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Brumett R, Danai L, Coffman A, Radwan Y, Teter M, Hayth H, Doe E, Pranger K, Thornburgh S, Dittmer A, Li Z, Kim TJ, Afonin KA, Khisamutdinov EF. Design and Characterization of Compact, Programmable, Multistranded Nonimmunostimulatory Nucleic Acid Nanoparticles Suitable for Biomedical Applications. Biochemistry 2024; 63:312-325. [PMID: 38271599 PMCID: PMC11587934 DOI: 10.1021/acs.biochem.3c00615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
We report a thorough investigation of the role of single-stranded thymidine (ssT) linkers in the stability and flexibility of minimal, multistranded DNA nanostructures. We systematically explore the impact of varying the number of ssTs in three-way junction motifs (3WJs) on their formation and properties. Through various UV melting experiments and molecular dynamics simulations, we demonstrate that while the number of ssTs minimally affects thermodynamic stability, the increasing ssT regions significantly enhance the structural flexibility of 3WJs. Utilizing this knowledge, we design triangular DNA nanoparticles with varying ssTs, all showing exceptional assembly efficiency except for the 0T triangle. All triangles demonstrate enhanced stability in blood serum and are nonimmunostimulatory and nontoxic in mammalian cell lines. The 4T 3WJ is chosen as the building block for constructing other polygons due to its enhanced flexibility and favorable physicochemical characteristics, making it a versatile choice for creating cost-effective, stable, and functional DNA nanostructures that can be stored in the dehydrated forms while retaining their structures. Our study provides valuable insights into the design and application of nucleic acid nanostructures, emphasizing the importance of understanding stability and flexibility in the realm of nucleic acid nanotechnology. Our findings suggest the intricate connection between these ssTs and the structural adaptability of DNA 3WJs, paving the way for more precise design and engineering of nucleic acid nanosystems suitable for broad biomedical applications.
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Affiliation(s)
- Ross Brumett
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Leyla Danai
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Abigail Coffman
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Yasmine Radwan
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Megan Teter
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Hannah Hayth
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Erwin Doe
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Katelynn Pranger
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Sable Thornburgh
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Allison Dittmer
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Zhihai Li
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Tae Jin Kim
- Department of Physical Sciences, West Virginia University Institute of Technology, Beckley, West Virginia 25801, United States
| | - Kirill A. Afonin
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Emil F. Khisamutdinov
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
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2
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Yin J, Feng Z, Li Z, Hu J, Hu Y, Cai X, Zhou H, Wang K, Tang N, Huang A, Huang L. Synthesis and evaluation of N-sulfonylpiperidine-3-carboxamide derivatives as capsid assembly modulators inhibiting HBV in vitro and in HBV-transgenic mice. Eur J Med Chem 2023; 249:115141. [PMID: 36709646 DOI: 10.1016/j.ejmech.2023.115141] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/13/2023] [Accepted: 01/18/2023] [Indexed: 01/24/2023]
Abstract
The hepatitis B virus (HBV) capsid assembly modulators (CAMs) have been developed as effective anti-HBV agents in the treatment of chronic HBV infection by targeting the HBV core protein and inducing the formation of aberrant or morphologically normal capsid. However, some CAMs have been observed adverse events such as ALT flares and rash. Therefore, finding new CAMs is of great importance. In this report, we synthesized N-sulfonylpiperidine-3-carboxamides (SPCs) derivatives and evaluated their anti-HBV activities. Among the SPC derivatives, compound C-49 notably suppressed HBV replication in HepAD38, HepG2-HBV1.3 and HepG2-NTCP cells. Moreover, treatment with C-49 for 12 days exhibited potent anti-HBV activity (100 mg/kg; 2.42 log reduction of serum HBV DNA) in HBV-transgenic mice without apparent hepatotoxicity. Our findings provided a new SPC derivative as HBV capsid assembly modulator for developing safe and efficient anti-HBV therapy.
