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Abstract
This protocol describes how to anneal synthetic sense and antisense siRNAs to form siRNA duplexes, as well as the analysis of siRNA duplexes using nondenaturing polyacrylamide gel electrophoresis.
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2
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Jeon Y, Choi YH, Jang Y, Yu J, Goo J, Lee G, Jeong YK, Lee SH, Kim IS, Kim JS, Jeong C, Lee S, Bae S. Direct observation of DNA target searching and cleavage by CRISPR-Cas12a. Nat Commun 2018; 9:2777. [PMID: 30018371 PMCID: PMC6050341 DOI: 10.1038/s41467-018-05245-x] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [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: 03/08/2018] [Accepted: 06/20/2018] [Indexed: 12/24/2022] Open
Abstract
Cas12a (also called Cpf1) is a representative type V-A CRISPR effector RNA-guided DNA endonuclease, which provides an alternative to type II CRISPR-Cas9 for genome editing. Previous studies have revealed that Cas12a has unique features distinct from Cas9, but the detailed mechanisms of target searching and DNA cleavage by Cas12a are still unclear. Here, we directly observe this entire process by using single-molecule fluorescence assays to study Cas12a from Acidaminococcus sp. (AsCas12a). We determine that AsCas12a ribonucleoproteins search for their on-target site by a one-dimensional diffusion along elongated DNA molecules and induce cleavage in the two DNA strands in a well-defined order, beginning with the non-target strand. Furthermore, the protospacer-adjacent motif (PAM) for AsCas12a makes only a limited contribution of DNA unwinding during R-loop formation and shows a negligible role in the process of DNA cleavage, in contrast to the Cas9 PAM.
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Affiliation(s)
- Yongmoon Jeon
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul, 02792, South Korea
| | - You Hee Choi
- Advanced Photonics Research Institute, Gwangju Institute of Science and Technology, Gwangju, 61005, South Korea
- Cell Logistics Research Center, Gwangju Institute of Science and Technology, Gwangju, 61005, South Korea
| | - Yunsu Jang
- Advanced Photonics Research Institute, Gwangju Institute of Science and Technology, Gwangju, 61005, South Korea
- Cell Logistics Research Center, Gwangju Institute of Science and Technology, Gwangju, 61005, South Korea
| | - Jihyeon Yu
- Department of Chemistry, Hanyang University, Seoul, 04763, South Korea
- Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Jiyoung Goo
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul, 02792, South Korea
- KHU-KIST Department of Converging Science and Technology, Kyunghee University, Seoul, 02447, South Korea
| | - Gyejun Lee
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul, 02792, South Korea
- KHU-KIST Department of Converging Science and Technology, Kyunghee University, Seoul, 02447, South Korea
| | - You Kyeong Jeong
- Department of Chemistry, Hanyang University, Seoul, 04763, South Korea
| | - Seung Hwan Lee
- Center for Genome Engineering, Institute for Basic Science, Seoul, 08826, South Korea
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, 28116, South Korea
| | - In-San Kim
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul, 02792, South Korea
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, 02841, South Korea
| | - Jin-Soo Kim
- Center for Genome Engineering, Institute for Basic Science, Seoul, 08826, South Korea
- Department of Chemistry, Seoul National University, Seoul, 08826, South Korea
| | - Cherlhyun Jeong
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul, 02792, South Korea.
- KHU-KIST Department of Converging Science and Technology, Kyunghee University, Seoul, 02447, South Korea.
| | - Sanghwa Lee
- Advanced Photonics Research Institute, Gwangju Institute of Science and Technology, Gwangju, 61005, South Korea.
- Cell Logistics Research Center, Gwangju Institute of Science and Technology, Gwangju, 61005, South Korea.
| | - Sangsu Bae
- Department of Chemistry, Hanyang University, Seoul, 04763, South Korea.
- Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 04763, South Korea.
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3
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Hum YF, Jinks-Robertson S. DNA strand-exchange patterns associated with double-strand break-induced and spontaneous mitotic crossovers in Saccharomyces cerevisiae. PLoS Genet 2018; 14:e1007302. [PMID: 29579095 PMCID: PMC5886692 DOI: 10.1371/journal.pgen.1007302] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [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: 12/19/2017] [Revised: 04/05/2018] [Accepted: 03/08/2018] [Indexed: 11/24/2022] Open
Abstract
Mitotic recombination can result in loss of heterozygosity and chromosomal rearrangements that shape genome structure and initiate human disease. Engineered double-strand breaks (DSBs) are a potent initiator of recombination, but whether spontaneous events initiate with the breakage of one or both DNA strands remains unclear. In the current study, a crossover (CO)-specific assay was used to compare heteroduplex DNA (hetDNA) profiles, which reflect strand exchange intermediates, associated with DSB-induced versus spontaneous events in yeast. Most DSB-induced CO products had the two-sided hetDNA predicted by the canonical DSB repair model, with a switch in hetDNA position from one product to the other at the position of the break. Approximately 40% of COs, however, had hetDNA on only one side of the initiating break. This anomaly can be explained by a modified model in which there is frequent processing of an early invasion (D-loop) intermediate prior to extension of the invading end. Finally, hetDNA tracts exhibited complexities consistent with frequent expansion of the DSB into a gap, migration of strand-exchange junctions, and template switching during gap-filling reactions. hetDNA patterns in spontaneous COs isolated in either a wild-type background or in a background with elevated levels of reactive oxygen species (tsa1Δ mutant) were similar to those associated with the DSB-induced events, suggesting that DSBs are the major instigator of spontaneous mitotic recombination in yeast.
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Affiliation(s)
- Yee Fang Hum
- Department of Molecular Genetics and Microbiology and the University Program in Genetics and Genomics, Duke University, Durham, North Carolina, United States of America
| | - Sue Jinks-Robertson
- Department of Molecular Genetics and Microbiology and the University Program in Genetics and Genomics, Duke University, Durham, North Carolina, United States of America
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4
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Ying N, Ju C, Sun X, Li L, Chang H, Song G, Li Z, Wan J, Dai E. Lateral flow nucleic acid biosensor for sensitive detection of microRNAs based on the dual amplification strategy of duplex-specific nuclease and hybridization chain reaction. PLoS One 2017; 12:e0185091. [PMID: 28945768 PMCID: PMC5612651 DOI: 10.1371/journal.pone.0185091] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [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: 02/03/2017] [Accepted: 09/06/2017] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs (miRNAs) constitute novel biomarkers for various diseases. Accurate and quantitative analysis of miRNA expression is critical for biomedical research and clinical theranostics. In this study, a method was developed for sensitive and specific detection of miRNAs via dual signal amplification based on duplex specific nuclease (DSN) and hybridization chain reaction (HCR). A reporter probe (RP), comprising recognition sequence (3’ end modified with biotin) for a target miRNA of miR-21 and capture sequence (5’ end modified with Fam) for HCR product, was designed and synthesized. HCR was initiated by partial sequence of initiator probe (IP), the other part of which can hybridize with capture sequence of RP, and was assembled by hairpin probes modified with biotin (H1-bio and H2-bio). A miR-21 triggered cyclical DSN cleavage of RP, which was immobilized to a streptavidin (SA) coated magnetic bead (MB). The released Fam labeled capture sequence then hybridized with the HCR product to generate a detectable dsDNA. This polymer was then dropped on lateral flow strip and positive result was observed. The proposed method allowed quantitative sequence-specific detection of miR-21 (with a detection limit of 2.1 fM, S/N = 3) in a dynamic range from 100 fM to 100 pM, with an excellent ability to discriminate differences in miRNAs. The method showed acceptable testing recoveries for the determination of miRNAs in serum.
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Affiliation(s)
- Na Ying
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
- East China Sea Fisheries Research Institute, China Academy of Fishery Sciences, Shanghai, China
| | - Chuanjing Ju
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
- The General Hospital of FAW, Changchun, China
- The Fourth Hospital of Jilin University, Changchun, China
| | - Xiuwei Sun
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Letian Li
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Hongbiao Chang
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
- School of Life Science and Technology, Changchun University of Science and Technology, Changchun, China
| | - Guangping Song
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - Zhongyi Li
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Jiayu Wan
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
- * E-mail: (JW); (ED)
| | - Enyong Dai
- Department of Oncology and Hematology, China-Japan Union Hospital of Jilin University, Changchun, China
- * E-mail: (JW); (ED)
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5
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Nishimasu H, Yamano T, Gao L, Zhang F, Ishitani R, Nureki O. Structural Basis for the Altered PAM Recognition by Engineered CRISPR-Cpf1. Mol Cell 2017; 67:139-147.e2. [PMID: 28595896 PMCID: PMC5957533 DOI: 10.1016/j.molcel.2017.04.019] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [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] [Received: 02/25/2017] [Revised: 04/13/2017] [Accepted: 04/25/2017] [Indexed: 12/27/2022]
Abstract
The RNA-guided Cpf1 nuclease cleaves double-stranded DNA targets complementary to the CRISPR RNA (crRNA), and it has been harnessed for genome editing technologies. Recently, Acidaminococcus sp. BV3L6 (AsCpf1) was engineered to recognize altered DNA sequences as the protospacer adjacent motif (PAM), thereby expanding the target range of Cpf1-mediated genome editing. Whereas wild-type AsCpf1 recognizes the TTTV PAM, the RVR (S542R/K548V/N552R) and RR (S542R/K607R) variants can efficiently recognize the TATV and TYCV PAMs, respectively. However, their PAM recognition mechanisms remained unknown. Here we present the 2.0 Å resolution crystal structures of the RVR and RR variants bound to a crRNA and its target DNA. The structures revealed that the RVR and RR variants primarily recognize the PAM-complementary nucleotides via the substituted residues. Our high-resolution structures delineated the altered PAM recognition mechanisms of the AsCpf1 variants, providing a basis for the further engineering of CRISPR-Cpf1.
