' end), quantification accuracies could be as low as ~0.1%. Furthermore, tests were run using a published pcrA primer set with mixtures of genomic DNA from strains known to harbor the target gene, and for some mixtures quantification accuracy was as low as ~0.8% or was non-detect. To overcome these limitations, a multiple primer set assay including minimal degeneracies was developed for pcrA genes. This assay resulted in nearly 100% accurate detection for all mixed microbial communities tested. The multi-primer set approach demonstrated herein can be broadly applied to other genes with known sequences.
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Affiliation(s)
- Brett M Ledeker
- Department of Civil and Environmental Engineering, Colorado State University, 1372 Campus Delivery, Fort Collins, CO 80523, USA.
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Hong G, Lee SH, Ge S, Zhou S. A novel low temperature PCR assured high-fidelity DNA amplification. Int J Mol Sci 2013; 14:12853-62. [PMID: 23787473 PMCID: PMC3709816 DOI: 10.3390/ijms140612853] [Citation(s) in RCA: 6] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 06/05/2013] [Accepted: 06/07/2013] [Indexed: 12/31/2022] Open
Abstract
As previously reported, a novel low temperature (LoTemp) polymerase chain reaction (PCR) catalyzed by a moderately heat-resistant (MHR) DNA polymerase with a chemical-assisted denaturation temperature set at 85 °C instead of the conventional 94-96 °C can achieve high-fidelity DNA amplification of a target DNA, even after up to 120 PCR thermal cycles. Furthermore, such accurate amplification is not achievable with conventional PCR. Now, using a well-recognized L1 gene segment of the human papillomavirus (HPV) type 52 (HPV-52) as the template for experiments, we demonstrate that the LoTemp high-fidelity DNA amplification is attributed to an unusually high processivity and stability of the MHR DNA polymerase whose high fidelity in template-directed DNA synthesis is independent of non-existent 3'-5' exonuclease activity. Further studies and understanding of the characteristics of the LoTemp PCR technology may facilitate implementation of DNA sequencing-based diagnostics at the point of care in community hospital laboratories.
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Affiliation(s)
- Guofan Hong
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China; E-Mails: (S.G.); (S.Z.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +86-21-5492-1223; Fax: +86-21-5492-1226
| | - Sin Hang Lee
- Milford Hospital and Milford Molecular Laboratory, 2044 Bridgeport Avenue, Milford, CT 06460, USA; E-Mail:
| | - Shichao Ge
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China; E-Mails: (S.G.); (S.Z.)
| | - Shaoxia Zhou
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China; E-Mails: (S.G.); (S.Z.)
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Fedorov DV, Koval'tsova SV, Evstukhina TA, Peshekhonov VT, Chernenkov AI, Korolev VG. [HSM6 gene is identical to PSY4 gene in Saccharomyces cerevisiae yeasts]. Genetika 2013; 49:328-336. [PMID: 23755532 DOI: 10.7868/s0016675813020069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Previously, we isolated mutant yeasts Saccharomyces cerevisiae with an increased rate of spontaneous mutagenesis. Here, we studied the properties of HSM6 gene, the hsm6-1 mutation of which increased the frequency of UV-induced mutagenesis and decreased the level of UV-induced mitotic crossover at the centromere gene region, ADE2. HSM6 gene was mapped on the left arm of chromosome 11 in the region where the PSY4 gene is located. The epistatic analysis has shown that the hsm6-1 mutation represents an allele of PSY4 gene. Sequencing of hsm6-1 mutant allele has revealed a frameshift mutation, which caused the substitution of Lys218Glu and the generation of a stop codon in the next position. The interactions of hsm6-1 and rad52 mutations were epistatic. Our data show that the PSY4 gene plays a key role in the regulation of cell withdrawal from checkpoint induced by DNA disturbances.
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Taylor SH, Harmse J, Arbuthnot P, Van Den Berg F, Weinberg MS, Rey MEC. Construction of effective inverted repeat silencing constructs using sodium bisulfite treatment coupled with strand-specific PCR. Biotechniques 2012; 52:254-62. [PMID: 22482441 DOI: 10.2144/0000113839] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [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: 03/25/2010] [Accepted: 02/21/2012] [Indexed: 11/23/2022] Open
Abstract
RNA silencing has been exploited to produce transgenic plants with resistance to viral pathogens via posttranscriptional gene silencing (PTGS). In some cases, this technology is difficult to apply due to the instability of inverted repeat (IR) constructs during cloning and plant transformation. Although such constructs have been shown to be stabilized with introns and efficiently induce RNA silencing, we found that the Pdk intron did not stabilize South African cassava mosaic virus (SACMV) silencing constructs. Therefore, we developed a method for producing long SACMV IR constructs through bisulfite-induced base pair mismatches on the sense arm prior to IR assembly. Expression of SACMV BC1 mismatched IR constructs in the model test plant Nicotiana benthamiana resulted in a reduction in viral BC1 transcript levels, hence viral replication, upon SACMV infection. Mismatched SACMV AC1 IR constructs induced PTGS more efficiently in a N. benthamiana callus system than nonmismatched IR constructs. Our novel method for IR construct generation should be applicable to many sequences where the generation of these constructs has proven difficult in the past.
