1
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Tong H, Liu N, Wei Y, Zhou Y, Li Y, Wu D, Jin M, Cui S, Li H, Li G, Zhou J, Yuan Y, Zhang H, Shi L, Yao X, Yang H. Programmable deaminase-free base editors for G-to-Y conversion by engineered glycosylase. Natl Sci Rev 2023; 10:nwad143. [PMID: 37404457 PMCID: PMC10317176 DOI: 10.1093/nsr/nwad143] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/13/2023] [Accepted: 05/13/2023] [Indexed: 07/06/2023] Open
Abstract
Current DNA base editors contain nuclease and DNA deaminase that enables deamination of cytosine (C) or adenine (A), but no method for guanine (G) or thymine (T) editing is available at present. Here we developed a deaminase-free glycosylase-based guanine base editor (gGBE) with G editing ability, by fusing Cas9 nickase with engineered N-methylpurine DNA glycosylase protein (MPG). By several rounds of MPG mutagenesis via unbiased and rational screening using an intron-split EGFP reporter, we demonstrated that gGBE with engineered MPG could increase G editing efficiency by more than 1500 fold. Furthermore, this gGBE exhibited high base editing efficiency (up to 81.2%) and high G-to-T or G-to-C (i.e. G-to-Y) conversion ratio (up to 0.95) in both cultured human cells and mouse embryos. Thus, we have provided a proof-of-concept of a new base editing approach by endowing the engineered DNA glycosylase the capability to selectively excise a new type of substrate.
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Affiliation(s)
| | | | | | | | | | | | - Ming Jin
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350004, China
| | - Shuna Cui
- HuidaGene Therapeutics Co., Ltd., Shanghai 200131, China
| | - Hengbin Li
- HuidaGene Therapeutics Co., Ltd., Shanghai 200131, China
| | - Guoling Li
- HuidaGene Therapeutics Co., Ltd., Shanghai 200131, China
| | - Jingxing Zhou
- HuidaGene Therapeutics Co., Ltd., Shanghai 200131, China
| | - Yuan Yuan
- HuidaGene Therapeutics Co., Ltd., Shanghai 200131, China
| | - Hainan Zhang
- HuidaGene Therapeutics Co., Ltd., Shanghai 200131, China
| | - Linyu Shi
- HuidaGene Therapeutics Co., Ltd., Shanghai 200131, China
| | - Xuan Yao
- HuidaGene Therapeutics Co., Ltd., Shanghai 200131, China
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2
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Schulze Johann K, Bauer H, Wiegand P, Pfeiffer H, Vennemann M. Detecting DNA damage in stored blood samples. Forensic Sci Med Pathol 2023; 19:50-59. [PMID: 36355320 PMCID: PMC10014702 DOI: 10.1007/s12024-022-00549-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/18/2022] [Indexed: 11/11/2022]
Abstract
Several commercially available quantitative real-time PCR (qPCR) systems enable highly sensitive detection of human DNA and provide a degradation index (DI) to assess DNA quality. From routine casework in forensic genetics, it was observed that DNA degradation in forensic samples such as blood samples stored under sub-optimal conditions leads to visible effects in multiplex analyses of short tandem repeat markers (STRs) due to decreased amplification efficiencies in longer amplicons. It was further noticed that degradation indices often remain below the value that is considered to be critical. Thus, the aim of this work was to systematically analyze this effect and to compare conventional qPCR assays with a modified qPCR approach using uracil DNA glycosylase (UNG) and DNA quality assessment methods based on electrophoresis. Blood samples were stored at three different storage temperatures for up to 316 days. Significantly increased DNA recovery was observed from samples stored at high temperatures (37 °C) compared samples stored at room temperature and 4 °C. We observed typical effects of degradation in STR analyses but no correlation between DI and storage time in any of the storage conditions. Adding UNG slightly increased the sensitivity of detecting DNA degradation in one of the qPCR kits used in this study. This observation was not confirmed when using a second qPCR system. Electrophoretic systems did also not reveal significant correlations between integrity values and time. Methods for detecting DNA degradation are usually limited to the detection of DNA fragmentation, and we conclude that degradation affecting forensic STR typing is more complex.
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Affiliation(s)
- Kristina Schulze Johann
- Institute of Legal Medicine, University of Münster, Röntgenstr. 23, 48149, Münster, Germany.
| | - Hannah Bauer
- Institute of Legal Medicine, University of Münster, Röntgenstr. 23, 48149, Münster, Germany
| | - Peter Wiegand
- Institute of Legal Medicine, University of Ulm, Albert-Einstein-Allee 23, 89081, Ulm, Germany
| | - Heidi Pfeiffer
- Institute of Legal Medicine, University of Münster, Röntgenstr. 23, 48149, Münster, Germany
| | - Marielle Vennemann
- Institute of Legal Medicine, University of Münster, Röntgenstr. 23, 48149, Münster, Germany
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3
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Schulze Johann K, Bauer H, Wiegand P, Pfeiffer H, Vennemann M. Whole-genome sequencing of artificial single-nucleotide variants induced by DNA degradation in biological crime scene traces. Int J Legal Med 2023; 137:33-45. [PMID: 36352329 PMCID: PMC9816238 DOI: 10.1007/s00414-022-02911-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/19/2022] [Indexed: 11/11/2022]
Abstract
The aim of this study was to identify artificial single-nucleotide variants (SNVs) in degraded trace DNA samples. In a preliminary study, blood samples were stored for up to 120 days and whole-genome sequencing was performed using the Snakemake workflow dna-seq-gatk-variant-calling to identify positions that vary between the time point 0 sample and the aged samples. In a follow-up study on blood and saliva samples stored under humid and dry conditions, potential marker candidates for the estimation of the age of a blood stain (= time since deposition) were identified. Both studies show that a general decrease in the mean fragment size of the libraries over time was observed, presumably due to the formation of abasic sites during DNA degradation which are more susceptible to strand breaks by mechanical shearing of DNA. Unsurprisingly, an increase in the number of failed genotype calls (no coverage) was detected over time. Both studies indicated the presence of artificial SNVs with the majority of changes happening at guanine and cytosine positions. This confirms previous studies and can be explained by depurination through hydrolytic attacks which more likely deplete guanine while deamination leads to cytosine to thymine variants. Even complete genotype switches from homozygote 0/0 genotypes to the opposite 1/1 genotypes were observed. While positions with such drastic changes might provide suitable candidate markers for estimating short-term time since deposition (TsD), 11 markers were identified which show a slower gradual change of the relative abundance of the artificial variant in both blood and saliva samples, irrespective of storage conditions.