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Affiliation(s)
- Jiaxin Yin
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Department of Infectious Diseases, Institute for Viral Hepatitis, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Zhongqi Feng
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Department of Infectious Diseases, Institute for Viral Hepatitis, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Zhi Li
- Department of Breast&thyroid Surgery, The Second Affiliated Hospital of Chongqing Medical University, Yuzhong District, Chongqing, 400010, China
| | - Jieli Hu
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Department of Infectious Diseases, Institute for Viral Hepatitis, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Yuan Hu
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Department of Infectious Diseases, Institute for Viral Hepatitis, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Xuefei Cai
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Department of Infectious Diseases, Institute for Viral Hepatitis, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Hui Zhou
- Chongqing Research Center for Pharmaceutical Engineering, College of Pharmacy, Chongqing Medical University, Chongqing, 400016, China
| | - Kai Wang
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Department of Infectious Diseases, Institute for Viral Hepatitis, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Ni Tang
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Department of Infectious Diseases, Institute for Viral Hepatitis, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Ailong Huang
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Department of Infectious Diseases, Institute for Viral Hepatitis, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Luyi Huang
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Department of Infectious Diseases, Institute for Viral Hepatitis, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China.
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3
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Andreychuk DB, Andriyasov AV, Nikonova ZB, Kozlov АА, Suarez DL, Chvala IA. Armoured exogenous internal control for real-time PCR diagnosis of avian influenza. Avian Pathol 2019; 48:492-498. [PMID: 31203638 DOI: 10.1080/03079457.2019.1628918] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
An exogenous "armoured" PCR internal control (IC) short RNA was analyzed in conjunction with real-time RT-PCR method for diagnosis of avian influenza. The resistance to nucleases and increased physical stability of the IC was ensured using branched polyethyleneimine (PEI) which was in complex with IC-RNA. The option to add the IC directly to pathological material suspensions allows measurement of the nucleic acids extraction efficiency. Stability of armoured RNA-IC during storage and tissue suspension preparation was shown. The advantage of exogenous "armoured" IC was demonstrated in the experiment with AIV genome detection by qPCR in samples from different species of wild birds. The exogenous IC gave reproducible homogeneous Ct values in all tests.
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Affiliation(s)
- D B Andreychuk
- Federal Centre for Animal Health , Vladimir , Russian Federation
| | - A V Andriyasov
- Federal Centre for Animal Health , Vladimir , Russian Federation
| | - Z B Nikonova
- Federal Centre for Animal Health , Vladimir , Russian Federation
| | - А А Kozlov
- Federal Centre for Animal Health , Vladimir , Russian Federation
| | - D L Suarez
- Southeast Poultry Research Laboratory, U.S. National Poultry Research Center , Athens , GA , USA
| | - Il A Chvala
- Federal Centre for Animal Health , Vladimir , Russian Federation
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Chang L, Wang G, Jia T, Zhang L, Li Y, Han Y, Zhang K, Lin G, Zhang R, Li J, Wang L. Armored long non-coding RNA MEG3 targeting EGFR based on recombinant MS2 bacteriophage virus-like particles against hepatocellular carcinoma. Oncotarget 2018; 7:23988-4004. [PMID: 26992211 PMCID: PMC5029679 DOI: 10.18632/oncotarget.8115] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 03/02/2016] [Indexed: 02/07/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most frequently diagnosed cancers worldwide. However, the treatment of patients with HCC is particularly challenging. Long non-coding RNA maternally expressed gene 3 (MEG3) has been identified as a potential suppressor of several types of tumors, but the delivery of long RNA remains problematic, limiting its applications. In the present study, we designed a novel delivery system based on MS2 virus-like particles (VLPs) crosslinked with GE11 polypeptide. This vector was found to be fast, effective and safe for the targeted delivery of lncRNA MEG3 RNA to the epidermal growth factor receptor (EGFR)-positive HCC cell lines without the activation of EGFR downstream pathways, and significantly attenuated both in vitro and in vivo tumor cell growth. Our study also revealed that the targeted delivery was mainly dependent on clathrin-mediated endocytosis and MEG3 RNA suppresses tumor growth mainly via increasing the expression of p53 and its downstream gene GDF15, but decreasing the expression of MDM2. Thus, this vector is promising as a novel delivery system and may facilitate a new approach to lncRNA based cancer therapy.