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Affiliation(s)
- Sarah H Taylor
- Plant Biotechnology Research Group, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa
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Wu H, Ma H, Ye C, Ramirez D, Chen S, Montoya J, Shankar P, Wang XA, Manjunath N. Improved siRNA/shRNA functionality by mismatched duplex. PLoS One 2011; 6:e28580. [PMID: 22174840 PMCID: PMC3235145 DOI: 10.1371/journal.pone.0028580] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Accepted: 11/10/2011] [Indexed: 11/26/2022] Open
Abstract
siRNA (small interfering RNA) and shRNA (small hairpin RNA) are powerful and commonly used tools in biomedical research. Currently, siRNAs are generally designed as two 21 nt strands of RNA that include a 19 nt completely complementary part and a 2 nt overhang. However, since the si/shRNAs use the endogenous miRNA machinery for gene silencing and the miRNAs are generally 22 nt in length and contain multiple internal mismatches, we tested if the functionality can be increased by designing the si/shRNAs to mimic a miRNA structure. We systematically investigated the effect of single or multiple mismatches introduced in the passenger strand at different positions on siRNA functionality. Mismatches at certain positions could significantly increase the functionality of siRNAs and also, in some cases decreased the unwanted passenger strand functionality. The same strategy could also be used to design shRNAs. Finally, we showed that both si and miRNA structured oligos (siRNA with or without mismatches in the passenger strand) can repress targets in all individual Ago containing cells, suggesting that the Ago proteins do not differentiate between si/miRNA-based structure for silencing activity.
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Affiliation(s)
- Haoquan Wu
- Center of Excellence in Infectious Disease Research, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, United States of America
- * E-mail: (HW); (NM)
| | - Hongming Ma
- Center of Excellence in Infectious Disease Research, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, United States of America
| | - Chunting Ye
- Center of Excellence in Infectious Disease Research, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, United States of America
| | - Danielle Ramirez
- Center of Excellence in Infectious Disease Research, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, United States of America
| | - Shuiping Chen
- Center of Excellence in Infectious Disease Research, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, United States of America
| | - Jessica Montoya
- Center of Excellence in Infectious Disease Research, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, United States of America
| | - Premlata Shankar
- Center of Excellence in Infectious Disease Research, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, United States of America
| | - Xiaozhong A. Wang
- Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, Evanston, Illinois, United States of America
| | - N. Manjunath
- Center of Excellence in Infectious Disease Research, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, United States of America
- * E-mail: (HW); (NM)
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Abstract
Adenosine-to-inosine modification of RNA molecules (A-to-I RNA editing) is an important mechanism that increases transciptome diversity. It occurs when a genomically encoded adenosine (A) is converted to an inosine (I) by ADAR proteins. Sequencing reactions read inosine as guanosine (G); therefore, current methods to detect A-to-I editing sites align RNA sequences to their corresponding DNA regions and identify A-to-G mismatches. However, such methods perform poorly on RNAs that underwent extensive editing ("ultra"-editing), as the large number of mismatches obscures the genomic origin of these RNAs. Therefore, only a few anecdotal ultra-edited RNAs have been discovered so far. Here we introduce and apply a novel computational method to identify ultra-edited RNAs. We detected 760 ESTs containing 15,646 editing sites (more than 20 sites per EST, on average), of which 13,668 are novel. Ultra-edited RNAs exhibit the known sequence motif of ADARs and tend to localize in sense strand Alu elements. Compared to sites of mild editing, ultra-editing occurs primarily in Alu-rich regions, where potential base pairing with neighboring, inverted Alus creates particularly long double-stranded RNA structures. Ultra-editing sites are underrepresented in old Alu subfamilies, tend to be non-conserved, and avoid exons, suggesting that ultra-editing is usually deleterious. A possible biological function of ultra-editing could be mediated by non-canonical splicing and cleavage of the RNA near the editing sites.
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Affiliation(s)
- Shai Carmi
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel.