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Affiliation(s)
- Hiroshi Nishimasu
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan; JST, PRESTO, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
| | - Takashi Yamano
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Linyi Gao
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ryuichiro Ishitani
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
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6
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Mazina OM, Keskin H, Hanamshet K, Storici F, Mazin AV. Rad52 Inverse Strand Exchange Drives RNA-Templated DNA Double-Strand Break Repair. Mol Cell 2017; 67:19-29.e3. [PMID: 28602639 DOI: 10.1016/j.molcel.2017.05.019] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [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] [Received: 01/03/2017] [Revised: 05/09/2017] [Accepted: 05/19/2017] [Indexed: 12/20/2022]
Abstract
RNA can serve as a template for DNA double-strand break repair in yeast cells, and Rad52, a member of the homologous recombination pathway, emerged as an important player in this process. However, the exact mechanism of how Rad52 contributes to RNA-dependent DSB repair remained unknown. Here, we report an unanticipated activity of yeast and human Rad52: inverse strand exchange, in which Rad52 forms a complex with dsDNA and promotes strand exchange with homologous ssRNA or ssDNA. We show that in eukaryotes, inverse strand exchange between homologous dsDNA and RNA is a distinctive activity of Rad52; neither Rad51 recombinase nor the yeast Rad52 paralog Rad59 has this activity. In accord with our in vitro results, our experiments in budding yeast provide evidence that Rad52 inverse strand exchange plays an important role in RNA-templated DSB repair in vivo.
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Affiliation(s)
- Olga M Mazina
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Havva Keskin
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Kritika Hanamshet
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Francesca Storici
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| | - Alexander V Mazin
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA.
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7
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Kulibaba RA, Liashenko YV. [Not Available]. Tsitol Genet 2016; 50:16-23. [PMID: 30480404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The formation of different types of the artifacts in the amplification reaction with using different classes of the molecular-genetic markers (Indel and SSR) was studied. It was shown that DNA heteroduplexes formed during amplification of heterozygous samples, as fragments of target genes and microsatellite loci. During the electrophoresis in native polyacrylamide gel of the amplification products of homozygous samples for microsatellite loci it was revealed specific additional fragments that do not belong to the class of heteroduplex DNA. It was supposed, that the additional fragments belong to a special type of homoduplex DNA – non-linear homoduplexes. The analysis revealed that the formation of a non-linear homoduplex DNA takes place on the 20–25 cycle of the PCR, both at the amplification of the individual samples, and individual DNA fragments that was cut out from the gel.
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8
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Bird JG, Strobel EJ, Roberts JW. A universal transcription pause sequence is an element of initiation factor σ70-dependent pausing. Nucleic Acids Res 2016; 44:6732-40. [PMID: 27098041 PMCID: PMC5001585 DOI: 10.1093/nar/gkw285] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 04/07/2016] [Indexed: 11/12/2022] Open
Abstract
The Escherichia coli σ70 initiation factor is required for a post-initiation, promoter-proximal pause essential for regulation of lambdoid phage late gene expression; potentially, σ70 acts at other sites during transcription elongation as well. The pause is induced by σ70 binding to a repeat of the promoter -10 sequence. After σ70 binding, further RNA synthesis occurs as DNA is drawn (or 'scrunched') into the enzyme complex, presumably exactly as occurs during initial synthesis from the promoter; this synthesis then pauses at a defined site several nucleotides downstream from the active center position when σ70 first engages the -10 sequence repeat. We show that the actual pause site in the stabilized, scrunched complex is the 'elemental pause sequence' recognized from its frequent occurrence in the E. coli genome. σ70 binding and the elemental pause sequence together, but neither alone, produce a substantial transcription pause.
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Affiliation(s)
- Jeremy G Bird
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Eric J Strobel
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Jeffrey W Roberts
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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9
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Hestand MS, Van Houdt J, Cristofoli F, Vermeesch JR. Polymerase specific error rates and profiles identified by single molecule sequencing. Mutat Res 2016; 784-785:39-45. [PMID: 26829216 DOI: 10.1016/j.mrfmmm.2016.01.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [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: 07/23/2015] [Revised: 12/16/2015] [Accepted: 01/14/2016] [Indexed: 06/05/2023]
Abstract
DNA polymerases have an innate error rate which is polymerase and DNA context specific. Historically the mutational rate and profiles have been measured using a variety of methods, each with their own technical limitations. Here we used the unique properties of single molecule sequencing to evaluate the mutational rate and profiles of six DNA polymerases at the sequence level. In addition to accurately determining mutations in double strands, single molecule sequencing also captures direction specific transversions and transitions through the analysis of heteroduplexes. Not only did the error rates vary, but also the direction specific transitions differed among polymerases.
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Affiliation(s)
- Matthew S Hestand
- Department of Human Genetics, KU Leuven, O&N I Herestraat 49-box 602, 3000 Leuven, Belgium
| | - Jeroen Van Houdt
- Department of Human Genetics, KU Leuven, O&N I Herestraat 49-box 602, 3000 Leuven, Belgium
| | - Francesca Cristofoli
- Department of Human Genetics, KU Leuven, O&N I Herestraat 49-box 602, 3000 Leuven, Belgium
| | - Joris R Vermeesch
- Department of Human Genetics, KU Leuven, O&N I Herestraat 49-box 602, 3000 Leuven, Belgium.
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10
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Abstract
Sea urchin embryos are a useful model system for investigating early developmental processes and the underlying gene regulatory networks. Most functional studies using sea urchin embryos rely on antisense morpholino oligonucleotides to knockdown gene functions. However, major concerns related to this technique include off-target effects, variations in morpholino efficiency, and potential morpholino toxicity; furthermore, such problems are difficult to discern. Recent advances in genome editing technologies have introduced the prospect of not only generating sequence-specific knockouts, but also providing genome-engineering applications. Two genome editing tools, zinc-finger nuclease (ZFN) and transcription activator-like effector nucleases (TALENs), have been utilized in sea urchin embryos, but the resulting efficiencies are far from satisfactory. The CRISPR (clustered regularly interspaced short palindromic repeat)-Cas9 (CRISPR-associated nuclease 9) system serves as an easy and efficient method with which to edit the genomes of several established and emerging model organisms in the field of developmental biology. Here, we apply the CRISPR/Cas9 system to the sea urchin embryo. We designed six guide RNAs (gRNAs) against the well-studied nodal gene and discovered that five of the gRNAs induced the expected phenotype in 60-80% of the injected embryos. In addition, we developed a simple method for isolating genomic DNA from individual embryos, enabling phenotype to be precisely linked to genotype, and revealed that the mutation rates were 67-100% among the sequenced clones. Of the two potential off-target sites we examined, no off-target effects were observed. The detailed procedures described herein promise to accelerate the usage of CRISPR/Cas9 system for genome editing in sea urchin embryos.
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Affiliation(s)
- Che-Yi Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Yi-Hsien Su
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan.
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Glushakova LG, Sharma N, Hoshika S, Bradley AC, Bradley KM, Yang Z, Benner SA. Detecting respiratory viral RNA using expanded genetic alphabets and self-avoiding DNA. Anal Biochem 2015; 489:62-72. [PMID: 26299645 PMCID: PMC4733849 DOI: 10.1016/j.ab.2015.08.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Revised: 08/07/2015] [Accepted: 08/13/2015] [Indexed: 11/23/2022]
Abstract
Nucleic acid (NA)-targeted tests detect and quantify viral DNA and RNA (collectively xNA) to support epidemiological surveillance and, in individual patients, to guide therapy. They commonly use polymerase chain reaction (PCR) and reverse transcription PCR. Although these all have rapid turnaround, they are expensive to run. Multiplexing would allow their cost to be spread over multiple targets, but often only with lower sensitivity and accuracy, noise, false positives, and false negatives; these arise by interactions between the multiple nucleic acid primers and probes in a multiplexed kit. Here we offer a multiplexed assay for a panel of respiratory viruses that mitigates these problems by combining several nucleic acid analogs from the emerging field of synthetic biology: (i) self-avoiding molecular recognition systems (SAMRSs), which facilitate multiplexing, and (ii) artificially expanded genetic information systems (AEGISs), which enable low-noise PCR. These are supplemented by “transliteration” technology, which converts standard nucleotides in a target to AEGIS nucleotides in a product, improving hybridization. The combination supports a multiplexed Luminex-based respiratory panel that potentially differentiates influenza viruses A and B, respiratory syncytial virus, severe acute respiratory syndrome coronavirus (SARS), and Middle East respiratory syndrome (MERS) coronavirus, detecting as few as 10 MERS virions in a 20-μl sample.