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Affiliation(s)
- Le Chang
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Guojing Wang
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Tingting Jia
- Department of Clinical Laboratory, Beijing Chaoyang Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Lei Zhang
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, People's Republic of China.,Peking University Fifth School of Clinical Medicine, Beijing, People's Republic of China
| | - Yulong Li
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Yanxi Han
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, People's Republic of China
| | - Kuo Zhang
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Guigao Lin
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, People's Republic of China
| | - Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, People's Republic of China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Lunan Wang
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
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5
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Armored DNA in recombinant Baculoviruses as controls in molecular genetic assays. Appl Microbiol Biotechnol 2017; 101:7259-7269. [DOI: 10.1007/s00253-017-8436-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 07/12/2017] [Accepted: 07/15/2017] [Indexed: 01/29/2023]
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6
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Zambenedetti MR, Pavoni DP, Dallabona AC, Dominguez AC, Poersch CDO, Fragoso SP, Krieger MA. Internal control for real-time polymerase chain reaction based on MS2 bacteriophage for RNA viruses diagnostics. Mem Inst Oswaldo Cruz 2017; 112:339-347. [PMID: 28403327 PMCID: PMC5398160 DOI: 10.1590/0074-02760160380] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Accepted: 01/17/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Real-time reverse transcription polymerase chain reaction (RT-PCR) is routinely used to detect viral infections. In Brazil, it is mandatory the use of nucleic acid tests to detect hepatitis C virus (HCV), hepatitis B virus and human immunodeficiency virus in blood banks because of the immunological window. The use of an internal control (IC) is necessary to differentiate the true negative results from those consequent from a failure in some step of the nucleic acid test. OBJECTIVES The aim of this study was the construction of virus-modified particles, based on MS2 bacteriophage, to be used as IC for the diagnosis of RNA viruses. METHODS The MS2 genome was cloned into the pET47b(+) plasmid, generating pET47b(+)-MS2. MS2-like particles were produced through the synthesis of MS2 RNA genome by T7 RNA polymerase. These particles were used as non-competitive IC in assays for RNA virus diagnostics. In addition, a competitive control for HCV diagnosis was developed by cloning a mutated HCV sequence into the MS2 replicase gene of pET47b(+)-MS2, which produces a non-propagating MS2 particle. The utility of MS2-like particles as IC was evaluated in a one-step format multiplex real-time RT-PCR for HCV detection. FINDINGS We demonstrated that both competitive and non-competitive IC could be successfully used to monitor the HCV amplification performance, including the extraction, reverse transcription, amplification and detection steps, without compromising the detection of samples with low target concentrations. In conclusion, MS2-like particles generated by this strategy proved to be useful IC for RNA virus diagnosis, with advantage that they are produced by a low cost protocol. An attractive feature of this system is that it allows the construction of a multicontrol by the insertion of sequences from more than one pathogen, increasing its applicability for diagnosing different RNA viruses.