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Rikimaru K, Komatsu M, Suzuki K, Uemoto Y, Takeda H, Takahashi H. Association between cholecystokinin type A receptor haplotypes and growth traits in Japanese Hinai-dori crossbred chickens. Mol Biol Rep 2011; 39:4479-84. [PMID: 21947885 DOI: 10.1007/s11033-011-1237-9] [Citation(s) in RCA: 12] [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] [Received: 02/02/2011] [Accepted: 09/13/2011] [Indexed: 11/26/2022]
Abstract
We previously identified quantitative trait loci for body weight and average daily gain in a common region between MCW0240 (chr 4: 69.9 Mb) and ABR0622 (chr 4: 86.3 Mb) on chicken chromosome 4 in an F(2) resource population produced by crossing low- and high-growth lines of the Hinai-dori breed. Cholecystokinin type A receptor (CCKAR) is a candidate gene affecting growth traits in the region. In this study, we genotyped polymorphisms of the CCKAR gene and investigated its association with growth traits in a Hinai-dori F(2) intercross population. All the exons of the CCKAR gene in the parental population were subjected to PCR amplification, nucleotide sequenced and haplotypes identified. To distinguish resultant diplotype individuals in the F(2) population, a mismatch amplification mutation assay was performed. Five haplotypes (Haplotypes 1-5) were accordingly identified. Six genotypes produced by the combination of three haplotypes (Haplotype 1, 3, and 4) were examined in order to identify associations between CCKAR haplotypes and growth traits. The data indicate that Haplotype 1 was superior to Haplotype 3 and 4 in body weight at 10 and 14 weeks of age, average daily gain between 4 and 10 weeks, 10 and 14 weeks, and 0 and 14 weeks of age. It was concluded that CCKAR is a useful marker of growth traits and could be used to develop strategies for improving growth traits in the Hinai-dori breed.
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Affiliation(s)
- Kazuhiro Rikimaru
- Livestock Experiment Station, Akita Prefectural Agriculture, Forestry, and Fisheries Research Center, Daisen, 019-1701, Japan
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Lu XJ, Yu DL, Wang JX, Pan XL, Jin P, Li SR, Sheng JQ. [Effect of estrogen on mismatch repair gene expression in colon cancer cells]. Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi 2011; 27:754-756. [PMID: 21722527] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
AIM To investigate the effect of estrogen on MMR gene expression in colon cancer cells COLO205. METHODS By employing semi-quantitative RT-PCR and Western blotting techniques, changes in the expression of MMR genes (hMLH1 and hMSH2) induced by different levels of estradiol (E2) and ICI182.780, an estrogen receptor inhibitor, was investigated in cultured COLO205 cells. The effect was then verified by real time RT-PCR. RESULTS E2 enhanced the expression of hMLH1 in COLO205 cells at transcriptional level, and a dose-response relationship was established when the concentration of E2 was between 10(-12);-10(-8); mol/L. The enhancement was suppressed by the estrogen receptor inhibitor ICI182.780. On the other hand, there was no significant effect of E2 on hMSH2 expression in COLO205 cells. CONCLUSION E2 can increase the expression of hMLH1 in colon cancer cells COLO205, and this finding sheds new light on the mechanism of estrogen protecting against colon cancer by regulating MMR system.
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Affiliation(s)
- Xiao-juan Lu
- Department of Gastroenterology, General Hospital of Beijing Military Command, Beijing, China.
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Li H, Zhang Y, Luo Y, Sun X. Nano-C(60) : a novel, effective, fluorescent sensing platform for biomolecular detection. Small 2011; 7:1562-1568. [PMID: 21520502 DOI: 10.1002/smll.201100068] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Revised: 02/22/2011] [Indexed: 05/30/2023]
Abstract
Water-soluble nano-C(60) can serve as a novel, effective, fluorescent sensing platform for biomolecular detection with high sensitivity and selectivity. In this paper, fluorescent detection of DNA and thrombin via nano-C(60) is demonstrated for the first time. The principle of the assay lies in the fact that the adsorption of the fluorescently labeled single-stranded DNA (ssDNA) probe by nano-C(60) leads to substantial fluorescence quenching. In the presence of a target, the biomolecular mutual interaction suppresses this quenching, signaling the existence of the target. This sensing system rivals graphene oxide but is superior to other carbon-structure-based systems. The present method can also achieve multiplex DNA detection and withstand the interference from human blood serum.