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Affiliation(s)
| | - Nidhi Sharma
- Foundation for Applied Molecular Evolution (FfAME), Alachua, FL 32615, USA
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution (FfAME), Alachua, FL 32615, USA
| | - Andrea C Bradley
- Foundation for Applied Molecular Evolution (FfAME), Alachua, FL 32615, USA
| | - Kevin M Bradley
- Foundation for Applied Molecular Evolution (FfAME), Alachua, FL 32615, USA
| | - Zunyi Yang
- Foundation for Applied Molecular Evolution (FfAME), Alachua, FL 32615, USA
| | - Steven A Benner
- Firebird Biomolecular Sciences, Alachua, FL 32615, USA; Foundation for Applied Molecular Evolution (FfAME), Alachua, FL 32615, USA.
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12
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Muterko A, Kalendar R, Cockram J, Balashova I. Discovery, evaluation and distribution of haplotypes and new alleles of the Photoperiod-A1 gene in wheat. Plant Mol Biol 2015; 88:149-164. [PMID: 25851614 DOI: 10.1007/s11103-015-0313-2] [Citation(s) in RCA: 3] [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: 10/18/2014] [Accepted: 03/29/2015] [Indexed: 06/04/2023]
Abstract
Photoperiod response in wheat is determined to a large extent by the homoeologous series of Photoperiod 1 (Ppd1) genes. In this study, Ppd-A1 genomic sequences from the 5' UTR and promoter region were analysed in 104 accessions of six tetraploid wheat species (Triticum dicoccoides, T. dicoccum, T. turgidum, T. polonicum, T. carthlicum, T. durum) and 102 accessions of six hexaploid wheat species (T. aestivum, T. compactum, T. sphaerococcum, T. spelta, T. macha, T. vavilovii). This data was supplemented with in silico analysis of publicly available sequences from 46 to 193 accessions of diploid and tetraploid wheat, respectively. Analysis of a region of the Ppd-A1 promoter identified thirteen haplotypes, which were divided in two haplogroups. Distribution of the Ppd-A1 haplogroups and haplotypes in wheat species, and their geographical distributions were analysed. Polymerase chain reaction combined with a heteroduplex mobility assay was subsequently used to efficiently discriminate between Ppd-A1 alleles, allowing identification of the Ppd-A1b haplotypes and haplogroups. The causes of anomalous migration of Ppd-A1 heteroduplexes in gels were found to be the localization of mismatches relative to the center of fragment, the cumulative effect of neighbouring polymorphic sites, and the location of mismatches within A/T-tracts. Analysis of the Ppd-A1 5' UTR in hexaploid wheat revealed a novel mutation within the "photoperiod critical" region in a subset of T. compactum accessions. This putative photoperiod insensitive allele (designated Ppd-A1a.4) includes a 684 bp deletion which spans region in common with deletions previously identified in other photoperiod insensitive Ppd1 alleles.
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Affiliation(s)
- Alexandr Muterko
- Department of Genomics and Biotechnology, Plant Breeding and Genetics Institute - National Center of Seed and Cultivar Investigation, Ovidiopolskaya Road 3, Odessa, 65036, Ukraine,
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13
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Dong CB, Mao JF, Suo YJ, Shi L, Wang J, Zhang PD, Kang XY. A strategy for characterization of persistent heteroduplex DNA in higher plants. Plant J 2014; 80:282-291. [PMID: 25073546 DOI: 10.1111/tpj.12631] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [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: 08/07/2013] [Revised: 07/24/2014] [Accepted: 07/25/2014] [Indexed: 06/03/2023]
Abstract
Heteroduplex DNA (hDNA) generated during homologous recombination (HR) is an important component that shapes genetic diversity in sexually reproducing organisms. However, studies of this process in higher plants are limited. This is because hDNAs are difficult to capture in higher plants as their reproductive developmental model only produces normal gametes and does not preserve the mitotic products of the post-meiotic segregation (PMS) process which is crucial for studying hDNAs. In this study, using the model system for tree and woody perennial plant biology (Populus), we propose a strategy for characterizing hDNAs in higher plants. We captured hDNAs by constructing triploid hybrids originating from a cross between unreduced 2n eggs (containing hDNA information as a result of inhibition chromosome segregation at the PMS stage) with normal male gametes. These triploid hybrids allowed us to detect the frequency and location of persistent hDNAs resulting from HR at the molecular level. We found that the frequency of persistent hDNAs, which ranged from 5.3 to 76.6%, was related to locations of the simple sequence repeat markers at the chromosomes, such as the locus-centromere distance, the surrounding DNA sequence and epigenetic information, and the richness of protein-coding transcripts at these loci. In summary, this study provides a method for characterizing persistent hDNAs in higher plants. When high-throughput sequencing techniques can be incorporated, genome-wide persistent hDNA assays for higher plants can be easily carried out using the strategy presented in this study.
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Affiliation(s)
- Chun-Bo Dong
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
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14
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Farjami E, Campos R, Ferapontova EE. Effect of the DNA end of tethering to electrodes on electron transfer in methylene blue-labeled DNA duplexes. Langmuir 2012; 28:16218-16226. [PMID: 23106377 DOI: 10.1021/la3032336] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Electron transfer (ET) in redox-labeled double-stranded (ds) DNA tethered to electrodes through the alkanethiol linker at either the 3' or 5' DNA end and bearing methylene blue (MB) conjugated to the opposite end of DNA is shown to depend on the DNA end of tethering to electrodes. For 3' tethering, a nanoscale diffusion of the positively charged MB redox probe (and thus of the individual DNA molecules) to the negatively charged electrode surface provided the highest apparent diffusion and ET rates as a result of the tilting of 3'-tethered DNA (as compared to 5'-tethered DNA) versus the normal to the surface. Dynamic values of the tilting angle varied between 57 and 45° for 16-mer and 22-mer 3'-tethered DNA, and 5'-tethering was correlated with an upright orientation of DNA at the electrode surface. The values of the diffusion coefficient D(MB) corrected for tilting angles were similar for 5'- and 3'-tethered DNA and ranged between 5.4 × 10(-12) and 2.5 × 10(-12) cm(2) s(-1), whereas the ET rate constant k(ET)(dif) fit the 4.7 × 10(-6)-10.3 × 10(-6) cm s(-1) range for 22-mer and 16-mer dsDNA, respectively. Those values, when related to the nanometer (10(-7) cm) diffusion distances (the length of the studied DNA), allow relatively fast diffusion-limited ET at an apparent rate that may exceed the rate of the corresponding surface-confined ET process. This phenomenon is of particular importance for molecular electronics and electrochemical genosensor development.
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Affiliation(s)
- Elaheh Farjami
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Denmark
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15
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Pande P, Das RS, Sheppard C, Kow YW, Basu AK. Repair efficiency of (5'S)-8,5'-cyclo-2'-deoxyguanosine and (5'S)-8,5'-cyclo-2'-deoxyadenosine depends on the complementary base. DNA Repair (Amst) 2012; 11:926-31. [PMID: 23063091 DOI: 10.1016/j.dnarep.2012.09.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [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] [Received: 06/08/2012] [Revised: 08/30/2012] [Accepted: 09/06/2012] [Indexed: 11/19/2022]
Abstract
5'-R and 5'-S diastereoisomers of 8,5'-cyclo-2'-deoxyadenosine (cdA) and 8,5'-cyclo-2'-deoxyguanosine (cdG) containing a base-sugar covalent bond are formed by hydroxyl radicals. R-cdA and S-cdA are repaired by nucleotide excision repair (NER) in mammalian cellular extracts. Here, we have examined seven purified base excision repair enzymes for their ability to repair S-cdG or S-cdA. We could not detect either excision or binding of these enzymes on duplex oligonucleotide substrates containing these lesions. However, both lesions were repaired by HeLa cell extracts. Dual incisions by human NER on a 136-mer duplex generated 24-32 bp fragments. The time course of dual incisions were measured in comparison to cis-anti-B[a]P-N(2)-dG, an excellent substrate for human NER, which showed that cis-anti-B[a]P-N(2)-dG was repaired more efficiently than S-cdG, which, in turn, was repaired more efficiently than S-cdA. When NER efficiency of S-cdG with different complementary bases was investigated, the wobble pair S-cdG·dT was excised more efficiently than the S-cdG·dC pair that maintains nearly normal Watson-Crick base pairing. But S-cdG·dA mispair with no hydrogen bonds was excised less efficiently than the S-cdG·dC pair. Similar pattern was noted for S-cdA. The S-cdA·dC mispair was excised much more efficiently than the S-cdA·dT pair, whereas the S-cdA·dA pair was excised less efficiently. This result adds to complexity of human NER, which discriminates the damaged base pairs on the basis of multiple criteria.
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Affiliation(s)
- Paritosh Pande
- Department of Chemistry, University of Connecticut, Storrs, CT 06269, USA
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16
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Limanskaia OI, Fesenko TV, Pokrovskiĭ VA, Mukhina TN, Stepanshina VN, Shemiakin IG, Limanskiĭ AP. [Characterization of oligonucleotides with LNA-monomers for PCR detection of point mutations in mycobacteria tuberculosis genome]. Biomed Khim 2012; 58:199-210. [PMID: 22724359 DOI: 10.18097/pbmc20125802199] [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: 11/23/2022]
Abstract
Point mutations associated with isoniazid resistance in Mycobacterium tuberculosis (MTB) have been analyzed in codon 315 of the katG gene by conventional polymerase chain reaction (PCR) using primers containing locked nucleic acid (LNA) modified nucleotides. Purity and structure of primers containing 5 LNA monomers of 17 nucleotides in length were characterized by matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) and a 17-mer duplex formed by two complementary oligonucleotides was characterized by the method of thermal denaturation. The duplex containing five LNA monomers per each strand was characterized by a higher melting temperature than it was expected using extrapolation of theoretical calculation for nucleotide modification of one strand of the duplex. Detection of any of six possible mutations in katG codon 315 (i.e. discrimination between sensitive and resistant MTB) requires just one PCR employing a set of two primers with one LNA-modified primer; this is an important advantage of oligonucleotides containing LNA over unmodified nucleotides: employment of multiplex PCR would require up to 12 primers. Problems of control of oligonucleotide modification by LNA monomers are discussed.