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Affiliation(s)
- Miriam Ribas Zambenedetti
- Fundação Oswaldo Cruz-Fiocruz, Instituto Carlos Chagas, Laboratório de Genômica, Curitiba, PR, Brasil.,Universidade Federal do Paraná, Departamento de Bioprocessos e Biotecnologia, Curitiba, PR, Brasil
| | - Daniela Parada Pavoni
- Fundação Oswaldo Cruz-Fiocruz, Instituto Carlos Chagas, Laboratório de Genômica, Curitiba, PR, Brasil
| | | | | | | | - Stenio Perdigão Fragoso
- Fundação Oswaldo Cruz-Fiocruz, Instituto Carlos Chagas, Laboratório de Genômica, Curitiba, PR, Brasil
| | - Marco Aurélio Krieger
- Fundação Oswaldo Cruz-Fiocruz, Instituto Carlos Chagas, Laboratório de Genômica, Curitiba, PR, Brasil.,Fundação Oswaldo Cruz-Fiocruz, Instituto de Biologia Molecular do Paraná, Curitiba, PR, Brasil
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7
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Wen AM, Steinmetz NF. Design of virus-based nanomaterials for medicine, biotechnology, and energy. Chem Soc Rev 2016; 45:4074-126. [PMID: 27152673 PMCID: PMC5068136 DOI: 10.1039/c5cs00287g] [Citation(s) in RCA: 246] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This review provides an overview of recent developments in "chemical virology." Viruses, as materials, provide unique nanoscale scaffolds that have relevance in chemical biology and nanotechnology, with diverse areas of applications. Some fundamental advantages of viruses, compared to synthetically programmed materials, include the highly precise spatial arrangement of their subunits into a diverse array of shapes and sizes and many available avenues for easy and reproducible modification. Here, we will first survey the broad distribution of viruses and various methods for producing virus-based nanoparticles, as well as engineering principles used to impart new functionalities. We will then examine the broad range of applications and implications of virus-based materials, focusing on the medical, biotechnology, and energy sectors. We anticipate that this field will continue to evolve and grow, with exciting new possibilities stemming from advancements in the rational design of virus-based nanomaterials.
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Affiliation(s)
- Amy M Wen
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH 44106, USA.
| | - Nicole F Steinmetz
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH 44106, USA. and Department of Radiology, Case Western Reserve University, Cleveland, OH 44106, USA and Department of Materials Science and Engineering, Case Western Reserve University, Cleveland, OH 44106, USA and Department of Macromolecular Science and Engineering, Case Western Reserve University, Cleveland, OH 44106, USA and Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
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8
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Zhang K, Huo H, Sun Y, Wang L, Zhang R, Lin G, Xie J, Wang Q, Li J. Application of HTB-SiHa cells transfected with a recombinant plasmid for external quality assessment of Chlamydia trachomatis PCR. Ann Lab Med 2014; 34:360-6. [PMID: 25187888 PMCID: PMC4151004 DOI: 10.3343/alm.2014.34.5.360] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 02/11/2014] [Accepted: 06/24/2014] [Indexed: 01/29/2023] Open
Abstract
Background The participation of laboratories in external quality assessment (EQA) programs is required for the quality assurance of nucleic acid amplification of Chlamydia trachomatis. This study aimed to construct a new quality control (QC) material applicated in EQA of C. trachomatis PCR. Methods A QC material-HTB-SiHa cells transfected with a recombinant plasmid containing the cryptic plasmid sequence-was constructed for C. trachomatis PCR detection, and four different panels, each consisting of 4 positive samples with serial dilution of the constructed QC material and 1 negative sample, were distributed by the National Center for Clinical Laboratories among four groups of 275, 268, 317, and 304 participants across China from 2011 through 2012. A total of eight commercial kits were used for C. trachomatis PCR detection in participants. Results Nine laboratories reported false-positive results (0.9%). As the series dilution increased, the correct reporting of the data sets decreased; the lowest correct rate was 96.3% in the weakest positive samples (104 copies/mL). Eight laboratories reported false-positive results, and 42 laboratories reported false-negative results in the EQA detection of C. trachomatis. No significant differences were observed in the detection of the constructed C. trachomatis positive samples (97.9%, 98.5%, 100%, 98.5%; P=0.36) and negative samples (100%, 99.0%, 100%, 99.0%; P=0.764) using four commercial kits commonly used in China. Conclusions The results of the EQA study indicated that the constructed material provides a noninfectious, stable control material with sufficient volume for PCR detection of C. trachomatis.