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Affiliation(s)
- Hailong Li
- Changchun Institute of Applied Chemistry, Changchun 130022, Jilin, People's Republic of China
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34
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Tang D, Lu P, Liao D, Yang X, Zhang Y, Yu C. Label-free detection of polynucleotide single-base mismatch via pyrene probe excimer emission. Spectrochim Acta A Mol Biomol Spectrosc 2011; 78:747-752. [PMID: 21195658 DOI: 10.1016/j.saa.2010.12.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2010] [Accepted: 12/06/2010] [Indexed: 05/30/2023]
Abstract
The pyrene probe and pyrene-labeled oligonucleotides (ODNs) probe are expected to be candidates as fluorescent probe for DNA assay. In particular, label-free detection is a very hot because of its simpleness, speediness and cheapness. Herein, we have investigated the use of a pyrenylakylammonium salt, a novel fluorescent probe for the detection of one single nucleotide polymorphism (SNP) in double stranded DNA. After S1 nuclease digestion, the pyrene probes bind electrostatically to the perfect complement DNA and emit a strong excimer emission. However, treatment of the non-complementary DNA with S1 nuclease caused nucleotide fragments of less than 5 bases, which could not induce excimer emission. By comparing ratio of excimer to monomer fluorescence between normal and mutant DNA after S1 nuclease digestion, One-base mutation in DNA was detected easily. This new method may be applied to the detection of SNP.
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Affiliation(s)
- Dan Tang
- Department of Animal Biotechnology, College of Animal Science and Veterinary Medicine, Jilin University, Changchun 130062, PR China
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35
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Nasirizadeh N, Zare HR, Pournaghi-Azar MH, Hejazi MS. Introduction of hematoxylin as an electroactive label for DNA biosensors and its employment in detection of target DNA sequence and single-base mismatch in human papilloma virus corresponding to oligonucleotide. Biosens Bioelectron 2010; 26:2638-44. [PMID: 21146975 DOI: 10.1016/j.bios.2010.11.026] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2010] [Accepted: 11/17/2010] [Indexed: 01/21/2023]
Abstract
For the detection of DNA hybridization, a new electrochemical biosensor was developed on the basis of the interaction of hematoxylin with 20-mer deoxyoligonucleotides (from human papilloma virus, HPV). The study was performed based on the interaction of hematoxylin with an alkanethiol DNA probe self-assembled gold electrode (ss-DNA/AuE) and its hybridization form (ds-DNA/AuE). The optimum conditions were found for the immobilization of HPV probe on the gold electrode (AuE) surface and its hybridization with the target DNA. Electrochemical detection of the self-assembled DNA and the hybridization process were performed by cyclic voltammetry (CV) and differential pulse voltammetry (DPV) over the potential range where the accumulated hematoxylin at the modified electrode was electroactive. Observing a remarkable difference between the voltammetric signals of the hematoxylin obtained from different hybridization samples (non-complementary, mismatch and complementary DNAs), we confirmed the potential of the developed biosensor in detecting and discriminating the target complementary DNA from non-complementary and mismatch oligonucleotides. Under optimum conditions, the electrochemical signal had a linear relationship with the concentration of the target DNA ranging from 12.5 nM to 350.0 nM, and the detection limit was 3.8 nM.
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Affiliation(s)
- Navid Nasirizadeh
- Department of Chemistry, Yazd University, P.O. Box 89195-741, Yazd, Iran
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Perrett CM, Harwood CA, McGregor JM, Warwick J, Cerio R, Karran P. Expression of DNA mismatch repair proteins and MSH2 polymorphisms in nonmelanoma skin cancers of organ transplant recipients. Br J Dermatol 2010; 162:732-42. [PMID: 19818066 DOI: 10.1111/j.1365-2133.2009.09550.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [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: 12/01/2022]
Abstract
BACKGROUND Organ transplant recipients (OTRs) have an increased risk of skin cancer. Treatment with azathioprine, commonly used in post-transplant immunosuppressive regimens, results in incorporation of 6-thioguanine (6-TG) into DNA. Mismatch repair (MMR)-defective cells are resistant to killing by 6-TG. Azathioprine exposure confers a survival advantage on MMR-defective cells, which are hypermutable and may therefore contribute to azathioprine-related nonmelanoma skin cancer, a phenomenon we have previously demonstrated in transplant-associated sebaceous carcinomas. The MSH2 protein is an important component of DNA MMR. The -6 exon 13 T>C MSH2 polymorphism is associated with impaired MMR, drug resistance and certain cancers. OBJECTIVES To investigate (i) whether loss of MMR protein expression and microsatellite instability are over-represented in squamous cell carcinomas (SCCs) from OTRs on azathioprine compared with SCCs from immunocompetent patients, and (ii) whether the MSH2 -6 exon 13 polymorphism is over-represented in OTRs with skin cancer on azathioprine. METHODS (i) Immunohistochemical staining was used to assess expression of the MMR proteins MSH2 and MLH1 in cutaneous SCCs from OTRs on azathioprine and from immunocompetent patients. (ii) Blood samples from OTRs on azathioprine with and without skin cancer were genotyped for the -6 exon 13 MSH2 polymorphism. RESULTS (i) MSH2 and MLH1 protein expression was not altered in SCCs from OTRs on azathioprine and there was no difference in expression between SCCs from OTRs and immunocompetent patients. (ii) There was no association between MSH2 polymorphism genotype frequency and OTR skin cancer status. CONCLUSIONS Despite previous findings in transplant-associated sebaceous carcinomas, defective MMR and the -6 exon 13 MSH2 polymorphism are unlikely to play a significant role in the development of SCC in OTRs on azathioprine.