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17
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Juliano JJ, Trottman P, Mwapasa V, Meshnick SR. Detection of the dihydrofolate reductase-164L mutation in Plasmodium falciparum infections from Malawi by heteroduplex tracking assay. Am J Trop Med Hyg 2008; 78:892-894. [PMID: 18541765 PMCID: PMC2601660] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023] Open
Abstract
Standard polymerase chain reaction methods often cannot detect drug-resistance mutations in Plasmodium falciparum infections if the mutation is present in < or = 20% of the parasites. A heteroduplex tracking assay was developed that can detect dihydrofolate reductase 164-L mutations in variants representing 1% of the parasites in an individual host. Using this assay, we confirmed the presence of the mutation in P. falciparum infections in Malawi.
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Affiliation(s)
- Jonathan J Juliano
- Division of Infectious Diseases, University of North Carolina, School of Medicine, Chapel Hill, North Carolina 27599-7300, USA.
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18
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Powell RLR, Urbanski MM, Nyambi PN. A heteroduplex assay for the rapid detection of dual Human Immunodeficiency Virus Type 1 infections. J Virol Methods 2008; 149:20-7. [PMID: 18314205 DOI: 10.1016/j.jviromet.2008.01.015] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2007] [Revised: 01/14/2008] [Accepted: 01/17/2008] [Indexed: 12/16/2022]
Abstract
The predominance of circulating and unique recombinant forms (URFs) of Human Immunodeficiency Virus Type 1 (HIV-1) in Cameroon suggests that dual infection occurs frequently in this region. Despite the potential impact of these infections on the evolution of HIV diversity, relatively few have been detected. The failure to detect dual infections may be attributable to the laborious and costly sequence analysis involved in their identification. As such, there is a need for a cost-effective, more rapid method to efficiently distinguish this subset of HIV-positive individuals, particularly in regions where HIV diversity is broad. In the present study, the heteroduplex assay (HDA) was developed to detect dual HIV-1 infection. This assay was validated on sequential specimens obtained from 20 HIV+ study subjects, whose single or dual infection status was determined by standard sequence analysis. By mixing gag fragments amplified from the sequential specimens from each study subject in HDA reactions, it was shown that single and dual infection status correlated with the absence and presence, respectively, of heteroduplex bands upon gel electrophoresis. Therefore, this novel assay is capable of identifying dual infections with a sensitivity and specificity equivalent to that of sequence analysis. Given the impact of dual infection on viral recombination and diversity, this simple technique will be beneficial to understanding HIV-1 evolution within an individual, as well as at a population level, in West-Central Africa and globally.
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Affiliation(s)
- Rebecca L R Powell
- Department of Microbiology, New York University School of Medicine, New York, NY 10010, USA
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19
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Alanen M, Wartiovaara J, Söderlund H. Sequences conserved in the defective interfering RNAs of Semliki Forest virus: an electron microscopic heteroduplex analysis. Hereditas 2008; 106:19-29. [PMID: 3583781 DOI: 10.1111/j.1601-5223.1987.tb00232.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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20
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Gumbiner-Russo LM, Rosenberg SM. Physical analyses of E. coli heteroduplex recombination products in vivo: on the prevalence of 5' and 3' patches. PLoS One 2007; 2:e1242. [PMID: 18043749 PMCID: PMC2082072 DOI: 10.1371/journal.pone.0001242] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [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: 08/15/2007] [Accepted: 10/15/2007] [Indexed: 11/18/2022] Open
Abstract
Background Homologous recombination in Escherichia coli creates patches (non-crossovers) or splices (half crossovers), each of which may have associated heteroduplex DNA. Heteroduplex patches have recombinant DNA in one strand of the duplex, with parental flanking markers. Which DNA strand is exchanged in heteroduplex patches reflects the molecular mechanism of recombination. Several models for the mechanism of E. coli RecBCD-mediated recombinational double-strand-end (DSE) repair specify that only the 3′-ending strand invades the homologous DNA, forming heteroduplex in that strand. There is, however, in vivo evidence that patches are found in both strands. Methodology/Principle Findings This paper re-examines heteroduplex-patch-strand polarity using phage λ and the λdv plasmid as DNA substrates recombined via the E. coli RecBCD system in vivo. These DNAs are mutant for λ recombination functions, including orf and rap, which were functional in previous studies. Heteroduplexes are isolated, separated on polyacrylamide gels, and quantified using Southern blots for heteroduplex analysis. This method reveals that heteroduplexes are still found in either 5′ or 3′ DNA strands in approximately equal amounts, even in the absence of orf and rap. Also observed is an independence of the RuvC Holliday-junction endonuclease on patch formation, and a slight but statistically significant alteration of patch polarity by recD mutation. Conclusions/Significance These results indicate that orf and rap did not contribute to the presence of patches, and imply that patches occurring in both DNA strands reflects the molecular mechanism of recombination in E. coli. Most importantly, the lack of a requirement for RuvC implies that endonucleolytic resolution of Holliday junctions is not necessary for heteroduplex-patch formation, contrary to predictions of all of the major previous models. This implies that patches are not an alternative resolution of the same intermediate that produces splices, and do not bear on models for splice formation. We consider two mechanisms that use DNA replication instead of endonucleolytic resolution for formation of heteroduplex patches in either DNA strand: synthesis-dependent-strand annealing and a strand-assimilation mechanism.
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Affiliation(s)
- Laura M. Gumbiner-Russo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Susan M. Rosenberg
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America
- * To whom correspondence should be addressed. E-mail:
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21
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Abstract
Aminoacylation of tRNA by aminoacyl-tRNA synthetases is the essential reaction that matches protein amino acids with the trinucleotide sequences specified in mRNA. Direct electrostatic interactions made by tRNA synthetases with discriminating functional groups on the tRNA bases have long been known to determine aminoacylation specificity. However, structural and biochemical studies have revealed a second "indirect readout" mechanism that makes an important contribution as well. In indirect readout, the sequence-dependent conformations of tRNA are recognized through protein contacts with the sugar-phosphate backbone and with nonspecific portions of the bases. This mechanism appears to function in single-stranded regions, in canonical A-type duplex segments, and in the complex tertiary core portion of the tRNA. Operation of the indirect mechanism is not exclusive of the direct mechanism, and both are further mediated by induced-fit rearrangements, in which enzyme and tRNA undergo precise conformational changes after formation of an initial encounter complex. The examples of indirect readout in tRNA synthetase complexes extend the concept beyond its traditional application to DNA duplexes and serve as models for the operation of this mechanism in more complex systems such as the ribosome.
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Affiliation(s)
- John J Perona
- Department of Chemistry and Biochemistry and Interdepartmental Program in Biomolecular Science and Engineering, University of California, Santa Barbara, California 93106-9510, USA.
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22
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Alam MR, Majumdar A, Thazhathveetil AK, Liu ST, Liu JL, Puri N, Cuenoud B, Sasaki S, Miller PS, Seidman MM. Extensive sugar modification improves triple helix forming oligonucleotide activity in vitro but reduces activity in vivo. Biochemistry 2007; 46:10222-33. [PMID: 17691818 DOI: 10.1021/bi7003153] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We are developing triple helix forming oligonucleotides (TFOs) for gene targeting. Previously, we synthesized bioactive TFOs containing 2'-O-methylribose (2'-OMe) and 2'-O-aminoethylribose (2'-AE) residues. Active TFOs contained four contiguous 2'-AE residues and formed triplexes with high thermal stability and rapid association kinetics. In an effort to further improve bioactivity, we synthesized three series of TFOs containing the 2'-AE patch and additional ribose modifications distributed throughout the remainder of the oligonucleotide. These were either additional 2'-AE residues, the conformationally locked BNA/LNA ribose with a 2'-O,4'-C-methylene bridge, or the 2'-O,4'-C-ethylene analogue (ENA). The additionally modified TFOs formed triplexes with greater thermal stability than the reference TFO, and some had improved association kinetics. However, the most active TFOs in the biochemical and biophysical assays were the least active in the bioassay. We measured the thermal stability of triplexes formed by the TFOs in each series on duplex targets containing a change in sequence at a single position. The Tm value of the variant sequence triplexes increased as the number of all additional modifications increased. A simple explanation for the failure of the improved TFOs in the bioassay was that the increased affinity for nonspecific targets lowered the effective nuclear concentration. Enhancement of TFO bioactivity will require chemical modifications that improve interaction with the specific targets while retaining selectivity against mismatched sequences.