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Affiliation(s)
- Kuo Zhang
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, China
| | - Hong Huo
- Department of Clinical Laboratory, Beijing Chaoyang Hospital Affiliated to the Capital University of Medical Sciences, Beijing, China
| | - Yu Sun
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, China
| | - Lunan Wang
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, China
| | - Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, China
| | - Guigao Lin
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, China
| | - Jiehong Xie
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, China
| | - Qingtao Wang
- Department of Clinical Laboratory, Beijing Chaoyang Hospital Affiliated to the Capital University of Medical Sciences, Beijing, China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, China
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9
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Goswami J, Davis MC, Andersen T, Alileche A, Hampikian G. Safeguarding forensic DNA reference samples with nullomer barcodes. J Forensic Leg Med 2013; 20:513-9. [PMID: 23756524 DOI: 10.1016/j.jflm.2013.02.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 10/30/2012] [Accepted: 02/05/2013] [Indexed: 11/18/2022]
Abstract
Unintended transfer of biological material containing DNA is a concern to all laboratories conducting PCR analysis. While forensic laboratories have protocols in place to reduce the possibility of contaminating casework samples, there is no way to detect when a reference sample is mislabeled as evidence, or contaminates a forensic sample. Thus there is public concern regarding the safeguarding of DNA submitted to crime labs. We demonstrate a method of introducing an internal amplification control to reference samples, in the form of a nullomer barcode which is based upon sequences absent or rare from publically accessible DNA databases. The detection of this barcode would indicate that the source of analyzed DNA was from a reference sample provided by an individual, and not from an evidence sample. We demonstrate that the nullomers can be added directly to collection devices (FTA paper) to allow tagging during the process of sample collection. We show that such nullomer oligonucleotides can be added to existing forensic typing and quantification kits, without affecting genotyping or quantification results. Finally, we show that even when diluted a million-fold and spilled on a knife, the nullomer tags can be clearly detected. These tags support the National Research Council of the National Academy recommendation that "Quality control procedures should be designed to identify mistakes, fraud, and bias" in forensic science (National Academy of Sciences, 2009).
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Affiliation(s)
- Jayita Goswami
- Department of Biology, Boise State University, Science-215, 1910 University Dr., Boise, ID 83725-1515, USA
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10
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Sun S, Meng S, Zhang R, Zhang K, Wang L, Li J. Development of a new duplex real-time polymerase chain reaction assay for hepatitis B viral DNA detection. Virol J 2011; 8:227. [PMID: 21569595 PMCID: PMC3116493 DOI: 10.1186/1743-422x-8-227] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Accepted: 05/14/2011] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Quantification of hepatitis B virus (HBV) DNA can be used for diagnosing HBV infection and monitoring the effect of antiviral therapy. However, probably because of mismatches between the template and primer/probe, HBV DNA in some HBV infections could not be detected using currently available commercial assays with single primer/probe. By aligning the HBV sequences, we developed a duplex real-time polymerase chain reaction (PCR) assay using two sets of primers/probes and a specific armored DNA as internal control (IC). RESULTS The limit of the duplex real-time PCR assay was 29.5 IU/ml, whereas the specificity was 100%. The within-run precision coefficient of variation (CV) ranged from 1.02% to 2.73%, while the between-run CV ranged from 0.83% to 1.25%. The optimal concentration of armored DNA IC in the HBV DNA duplex real-time PCR assay was 1 000 copies/ml. Data from 69 serum samples with HBV infection showed that the performance of the duplex real-time PCR assay was comparable to that of the COBAS Ampliprep/Cobas Taqman (CAP/CTM) HBV assay and was superior to those of the domestic commercial HBV assays. CONCLUSIONS The duplex real-time PCR assay is sufficiently sensitive, specific, accurate, reproducible and cost-effective for the detection of HBV DNA. It is suitable for high throughput screening and frequent HBV DNA level monitoring.
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Affiliation(s)
- Shipeng Sun
- National Center for Clinical Laboratories, Beijing Hospital, People's Republic of China
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