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Affiliation(s)
- C M Perrett
- Centre for Cutaneous Research and Department of Dermatology, Institute of Cell and Molecular Science, Barts and The London School of Medicine and Dentistry, Queen Mary, University of London, 4 Newark Street, London E1 2AT, U.K.
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Houdayer C, Moncoutier V, Champ J, Weber J, Viovy JL, Stoppa-Lyonnet D. Enhanced mismatch mutation analysis: simultaneous detection of point mutations and large scale rearrangements by capillary electrophoresis, application to BRCA1 and BRCA2. Methods Mol Biol 2010; 653:147-180. [PMID: 20721742 DOI: 10.1007/978-1-60761-759-4_9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [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: 05/29/2023]
Abstract
We present the routine diagnostic application of EMMA (Enhanced Mismatch Mutation Analysis, Fluigent), a new, fast, reliable, and cost-effective method for mutation screening. This method is based on heteroduplex analysis by capillary electrophoresis and relies on the use of innovative matrices increasing the electrophoretic mobility differences between homoduplex and heteroduplex DNA, which is further enhanced by the addition of nucleosides in the separation matrix. Nucleosides interact with heteroduplex mismatched bases, hence increasing mobility difference with homoduplex. As separations are performed by multi-capillary electrophoresis, it allows for high automation, low cost, and high throughput. Moreover, EMMA, in combination with limiting PCR conditions, can be used to achieve the simultaneous detection of point mutation and large scale rearrangement in a single run.We now report on the routine diagnostic use of this method for BRCA1 and BRCA2 screening. The coding sequence and exon-intron junctions of BRCA1 and BRCA2 were amplified in 24 multiplex PCRs using a single condition. PCRs were electrophoresed with a single analytical condition on an ABI3100, and data were analyzed using dedicated software (Emmalys).The strength of this new method relies on the following assets: (1) a single condition of analysis: modeling related to melting domain is not required (2) simultaneous detection of point mutations and large scale rearrangements, (3) optimized and ready-to-use polymer that can be used on various ABI sequencers, (4) easy to use, (5) low reagent costs, and (6) throughput.
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Affiliation(s)
- Claude Houdayer
- Service de Génétique Oncologique, Institut Curie Hôpital, Paris, France
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Abstract
The single-crystal structure of a DNA Holliday junction assembled from four unique sequences shows a structure that conforms to the general features of models derived from similar constructs in solution. The structure is a compact stacked-X form junction with two sets of stacked B-DNA-type arms that coaxially stack to form semicontinuous duplexes interrupted only by the crossing of the junction. These semicontinuous helices are related by a right-handed rotation angle of 56.5 degrees, which is nearly identical to the 60 degree angle in the solution model but differs from the more shallow value of approximately 40 degrees for previous crystal structures of symmetric junctions that self-assemble from single identical inverted-repeat sequences. This supports the model in which the unique set of intramolecular interactions at the trinucleotide core of the crossing strands, which are not present in the current asymmetric junction, affects both the stability and geometry of the symmetric junctions. An unexpected result, however, is that a highly wobbled A.T base pair, which is ascribed here to a rare enol tautomer form of the thymine, was observed at the end of a CCCC/GGGG sequence within the stacked B-DNA arms of this 1.9 A resolution structure. We suggest that the junction itself is not responsible for this unusual conformation but served as a vehicle for the study of this CG-rich sequence as a B-DNA duplex, mimicking the form that would be present in a replication complex. The existence of this unusual base lends credence to and defines a sequence context for the "rare tautomer hypothesis" as a mechanism for inducing transition mutations during DNA replication.