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Affiliation(s)
- Md Rowshon Alam
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, USA
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23
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Teletchéa S, Komeda S, Teuben JM, Elizondo-Riojas MA, Reedijk J, Kozelka J. A pyrazolato-bridged dinuclear platinum(II) complex induces only minor distortions upon DNA-binding. Chemistry 2007; 12:3741-53. [PMID: 16514681 DOI: 10.1002/chem.200500923] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [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: 11/12/2022]
Abstract
The cytotoxic, pyrazolato-bridged dinuclear platinum(II) complex [(cis-{Pt(NH3)2})2(mu-OH)(mu-pz)]2+ (pz=pyrazolate) has been found to cross-link two adjacent guanines of a double-stranded DNA decamer without destabilizing the duplex and without changing the directionality of the helix axis. A 1H NMR study of the oligonucleotide d(CTCTG*G*TCTC)-d(GAGACCAGAG), cross-linked at the two G* guanines by [(cis-{Pt(NH3)2})2(mu-pz)]3+, and molecular dynamics simulations of the explicitly solvated duplex were performed to characterize the structural details of the adduct. The dinuclear platinum cross-link unwinds the helix by approximately 15 degrees , that is, to a similar extent as the widely used antitumor drug cisplatin, but, in contrast to the latter, induces no significant bend in the helix axis. The Watson-Crick base-pairing remains intact, and the melting temperature of the duplex is unaffected by the cross-link. The helical twist is considerably reduced between the two platinated bases, as becomes manifest in an unusually short sequential H1'-H1' distance. This unwinding also affects the sugar ring of the guanosine in the 3'-position to the cross-link, which presents an N<-->S equilibrium. This is the first cytotoxic platinum complex that has been successfully designed by envisioning the structural consequences of its binding to DNA.
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Affiliation(s)
- Stéphane Teletchéa
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université René Descartes, UMR 8601 CNRS, 45, rue des Saints-Pères, 75270 Paris Cedex 06, France
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24
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Nakano SI, Uotani Y, Anno Y, Fujii M, Sugimoto N. Conformational change of a nucleotide by a base-pair mimic nucleoside in the complementary DNA strand. ACTA ACUST UNITED AC 2007:259-60. [PMID: 17150577 DOI: 10.1093/nass/48.1.259] [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: 11/14/2022]
Abstract
On the basis of the non-covalent bond interactions in nucleic acids, we have synthesized a novel adenosine derivative tethering a phenyl group. Structure and thermal stability of the DNA duplexes bearing the adenosine derivative in the middle of a strand were investigated by CD spectra and the UV melting curves. We found that the conformation and the interactions of the duplexes were similar regardless of the nucleotide facing with the adenosine derivative in a duplex. This observation suggests the base pair-mimic geometry of the adenosine derivative accompanied with a conformational change of the nucleotide in the complementary strand.
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Affiliation(s)
- Shu-ichi Nakano
- Frontier Institute for Biomolecular Engineering Research, Konan University, Okamoto, Higashinada-ku, Kobe 658-8501, Japan
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25
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Bender M, Holben WE, Sørensen SJ, Jacobsen CS. Use of a PNA probe to block DNA-mediated PCR product formation in prokaryotic RT-PCR. Biotechniques 2007; 42:609-10, 612-4. [PMID: 17515199 DOI: 10.2144/000112437] [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] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
A novel method eliminating DNA-mediated PCR product formation in reverse transcription PCR (RT-PCR) amplification of specific RNA sequences is described. The method exploits the higher melting temperature values of peptide nucleic acid (PNA)/DNA duplexes compared with DNA/DNA duplexes by binding a sequence-specific PNA probe to a genomic sequence immediately overlapping one of the PCR-primer attachment sites within the sequence of interest. Hybridization of the blocking probe precludes primer attachment to DNA without affecting attachment of the same primer to the reverse transcription-generated cDNA sequence. A four-step PCR cycle is used that allows the PNA probe to hybridize to the DNA strand at a higher temperature just prior to the primer annealing step.
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Affiliation(s)
- Mikkel Bender
- Geological Survey of Denmark and Greenland, Copenhagen
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26
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Wu Y, Bhattacharyya D, King CL, Baskerville-Abraham I, Huh SH, Boysen G, Swenberg JA, Temple B, Campbell SL, Chaney SG. Solution structures of a DNA dodecamer duplex with and without a cisplatin 1,2-d(GG) intrastrand cross-link: comparison with the same DNA duplex containing an oxaliplatin 1,2-d(GG) intrastrand cross-link. Biochemistry 2007; 46:6477-87. [PMID: 17497831 PMCID: PMC2129171 DOI: 10.1021/bi062291f] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [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: 02/07/2023]
Abstract
Proteins that discriminate between cisplatin-DNA adducts and oxaliplatin-DNA adducts are thought to be responsible for the differences in tumor range, toxicity, and mutagenicity of these two important chemotherapeutic agents. However, the structural basis for differential protein recognition of these adducts has not been determined and could be important for the design of more effective platinum anticancer agents. We have determined high-resolution NMR structures for cisplatin-GG and undamaged DNA dodecamers in the AGGC sequence context and have compared these structures with the oxaliplatin-GG structure in the same sequence context determined previously in our laboratory. This structural study allows the first direct comparison of cisplatin-GG DNA and oxaliplatin-GG DNA solution structures referenced to undamaged DNA in the same sequence context. Non-hydrogen atom rmsds of 0.81 and 1.21 were determined for the 15 lowest-energy structures for cisplatin-GG DNA and undamaged DNA, respectively, indicating good structural convergence. The theoretical NOESY spectra obtained by back-calculation from the final average structures showed excellent agreement with the experimental data, indicating that the final structures are consistent with the NMR data. Several significant conformational differences were observed between the cisplatin-GG adduct and the oxaliplatin-GG adduct, including buckle at the 5' G6.C19 base pair, opening at the 3' G7.C18 base pair, twist at the A5G6.T20C19 base pair step, slide, twist, and roll at the G6G7.C19C18 base pair step, slide at the G7C8.C18G17 base pair step, G6G7 dihedral angle, and overall bend angle. We hypothesize that these conformational differences may be related to the ability of various DNA repair proteins, DNA binding proteins, and DNA polymerases to discriminate between cisplatin-GG and oxaliplatin-GG adducts.
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Affiliation(s)
- Yibing Wu
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599-7260
| | - Debadeep Bhattacharyya
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599-7260
| | - Candice L. King
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599-7260
| | - Irene Baskerville-Abraham
- Department of Environmental Sciences and Engineering, School of Public Health, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Sung-Ho Huh
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Gunnar Boysen
- Department of Environmental Sciences and Engineering, School of Public Health, University of North Carolina, Chapel Hill, North Carolina 27599
| | - James A. Swenberg
- Department of Environmental Sciences and Engineering, School of Public Health, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Brenda Temple
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Sharon L. Campbell
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599-7260
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
- * To whom correspondence should be addressed: Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, NC 27599-7260. Telephone: (919) 966-3286. E-mail: or
| | - Stephen G. Chaney
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599-7260
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
- * To whom correspondence should be addressed: Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, NC 27599-7260. Telephone: (919) 966-3286. E-mail: or
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27
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Abstract
We report the syntheses of chimeras of peptide nucleic acid (PNA) with DNA and 2'-deoxy 2'-fluoroarabinonucleic acid (2'-FANA). Chimeric oligomers possessing a single central PNA insert were capable of forming hybrid duplexes with complementary RNA, although with diminished thermal stability in comparison to the unmodified oligomers. We subsequently determined the ability of the DNA and 2'-FANA oligomers of mixed-base composition to elicit human RNase H1 degradation of complementary RNA that was either unstructured or as a hairpin. In the case of the more rigid FANA strand, a PNA insert led to a higher ability of the chimera to direct the degradation of both types of RNA targets. Generally, the enhancement observed was greater for a butanediol linker than for a more rigid PNA linker. Along with previous work, these studies suggest that the general flexibility associated with an acyclic insert (e.g., butyl vs PNA)--and not necessarily the presence of local structural imperfections in the heteroduplex--is beneficial for RNase H1 activity. As well, there are implications to the charge nature of non-nucleotide inserts (neutral vs negative) and their ability to maintain RNase H activity that may serve to direct further design considerations. Together, these studies support the notion that flexibility of antisense oligonucleotide (AON)/RNA hybrids is essential for high RNase H catalysis, in which an enzyme-induced altered trajectory of the bound AON/RNA substrate could facilitate optimal interaction with the catalytic site of RNase H.
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28
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Ghodke HB, Krishnan R, Vignesh K, Kumar GVP, Narayana C, Krishnan Y. The I-Tetraplex Building Block: Rational Design and Controlled Fabrication of Robust 1D DNA Scaffolds through Non-Watson–Crick Interactions. Angew Chem Int Ed Engl 2007; 46:2646-9. [PMID: 17330917 DOI: 10.1002/anie.200604461] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Harshad B Ghodke
- National Centre for Biological Sciences, TIFR, Bellary Road, Bangalore, India
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29
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Abstract
Pax-8 is a member of the Pax family of transcription factors and is essential in the development of thyroid follicular cells. Pax-8 has two DNA-binding domains: the paired domain and the homeo domain. In this study, a preliminary X-ray diffraction analysis of the mammalian Pax-8 paired domain in complex with the C-site of the thyroglobulin promoter was achieved. The Pax-8 paired domain was crystallized by the hanging-drop vapor-diffusion method in complex with both a blunt-ended 26 bp DNA fragment and with a sticky-ended 24 bp DNA fragment with two additional overhanging bases. Crystallization experiments make clear that the growth of transparent crystals with large dimensions and regular shape is particularly influenced by ionic strength. The crystals of Pax-8 complex with blunt-ended and sticky-ended DNA, diffracted synchrotron radiation to 6.0 and 8.0 A resolution and belongs both to the C centered monoclinic system with cell dimensions: a = 89.88 A, b = 80.05 A, c = 67.73 A, and beta = 124.3 degrees and a = 256.56, b = 69.07, c = 99.32 A, and beta = 98.1 degrees , respectively. Fluorescence experiments suggest that the crystalline disorder, deduced by the poor diffraction, can be attributed to the low homogeneity of the protein-DNA sample. The theoretical comparative model of the Pax-8 paired domain complexed with the C-site of the thyroglobulin promoter shows the probable presence of some specific protein-DNA interactions already observed in other Pax proteins and the important role of the cysteine residues of PAI subdomain in the redox control of the DNA recognition.