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Affiliation(s)
- Patricia Khuu
- Department of Biochemistry and Biophysics, ALS 2011, Oregon State University, Corvallis, OR 97331
| | - P. Shing Ho
- Department of Biochemistry and Biophysics, ALS 2011, Oregon State University, Corvallis, OR 97331
- Department of Biochemistry and Molecular Biology, 1870 Campus Delivery, Colorado State University, Fort Collins, CO 80523
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Niessen RC, Sijmons RH, Berends MJW, Ou J, Hofstra RMW, Kleibeuker JH. Hereditary non-polyposis colorectal cancer: identification of mutation carriers and assessing pathogenicity of mutations. Scand J Gastroenterol 2009:70-7. [PMID: 15696853 DOI: 10.1080/00855920410010915] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
Hereditary non-polyposis colorectal cancer (HNPCC), also referred to as Lynch syndrome, is an autosomal dominantly inherited disorder that is characterized by susceptibility to colorectal cancer and extracolonic malignancies, in particular endometrial cancer. HNPCC is caused by pathogenic mutations in the mismatch repair (MMR) genes, which play an important role in maintaining genomic stability during DNA replication. Identification of MMR gene mutation carriers is important as this enables them to enrol in surveillance programmes, thus reducing their risk of cancer and increasing survival. Clinical criteria as well as non-clinical criteria have been formulated to select patients for mutation analysis. In this paper we review the approaches used to select patients for mutation analysis. Mutation analysis in the MMR genes may yield mutations of which the pathogenic nature is unclear. Criteria to determine the pathogenicity of such variants are discussed, as well as differences in design of functional assays to assess pathogenicity.
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Affiliation(s)
- R C Niessen
- Dept. of Clinical Genetics, University Hospital Groningen, Groningen, The Netherlands
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De Bruin JHFM, Ligtenberg MJL, Nagengast FM, Adang EMM, Van Krieken JHJM, Hoogerbrugge N. Optimizing the detection of hereditary non-polyposis colorectal cancer: An update. Scand J Gastroenterol 2009:146-52. [PMID: 16782634 DOI: 10.1080/00365520600664508] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Hereditary non-polyposis colorectal cancer (HNPCC) is a dominant inherited disease and accounts for up to 5% of all colorectal cancer (CRC) patients. Despite the optimization of selection criteria and enhancements in molecular techniques for identifying more families with HNPCC, most cases are not recognized. Poor patient recollection of family history and inadequate family history-taking are main causative factors. We propose a new strategy for detecting HNPCC, one in which the pathologist selects patients for microsatellite instability (MSI) testing. Criteria for MSI analysis are: (1) CRC before the age of 50 years, (2) second CRC before 70 years, (3) CRC and HNPCC-associated cancer before 70 years, or (4) adenoma before 40 years. Additionally, patients with a positive MSI test and patients with a positive family history are offered referral for genetic counselling. With this strategy, at least twice the number of HNPCC patients will be identified among a population of CRC patients, and in a cost-effective, efficient and feasible way. The identification of patients with HNPCC is important because intensive surveillance can prevent death from CRC.
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Affiliation(s)
- J H F M De Bruin
- Department of Human Genetics, Radboud University Medical Centre Nijmegen, The Netherlands
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Mehigan BJ, Ashman JNE, Baker RP, Macdonald A, Greenman J, Monson JRT, Cawkwell L. Mismatch repair, p53 and chromosomal aberrations in primary colorectal carcinomas. Acta Oncol 2009; 45:61-6. [PMID: 16464797 DOI: 10.1080/02841860500374463] [Citation(s) in RCA: 2] [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: 10/25/2022]
Abstract
Colorectal carcinoma progresses via at least two genetic pathways. Microsatellite instability, due to defective mismatch repair genes, characterizes one pathway and gross chromosomal instability another. The involvement of p53 and mismatch repair gene abnormalities within these pathways has not been fully explored. We aimed to investigate the relationships of p53 and mismatch repair gene defects on gross chromosomal aberrations detected by comparative genomic hybridization in 49 colorectal carcinomas. Tumours demonstrating loss of expression for hMLH1 or hMSH2 proteins demonstrated a highly significant attenuation in the number of gross chromosomal aberrations (p = 0.007) and were less likely to show p53 overexpression (p = 0.02). Within the mismatch repair normal tumours, p53 status did not affect the total number of chromosomal aberrations but p53 overexpression was significantly associated with a higher frequency of amplifications at 8q22-ter and at 13q21-22. Colorectal cancer demonstrates distinct molecular phenotypes and should be sub-classified accordingly.
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Affiliation(s)
- Brian J Mehigan
- Postgraduate Medical Institute of the University of Hull and Hull York Medical School, University of Hull, UK
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Abstract
DNA strand exchange is of great importance in vivo for genetic recombination and DNA repair. The detailed mechanism of strand exchange is not understood in full detail despite extensive studies. Simplistic model systems in which molecular parameters can be varied independently are therefore of interest to study. We chose the surface of a positively charged liposome as a scaffold, which we recently demonstrated to be able to catalyze the exchange of fully complementary DNA oligonucleotides. We here study how single base pair mismatches affect the rate of strand exchange on the liposome surface. Interestingly, the rate of the exchange does not simply follow the stability of the duplex in solution, as determined by melting temperatures, but also depends sensitively on the position of the mismatch. For duplexes with similar melting temperatures, the exchange is much faster for a mismatch close to the end than for a mismatch in the middle of the sequence. Our results suggest that the single strands are stabilized by the liposome surface; therefore, the duplex is fraying more and the DNA opens up in a zipperlike fashion on the surface, increasing the probability of strand exchange. We also show that the competition between greater stability (higher Tm in solution) and higher concentration is important for the final composition of the duplex when a large excess of single strands is added to a complementary double-stranded DNA. Finally, the similar exchange rate constants for fully base-paired duplexes on the liposome surface when adding fully matched single strands or single strands with a mismatched base indicate that the rate is governed largely by separation of the initial duplex and not by the formation of the product duplex.
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Affiliation(s)
- Karolin Frykholm
- Department of Chemical and Biological Engineering, Chemistry and Biochemistry, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
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Abstract
AIM The aim of this study was to perform quality control (QC) and initial family-based association analyses on the major histocompatibility complex (MHC) single nucleotide polymorphism (SNP) and microsatellite marker data for the MHC Fine Mapping Workshop through the Type 1 Diabetes Genetics Consortium (T1DGC). METHODS A random sample of blind duplicates was sent for analysis of QC. DNA samples collected from participants were shipped to the genotyping laboratory from several T1DGC DNA Repository sites. Quality checks including examination of plate-panel yield, marker yield, Hardy-Weinberg equilibrium, mismatch error rate, Mendelian error rate and allele distribution across plates were performed. RESULTS Genotypes from 2325 families within nine cohorts were obtained and subjected to QC procedures. The MHC project consisted of three marker panels - two 1536 SNP sets (Illumina Golden Gate platform performed at the Wellcome Trust Sanger Institute, Cambridge, UK) and one 66 microsatellite marker panel (performed at deCODE). In the raw SNP data, the overall concordance rate was 99.1% (+/-0.02). CONCLUSIONS The T1DGC MHC Fine Mapping project resulted in a 2300 family, 9992 genotyped individuals database comprising of two 1536 SNP panels and a 66 microsatellite panel to densely cover the 4 Mb MHC core region for use in statistical genetic analyses.
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Affiliation(s)
- W M Brown
- Division of Public Health Sciences, Wake Forest University Health Sciences, Winston-Salem, NC, USA.
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Tabone T, Sallmann G, Cotton RGH. Mismatch oxidation assay: detection of DNA mutations using a standard UV/Vis microplate reader. Methods Mol Biol 2009; 578:235-242. [PMID: 19768598 DOI: 10.1007/978-1-60327-411-1_15] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Simple, low-cost mutation detection assays that are suitable for low-throughput analysis are essential for diagnostic applications where the causative mutation may be different in every family. The mismatch oxidation assay is a simple optical absorbance assay to detect nucleotide substitutions, insertions, and deletions in heteroduplex DNA. The method relies on detecting the oxidative modification products of mismatched thymine and cytosine bases by potassium permanganate as it is reduced to manganese dioxide. This approach, unlike other methods commonly used to detect sequence variants, does not require costly labeled probes or primers, toxic chemicals, or a time-consuming electrophoretic separation step. The oxidation rate, and hence the presence of a sequence variant, is detected by measuring the formation of the potassium permanganate reduction product (hypomanganate diester), which absorbs at the 420-nm visible wavelength, using a standard UV/vis microplate reader.
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Affiliation(s)
- Tania Tabone
- Ludwig Institute for Cancer Research, Parkville, Victoria, Australia
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Tabone T, Sallmann G, Cotton RGH. The chemical cleavage of mismatch for the detection of mutations in long DNA fragments. Methods Mol Biol 2009; 578:223-234. [PMID: 19768597 DOI: 10.1007/978-1-60327-411-1_14] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Methods to rapidly scan large regions of DNA that are not dependent on highly specific melting temperatures or suitable only for large-scale discovery are important to reduce the amount of sequencing required for DNA samples that appear to contain a mutation. This protocol describes the chemical cleavage of mismatch method to assess if a region of DNA contains a mutation and accurately localize the position of the mutation in the same reaction. To detect mutations, PCR heteroduplexes are incubated with two mismatch-specific reagents. Hydroxylamine modifies mismatched cytosine residues and potassium permanganate modifies mismatched thymine residues. The samples are then incubated with piperidine, which cleaves the DNA backbone at the site of the modified mismatched base. Cleavage products are separated by electrophoresis, revealing the identity and location of the mutation. The chemical cleavage of mismatch method can efficiently detect point mutations as well as insertions and deletions.