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Affiliation(s)
- M Campagnolo
- Department of Chemical Sciences and Centre of Excellence in Biocrystallography, University of Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy
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30
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Affiliation(s)
- Sandra Thoeni
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland
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Wang P, Guo X, Zhang Q. Further evidence of autosomal-dominant Leber congenital amaurosis caused by heterozygous CRX mutation. Graefes Arch Clin Exp Ophthalmol 2007; 245:1401-2. [PMID: 17347810 DOI: 10.1007/s00417-007-0554-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2006] [Revised: 02/02/2007] [Accepted: 02/11/2007] [Indexed: 11/28/2022] Open
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32
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Balkwill GD, Williams HEL, Searle MS. Structure and folding dynamics of a DNA hairpin with a stabilising d(GNA) trinucleotide loop: influence of base pair mis-matches and point mutations on conformational equilibria. Org Biomol Chem 2007; 5:832-9. [PMID: 17315071 DOI: 10.1039/b616820e] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hairpins are known to play specific roles in DNA- and RNA--protein recognition. Various disease states are thought to originate from the ill-timed formation of a hairpin loop during transcription, particularly in the context of triplet repeats which are associated with myotonic dystrophy, fragile X syndrome and other genetic disorders. An understanding of nucleic acid folding mechanisms requires a detailed appreciation of the timescales of these local folding events, a characterisation of the conformational equilibria that exist in solution and the influence of point mutations on the relative stabilities of the different species. We investigate using NMR and CD spectroscopy the structure and dynamics of a DNA hairpin containing a highly stabilising cGNAg loop. The single-stranded 13-mer 5'-d(GCTACGNAGTCGC) with N = T folds to form a hairpin structure which accommodates a C-T mis-matched base pair within the double-stranded stem region. The hairpin is in equilibrium with a double-stranded duplex form with the mixture of two interconverting conformations in slow exchange on the NMR timescale (1-2 s(-1) at 308 K). We are able to characterise the dynamics of the interconversion process by NMR magnetisation transfer and by CD stopped-flow kinetic experiments. The latter shows that the hairpin folds too rapidly to detect by this method (>500 s(-1)) and forms in a "kinetic overshoot" followed by a much slower equilibration to a mixture of conformations ( approximately 0.13 s(-1) at 298 K). A point mutation that converts the GTA to a GAA loop sequence destabilises the intermolecular duplex structure and enables us to unambiguously assign the various dynamic processes that are taking place.
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Affiliation(s)
- Graham D Balkwill
- Centre for Biomolecular Sciences, School of Chemistry, University Park, Nottingham, NG7 2RD, UK.
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Fuentes-Cabrera M, Sumpter BG, Sponer JE, Sponer J, Petit L, Wells JC. Theoretical Study on the Structure, Stability, and Electronic Properties of the Guanine−Zn−Cytosine Base Pair in M-DNA. J Phys Chem B 2007; 111:870-9. [PMID: 17249831 DOI: 10.1021/jp066465e] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
M-DNA is a type of metalated DNA that forms at high pH and in the presence of Zn, Ni, and Co, with the metals placed in between each base pair, as in G-Zn-C. Experiments have found that M-DNA could be a promising candidate for a variety of nanotechnological applications, as it is speculated that the metal d-states enhance the conductivity, but controversy still clouds these findings. In this paper, we carry out a comprehensive ab initio study of eight G-Zn-C models in the gas phase to help discern the structure and electronic properties of Zn-DNA. Specifically, we study whether a model prefers to be planar and has electronic properties that correlate with Zn-DNA having a metallic-like conductivity. Out of all the studied models, there is only one which preserves its planarity upon full geometry optimization. Nevertheless, starting from this model, one can deduce a parallel Zn-DNA architecture only. This duplex would contain the imino proton, in contrast to what has been proposed experimentally. Among the nonplanar models, there is one that requires less than 8 kcal/mol to flatten (both in gas and solvent conditions), and we propose that it is a plausible model for building an antiparallel duplex. In this duplex, the imino proton would be replaced by Zn, in accordance with experimental models. Neither planar nor nonplanar models have electronic properties that correlate with Zn-DNA having a metallic-like conductivity due to Zn d-states. To understand whether density functional theory (DFT) can describe appropriately the electronic properties of M-DNAs, we have investigated the electronic properties of G-Co-C base pairs. We have found that when self-interaction corrections (SIC) are not included the HOMO state contains Co d-levels, whereas these levels are moved below the HOMO state when SIC are considered. This result indicates that caution should be exercised when studying the electronic properties of M-DNAs with functionals that do not account for strong electronic correlations.
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Affiliation(s)
- Miguel Fuentes-Cabrera
- Center for Nanophase Materials Sciences, and Computer Science and Mathematics Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee 37831-6494, USA.
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Lee H, Diavatis T, Tennakoon S, Yu P, Gao X. Solution structure of DNA/RNA hybrid duplex with C8-propynyl 2'-deoxyadenosine modifications: Implication of RNase H and DNA/RNA duplex interaction. Biochim Biophys Acta 2007; 1769:20-8. [PMID: 17196678 DOI: 10.1016/j.bbaexp.2006.11.004] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2006] [Revised: 10/10/2006] [Accepted: 11/06/2006] [Indexed: 05/13/2023]
Abstract
Solution structures of DNA/RNA hybrid duplexes, d(GCGCA*AA*ACGCG): r(cgcguuuugcg)d(C) (designated PP57), containing two C8-propynyl 2'-deoxyadenosines (A*) and unmodified hybrid (designated U4A4) are solved. The C8-propynyl groups on 2'-deoxyadenosine perturb the local structure of the hybrid duplex, but overall the structure is similar to that of canonical DNA/RNA hybrid duplex except that Hoogsteen hydrogen bondings between A* and U result in lower thermal stability. RNase H is known to cleave RNA only in DNA/RNA hybrid duplexes. Minor groove widths of hybrid duplexes, sugar puckerings of DNA are reported to be responsible for RNase H mediated cleavage, but structural requirements for RNase H mediated cleavage still remain elusive. Despite the presence of bulky propynyl groups of PP57 in the minor groove and greater flexibility, the PP57 is an RNase H substrate. To provide an insight on the interactions between RNase H and substrates we have modeled Bacillus halodurans RNase H-PP57 complex, our NMR structure and modeling study suggest that the residue Gly(15) and Asn(16) of the loop residues between first beta sheet and second beta sheet of RNase HI of Escherichia coli might participate in substrate binding.
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Affiliation(s)
- Hunjoong Lee
- Department of Chemistry, University of Houston, 136 Fleming Building, Houston, TX 77204-5003, USA.
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35
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Abstract
Supravalvular aortic stenosis (SVAS) is a congenital heart disease that can occur as an isolated autosomal-dominant condition or as part of the developmental disorder Williams-Beuren syndrome (WBS) and is caused by heterozygous genetic lesions involving the elastin (ELN) gene locus on chromosome 7ql 1.23. SVAS is one of many phenotypic features associated with the contiguous gene microdeletion disorder, WBS, and is caused by deletion of the ELN locus on one chromosome 7 homolog. Point mutations, chromosomal deletions, and translocation involving ELN have also been described in individuals with nonsyndromic SVAS. In addition, ELN is involved in the connective tissue disorder, autosomal-dominant cutis laxa, and has been implicated as a susceptibility gene for hypertension and intracranial aneurysms. The molecular analysis of ELN defects is, therefore, an area of significant interest. Genetic screening can be achieved using a variety of techniques to detect both mutations and gross chromosome rearrangements involving the ELN locus, providing the ability to screen families and individuals with SVAS and associated elastinopathies.
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Affiliation(s)
- May Tassabehji
- Academic Unit of Medical Genetics, The University of Manchester, St Mary's Hospital, Manchester, United Kingdom
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36
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Abstract
CoiA is a transient protein expressed specifically during competence and required for genetic transformation in Streptococcus pneumoniae, but not for DNA uptake. It is widely conserved among Gram-positive bacteria but its function is unknown. Here we report that although the rate of DNA uptake was not affected in a coiA mutant, the internalized donor DNA did not recombine into the host chromosome to form a physical and genetic heteroduplex. Instead, DNA taken up by a coiA mutant accumulated in the form of a single-stranded (ss) DNA-protein complex indistinguishable from the eclipse complex formed as a recombination intermediate in wild-type competent cells. Internalized donor DNA in a dprA mutant did not accumulate either as ss DNA or as an eclipse complex. Together, these results establish that a coiA mutant exhibits a phenotype different from that of dprA or recA mutants, and that CoiA functions at a later step in promoting recombination during genetic transformation in Streptococcus pneumoniae.