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Affiliation(s)
- Tania Tabone
- Ludwig Institute for Cancer Research, Parkville, Victoria, Australia
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Bannwarth S, Procaccio V, Paquis-Flucklinger V. Rapid identification of unknown heteroplasmic mitochondrial DNA mutations with mismatch-specific surveyor nuclease. Methods Mol Biol 2009; 554:301-313. [PMID: 19513682 DOI: 10.1007/978-1-59745-521-3_19] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [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: 05/27/2023]
Abstract
Identification of mitochondrial DNA (mtDNA) mutations is essential for diagnosis and genetic counseling of mitochondrial diseases. In this chapter, we describe a strategy for the rapid identification of heteroplasmic mtDNA mutations that can be used routinely in molecular genetic laboratories. This protocol involves the following three steps: (i) PCR amplification of the entire human mitochondrial genome with 17 overlapping PCR products, (ii) localization of mtDNA mismatch(es) after digestion of the 17 amplicons by Surveyor Nuclease, a member of a family of plant DNA endonucleases that cleave double-strand DNA at any mismatch site, and (iii) identification of the mutation by sequencing the region containing the mismatch.
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Affiliation(s)
- Sylvie Bannwarth
- Department of Medical Genetics, Archet 2 Hospital, CHU Nice, France
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Abstract
We describe simple and efficient construction of mismatch repair (MMR) substrates, by generation of gapped plasmids using one sequence-specific nicking endonuclease (N.BstNBI), ligation of synthetic oligomers into the gaps, and introduction of defined single nicks for initiation of MMR excision using a second such endonuclease (N.AlwI). We further describe measurement of completed mismatch correction and a sensitive quantitative assay for MMR excision intermediates. These methods can be easily adapted for construction of substrates containing defined DNA lesions, for analysis of MMR responses to DNA damage and for studies of other DNA repair pathways.
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Affiliation(s)
- Huixian Wang
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, USA
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Abstract
We present a thin membrane transducer (TMT) that can detect nucleic acid based biomolecular reactions including DNA hybridization and protein recognition by aptamers. Specific molecular interactions on an extremely thin and flexible membrane surface cause the deflection of the membrane due to surface stress change which can be measured by a compact capacitive circuit. A gold-coated thin PDMS membrane assembled with metal patterned glass substrate is used to realize the capacitive detection. It is demonstrated that perfect match and mismatch hybridizations can be sharply discriminated with a 16-mer DNA oligonucleotide immobilized on the gold-coated surface. While the mismatched sample caused little capacitance change, the perfectly matched sample caused a well-defined capacitance decrease vs. time due to an upward deformation of the membrane by a compressive surface stress. Additionally, the TMT demonstrated the single nucleotide polymorphism (SNP) capabilities which enabled a detection of mismatching base pairs in the middle of the sequence. It is intriguing that the increase of capacitance, therefore a downward deflection due to tensile stress, was observed with the internal double mismatch hybridization. We further present the detection of thrombin protein through ligand-receptor type recognition with 15-mer thrombin aptamer as a receptor. Key aspects of this detection such as the effect of concentration variation are investigated. This capacitive thin membrane transducer presents a completely new approach for detecting biomolecular reactions with high sensitivity and specificity without molecular labelling and optical measurement.
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Affiliation(s)
- Misun Cha
- School of Mechanical and Aerospace Engineering, Seoul National University, San 56-1, Shinlim, Kwanak, Seoul, 151-742, Korea
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Wain AJ, Zhou F. Scanning electrochemical microscopy imaging of DNA microarrays using methylene blue as a redox-active intercalator. Langmuir 2008; 24:5155-5160. [PMID: 18355100 DOI: 10.1021/la703922v] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Scanning electrochemical microscopy (SECM) has been employed in the imaging of DNA microarrays fabricated on gold substrates using methylene blue (MB) as a redox-active intercalator and ferrocyanide as the SECM mediator in solution. MB intercalated between base pairs of immobilized ds-DNA is electrochemically reduced via electron transfer from the underlying gold substrate, and the product is reoxidized in solution by SECM tip-generated ferricyanide. The resulting feedback current allows a heterogeneous electron-transfer rate constant for the MB-intercalated DNA to be deduced. Moreover, DNA microarray spots can be imaged at a detection level of 14 fmol/spot for ds-DNA consisting of 15 base pairs. Microarrays prepared using 20 microM DNA solutions are easily visualized, and the feasibility of detecting base pair mismatches is also demonstrated.
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Affiliation(s)
- Andrew J Wain
- Department of Chemistry and Biochemistry, California State University-Los Angeles, Los Angeles, California 90032, USA
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