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Affiliation(s)
- Bhushan V Desai
- Laboratory for Molecular Biology, Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
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37
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Lima WF, Rose JB, Nichols JG, Wu H, Migawa MT, Wyrzykiewicz TK, Vasquez G, Swayze EE, Crooke ST. The positional influence of the helical geometry of the heteroduplex substrate on human RNase H1 catalysis. Mol Pharmacol 2006; 71:73-82. [PMID: 17028157 DOI: 10.1124/mol.106.025429] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
In a companion study published in this issue (p. 83), we showed that chimeric substrates containing 2'-methoxyethyl (MOE) nucleotides inhibited human RNase H1 activity. In this study, we prepared chimeric substrates containing a central DNA region with flanking northern-biased MOE nucleotides hybridized to complementary RNA. Conformationally biased and flexible modified nucleotides were positioned at the junctions between the DNA and MOE residues of the chimeric substrates to modulate the effects of the MOE residues on human RNase H1 activity. The strong northern-biased locked-nucleic acid modification exacerbated the negative effects of the MOE modifications resulting in slower human RNase H1 cleavage rates. Enhanced cleavage rates were observed for the eastern-biased 2'-ara-fluorothymidine and bulge inducing N-methylthymidine modifications positioned at the 5'-DNA/3'-MOE junction as well as the southern-biased 2'-methylthiothymidine and conformationally flexible tetrafluoroindole (TFI) modifications positioned at the 5'-MOE/3'-DNA junction. The heterocycle of the ribonucleotide opposing the TFI deoxyribonucleotide had no effect on the human RNase H1 activity, whereas nucleotide substitutions adjacent the TFI significantly affected the cleavage rate. Mismatch base pair(s) exhibited similar effects on human RNase H1 activity as the TFI modifications. The effects of the TFI modification and mismatch base pair(s) on human RNase H1 activity were influenced by the position of the modification relative to the nucleotides interacting with the catalytic site of the enzyme rather than the juxtaposition of the modification to the MOE residues. Finally, these results provide a method for enhancing the human RNase H1 activity of chimeric antisense oligonucleotides (ASO) as well as the design of more potent ASO drugs.
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Affiliation(s)
- Walt F Lima
- Department of Molecular and Structural Biology, Isis Pharmaceuticals, Carlsbad, California, USA.
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38
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Lima WF, Rose JB, Nichols JG, Wu H, Migawa MT, Wyrzykiewicz TK, Siwkowski AM, Crooke ST. Human RNase H1 discriminates between subtle variations in the structure of the heteroduplex substrate. Mol Pharmacol 2006; 71:83-91. [PMID: 17028158 DOI: 10.1124/mol.106.025015] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In a previous study, we demonstrated that the sugar conformation and helical geometry of the heteroduplex substrate at the catalytic site of human RNase H1 directs the selective recognition of the substrate by the enzyme (J Biol Chem 279: 36317-36326, 2004). In this study, we systematically introduced 2'-methoxyethoxy (MOE) nucleotides into the antisense oligodeoxyribonucleotide (ASO) of the heteroduplex to alter the helical geometry of the substrate. The MOE substitutions at the 3' and 5' poles of the ASO resulted in fewer cleavage sites and slower cleavage rates compared with the unmodified substrates. Furthermore, a greater reduction in cleavage activity was observed for MOE substitutions at the 5' pole of the ASO. The 3'- and 5'-most cleavage sites were positioned two and four to five base pairs, respectively, from the nearest MOE residues, suggesting a conformational transmission of the MOE/RNA helical geometry into the DNA/RNA portion of the heteroduplex. Similar conformational transmission was observed for Okazaki-like substrates containing deoxyribonucleotide substitutions at the 3' pole of the oligoribonucleotide. Finally, the heteroduplex substrates exhibited preferred cleavage sites that were cleaved 2- to 3-fold faster than other sites in the substrate, and these sites exhibited the greatest influence on the initial cleavage rates. The data presented here offer further insights into the role substrate structure plays in directing human RNase H1 activity as well as the design of effective ASOs.
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Affiliation(s)
- Walt F Lima
- Department of Molecular and Structural Biology, Isis Pharmaceuticals, Carlsbad, California, USA.
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Sehnert AJ. Use of Denaturing High-Performance Liquid Chromatography to Detect Mutations in Pediatric Cardiomyopathies. CONGENIT HEART DIS 2006; 126:257-70. [PMID: 16930018 DOI: 10.1385/1-59745-088-x:257] [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] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
This chapter describes the use of denaturing high-performance liquid chromatography as a high-throughput method to detect genetic mutations in pediatric cardiomyopathies. An overview of the classification, incidence, and etiologies of the major cardiomyopathies is provided, with emphasis on the special circumstances of the pediatric patient. During the past 15 yr, the genetic bases of inherited dilated, hypertrophic, and restrictive cardiomyopathy have been elucidated. As the list of known and candidate cardiomyopathy genes continues to grow and our ability to screen for genetic mutations improves, the cause of cardiomyopathy will be identified in a larger percentage of cases. This outcome is highly relevant to children with cardiomyopathy as well as those at risk for developing the disease because of their family history.
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Affiliation(s)
- Amy J Sehnert
- Department of Pediatrics, University of California, Pediatrics Heart Center, San Francisco, CA, USA
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40
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Abstract
A general analytical description of the equilibrium and reaction kinetics of DNA multiplex hybridization has been developed. In this approach, multiplex hybridization is considered to be a competitive multichannel reaction process: a system wherein many species can react both specifically and nonspecifically with one another. General equations are presented that can consider equilibrium and kinetic models of multiplex hybridization systems comprised, in principle, of any number of targets and probes. Numerical solutions to these systems for both equilibrium and kinetic behaviors are provided. Practical examples demonstrate clear differences between results obtained from more common simplex methods, in which individual hybridization reactions are considered to occur in isolation; and multiplex hybridization, where desired and competitive cross-hybrid reactions between all possible pairs of strands are considered. In addition, sensitivities of the hybridization process of the perfect match duplex, to temperature, target concentration, and existence of sequence homology with other strands, are examined. This general approach also considers explicit sequence-dependent interactions between targets and probes involved in the reactions. Sequence-dependent stabilities of all perfect match and mismatch duplex complexes are explicitly considered and effects of relative stability of cross-hybrid complexes are also explored. Results reveal several interdependent factors that strongly influence DNA multiplex hybridization behavior. These include: relative concentrations of all probes and targets; relative thermodynamic stability of all perfect match and mismatch complexes; sensitivity to temperature, particularly for mismatches; and amount of sequence homology shared by the probe and target strands in the multiplex mix.
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Affiliation(s)
- M T Horne
- Department of Chemistry, Portland State University, Portland, OR, USA
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41
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Abstract
Double-wide pyrimidine bases can assemble into helical, sequence-specific DNA complexes.
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42
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Hianik T, Wang X, Andreev S, Dolinnaya N, Oretskaya T, Thompson M. DNA-duplexes containing abasic sites: correlation between thermostability and acoustic wave properties. Analyst 2006; 131:1161-6. [PMID: 17003865 DOI: 10.1039/b605648m] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aldehydic apurinic or apyrimidinic sites that lack a nucleobase moiety are one of the most common forms of toxic lesions in DNA. In the present study, a close structural analog of such a site, the 2-(hydroxymethyl) tetrahydrofuranyl residue, was synthesized in order to act as a model for damaged nucleic acid probes. Prepared oligodeoxyribonucleotides containing one, two or three abasic sites were hybridized to complementary sequences immobilized on a gold surface using the neutravidin-biotin interaction for study by thickness shear mode acoustic wave detector. Measurement of the complex electrical impedance of an AT-cut quartz device with immobilized biotinylated nucleotide allowed the detection of changes of series resonance frequency, Deltafs, and motional resistance, Rm, associated with duplex formation. The changes as detected by the acoustic wave method correlated well with the thermostability of DNA duplexes in solution. With respect to the latter, UV-monitored melting curves indicate that both the number of sites and their localization in the double-stranded structure influence the amount by which a 19 b.p. duplex is destabilized. The presence of 3 abasic sites completely destabilized the DNA duplex.
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Affiliation(s)
- T Hianik
- Laboratory of Biophysics, Faculty of Mathematics, Physics and Computer Science, Comenius University, Mlynská dolina F1, 842 48 Bratislava, Slovak Republic
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Li W, Zhang M, Zhang JL, Li HQ, Zhang XC, Sun Q, Qiu CM. Interactions of daidzin with intramolecular G-quadruplex. FEBS Lett 2006; 580:4905-10. [PMID: 16920104 DOI: 10.1016/j.febslet.2006.08.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2006] [Revised: 07/06/2006] [Accepted: 08/01/2006] [Indexed: 02/01/2023]
Abstract
The potential interaction of daidzin, an ingredient of soy isoflavones, with human telomeric antiparallel G-quadruplex dAG(3)(T(2)AG(3))(3) was studied using ESI-MS, PAGE, CD and molecular simulation. Experimental studies indicated that daidzin molecules interacted with dAG(3)(T(2)AG(3))(3) and formed DNA-daidzin complex with the stoichiometric ratio of 1:1 and 1:2. The transition temperature of the G-quadruplex increased at higher ratio of daidzin to DNA. Under molecular crowding conditions the interactions between daidzin and the G-quadruplex become much stronger. Combining computational simulation and experimental results, it is demonstrated that the dAG(3)(T(2)AG(3))(3)/daidzin complex with a stoichiometric ratio of 1:1 is stabilized through the pi-pi conjugacy interactions and hydrogen bondings between daidzin and the bases of G-quadruplex. This work provides guidance not only on exploring the molecular anti-cancer mechanism of dietary isoflavones, but also searching small natural products as promising anticancer candidates that can inhibit telomerase activity.
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Affiliation(s)
- Wei Li
- Department of Chemical Technology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
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44
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Sharanov YS, Zvereva MI, Dontsova OA. Saccharomyces cerevisiaetelomerase subunit Est3p binds DNA and RNA and stimulates unwinding of RNA/DNA heteroduplexes. FEBS Lett 2006; 580:4683-90. [PMID: 16884717 DOI: 10.1016/j.febslet.2006.07.048] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2006] [Revised: 05/29/2006] [Accepted: 07/17/2006] [Indexed: 10/24/2022]
Abstract
Telomerase is a key participant of telomere length maintenance system in majority of eukaryotes. It synthesizes telomere repeats at 3'-end of telomere DNA according to its own RNA template. In addition to the reverse transcriptase subunit Est2p and telomerase RNA TLC1, yeast telomerase contain Est1p, necessary for telomerase attachment to telomere and telomerase activation, and Est3p, a subunit with unknown function. We have isolated Est3p and examined its biochemical properties. Est3p binds both DNA and RNA oligonucleotides containing telomere repeat sequences and stimulates dissociation of RNA/DNA heteroduplexes. The importance of these properties of Est3p for telomerase function is discussed.
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Affiliation(s)
- Yu S Sharanov
- Division of Chemistry of Natural Compounds, Department of Chemistry, M.V. Lomonosov Moscow State University, Vorobievi Gori 1, Building 40, 119992 Moscow, Russia
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Yang D, Goldsmith EB, Lin Y, Waldman BC, Kaza V, Waldman AS. Genetic exchange between homeologous sequences in mammalian chromosomes is averted by local homology requirements for initiation and resolution of recombination. Genetics 2006; 174:135-44. [PMID: 16816418 PMCID: PMC1569803 DOI: 10.1534/genetics.106.060590] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We examined the mechanism by which recombination between imperfectly matched sequences (homeologous recombination) is suppressed in mammalian chromosomes. DNA substrates were constructed, each containing a thymidine kinase (tk) gene disrupted by insertion of an XhoI linker and referred to as a "recipient" gene. Each substrate also contained one of several "donor" tk sequences that could potentially correct the recipient gene via recombination. Each donor sequence either was perfectly homologous to the recipient gene or contained homeologous sequence sharing only 80% identity with the recipient gene. Mouse Ltk(-) fibroblasts were stably transfected with the various substrates and tk(+) segregants produced via intrachromosomal recombination were recovered. We observed exclusion of homeologous sequence from gene conversion tracts when homeologous sequence was positioned adjacent to homologous sequence in the donor but not when homeologous sequence was surrounded by homology in the donor. Our results support a model in which homeologous recombination in mammalian chromosomes is suppressed by a nondestructive dismantling of mismatched heteroduplex DNA (hDNA) intermediates. We suggest that mammalian cells do not dismantle mismatched hDNA by responding to mismatches in hDNA per se but rather rejection of mismatched hDNA appears to be driven by a requirement for localized homology for resolution of recombination.
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Affiliation(s)
- Derek Yang
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208, USA
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46
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Abstract
We are developing triple helix-forming oligonucleotides (TFOs) as gene targeting reagents in mammalian cells. We have described psoralen-conjugated TFOs containing 2'-O-methyl (2'OMe) and 2'-O-aminoethoxy (AE) ribose substitutions. TFOs with a cluster of 3-4 AE residues, with all other sugars as 2'OMe, were bioactive in a gene knockout assay in mammalian cells. In contrast, TFOs with one or two clustered, or three dispersed, AE residues were inactive. Thermal stability analysis of the triplexes indicated that there were only incremental differences between the active and inactive TFOs. However the active and inactive TFOs could be distinguished by their association kinetics. The bioactive TFOs showed markedly greater on-rates than the inactive TFOs. It appears that the on-rate is a better predictor of TFO bioactivity than thermal stability. Our data are consistent with a model in which a cluster of 3-4 AE residues stabilizes the nucleation event that precedes formation of a complete triplex. It is likely that triplexes in cells are much less stable than triplexes in vitro probably as a result of elution by chromatin-associated translocases and helicases. Consequently the biologic assay will favor TFOs that can bind and rebind genomic targets quickly.
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Affiliation(s)
- Michael M Seidman
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, 5600 Nathan Shock Drive, Baltimore, MD 21224, USA.
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47
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Otagiri T, Sugai K, Kijima K, Arai H, Sawaishi Y, Shimohata M, Hayasaka K. Periaxin mutation in Japanese patients with Charcot-Marie-Tooth disease. J Hum Genet 2006; 51:625-8. [PMID: 16770524 DOI: 10.1007/s10038-006-0408-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2006] [Accepted: 03/27/2006] [Indexed: 11/29/2022]
Abstract
Periaxin (PRX) plays an important role in the myelination of the peripheral nerve and consequently in the pathogenesis of Charcot-Marie-Tooth disease (CMT). To date, nine nonsense or frameshift PRX mutations have been reported in eight families with CMT. The patients with PRX mutations appeared to show characteristic clinical features with early onset but slow or no progression, a common result of mutations that lead to missing a C-terminal acidic domain. Here, we report a Japanese CMT patient with these characteristic clinical features, who was a compound heterozygote for PRX R1070X and L132FsX153 mutations. We previously reported that three Japanese isolated families also had the homozygous R1070X mutation. To examine the potential founder effect of the R1070X mutation in the Japanese population, we performed haplotype analysis and found that each R1070X allele lay on a different haplotype background in these four families. Therefore, the high frequency of the R1070X mutation among the Japanese population is not likely the consequence of a founder effect, but probably a result of a mutation hot spot.
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Affiliation(s)
- Tesshu Otagiri
- Department of Pediatrics, Yamagata University School of Medicine, 2-2-2 Iida-nishi, Yamagata 990-9585, Japan
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48
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Xu H, Zhang H, Qu X. Interactions of the human telomeric DNA with terbium-amino acid complexes. J Inorg Biochem 2006; 100:1646-52. [PMID: 16842855 DOI: 10.1016/j.jinorgbio.2006.05.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2006] [Revised: 05/24/2006] [Accepted: 05/29/2006] [Indexed: 10/24/2022]
Abstract
The human telomeric DNA can form four-stranded structures: the G-rich strand adopts a G-quadruplex conformation stabilized by G-quartets and the C-rich strand may fold into an I-motif based on intercalated C.C(+) base pairs. There is intense interests in the design and synthesis of compounds which can target telomeric DNA and inhibit the telomerase activity. Here we report the thermodynamic studies of the two newly synthesized terbium-amino acid complexes bound to the human telomeric G-quadruplex and I-motif DNA which were studied by means of UV-Visible, DNA meltings, fluorescence and circular dichroism. These two complexes can bind to the human telomeric DNA and have shown different features on DNA stability, binding stoichiometry, and sequence-dependent fluorescence enhancement. To our knowledge, this is the first report to show terbium-amino acid complexes can interact with the human telomeric DNA.
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Affiliation(s)
- Haixia Xu
- Division of Biological Inorganic Chemistry, Key Laboratory of Rare Earth Chemistry and Physics, Graduate School of the Chinese Academy of Sciences, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
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49
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Abstract
G-quadruplexes and Z-DNA are two important non-B forms of DNA architecture. Results on novel structural elements, folding and unfolding kinetics, and interactions with small molecules and proteins have been reported recently for these forms. These results will enhance our understanding of the biology of these structures and provide a platform for drug design.
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Affiliation(s)
- Anh Tuân Phan
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA.
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50
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Abstract
Pyrrolo-C (PC), or 3-[beta-D-2-ribofuranosyl]-6-methylpyrrolo[2,3-d]pyrimidin-2(3H)-one, is a fluorescent analog of the nucleoside cytidine that retains its Watson-Crick base-pairing capacity with G. Due to its red-shifted absorbance, it can be selectively excited in the presence of natural nucleosides, making it a potential site-specific probe for RNA structure and dynamics. Similar to 2-aminopurine nucleoside, which base-pairs with uridine (or thymidine), PC's fluorescence becomes reversibly quenched upon base-pairing, most likely due to stacking interactions with neighboring bases. To test its utility as an RNA probe, we examined PC's fluorescent properties over a wide range of ionic strengths, pH, organic cosolvents, and temperatures. Incorporation of PC into a single-stranded RNA results in an approximately 60% reduction of fluorescence intensity, while duplex formation reduces the fluorescence by approximately 75% relative to the free ribonucleoside. We find that the fluorescence intensity of PC is only moderately affected by ionic strength, pH, and temperature, while it is slightly enhanced by organic cosolvents, making it a versatile probe for a broad range of buffer conditions. We demonstrate two applications for PC: fluorescent measurements of the kinetics of formation and dissociation of an RNA/DNA complex, and fluorescent monitoring of the thermal denaturation of the central segment of an RNA duplex. Taken together, our data showcase the potential of pyrrolo-C as an effective fluorescent probe to study RNA structure, dynamics, and function, complementary to the popular 2-aminopurine ribonucleoside.
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Affiliation(s)
- Rebecca A Tinsley
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
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