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Affiliation(s)
| | - Hannah Bauer
- Institute of Legal Medicine, University of Münster, Röntgenstr. 23, 48149 Münster, Germany
| | - Peter Wiegand
- Institute of Legal Medicine, University of Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Heidi Pfeiffer
- Institute of Legal Medicine, University of Münster, Röntgenstr. 23, 48149 Münster, Germany
| | - Marielle Vennemann
- Institute of Legal Medicine, University of Münster, Röntgenstr. 23, 48149 Münster, Germany
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4
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Wang M, Tsukamoto M, Sergeyev VG, Zinchenko A. Metal Ions Sensing by Biodots Prepared from DNA, RNA, and Nucleotides. BIOSENSORS 2021; 11:333. [PMID: 34562923 PMCID: PMC8466223 DOI: 10.3390/bios11090333] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/05/2021] [Accepted: 09/09/2021] [Indexed: 01/20/2023]
Abstract
Nucleic acids that exhibit a high affinity toward noble and transition metal ions have attracted growing attention in the fields of metal ion sensing, toxic metal ion removal, and the construction of functional metal nanostructures. In this study, fluorescent nanoparticles (biodots) were synthesized from DNA, RNA, and RNA nucleotides (AMP, GMP, UMP, and CMP) using a hydrothermal (HT) method, in order to study their metal ion sensing characteristics. The fluorescent properties of biodots differ markedly between those prepared from purine and pyrimidine nucleobases. All biodots demonstrate a high sensitivity to the presence of mercury cations (Hg2+), while biodots prepared from DNA, RNA, and guanosine monophosphate (GMP) are also sensitive to Ag+ and Cu2+ ions, but to a lesser extent. The obtained results show that biodots inherit the metal ion recognition properties of nucleobases, while the nucleobase composition of biodot precursors affects metal ion sensitivity and selectivity. A linear response of biodot fluorescence to Hg2+ concentration in solution was observed for AMP and GMP biodots in the range 0-250 μM, which can be used for the analytic detection of mercury ion concentration. A facile paper strip test was also developed that allows visual detection of mercury ions in solutions.
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Affiliation(s)
- Maofei Wang
- Graduate School of Environmental Studies, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan;
| | - Masaki Tsukamoto
- Graduate School of Informatics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan;
| | - Vladimir G. Sergeyev
- Department of Chemistry, Lomonosov Moscow State University, 119899 Moscow, Russia;
| | - Anatoly Zinchenko
- Graduate School of Environmental Studies, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan;
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5
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Bathrick AS, Norsworthy S, Plaza DT, McCormick MN, Slack D, Ramotowski RS. DNA recovery after sequential processing of latent fingerprints on copy paper. J Forensic Sci 2021; 67:149-160. [PMID: 34498754 PMCID: PMC9291209 DOI: 10.1111/1556-4029.14881] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 07/22/2021] [Accepted: 08/17/2021] [Indexed: 12/01/2022]
Abstract
Forensic examiners must determine whether both latent fingerprint development and DNA profiling can be performed on the same area of an evidence item and, if only one is possible, which examination offers the best chance for identification. Latent fingerprints can be enhanced by targeting different components of fingerprint residues with sequential chemical treatments. This study investigated the effects of single-reagent and sequential latent fingerprint development processes on downstream DNA analysis to determine the point at which latent fingerprint development should be stopped to allow for DNA recovery. Latent fingerprints deposited on copy paper by one donor were developed using three sequential processes: 1,8-diazafluoren-9-one (DFO) → ninhydrin → physical developer (PD); 1,2-indanedione-zinc (IND-Zn) → ninhydrin → PD; and IND-Zn → ninhydrin → Oil Red O (ORO) → PD. Samples were examined after the addition of each chemical treatment. DNA was collected with cotton swabs, extracted, quantified, and amplified. DNA yields, peak heights, number of alleles obtained, and percentage of DNA profiles eligible for CODIS upload were examined. DNA profiles were obtained with varying degrees of success, depending on the number and type of treatments used for latent fingerprint development. The treatments that were found to be the least harmful to downstream DNA analysis were IND-Zn and IND-Zn/laser, and the most detrimental treatments were DFO, DFO/laser, and PD. In general, as the number of treatments increase, the opportunities for DNA loss or damage also increase, and it is preferable to use fewer treatments when developing latent fingerprints prior to downstream DNA processing.
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Affiliation(s)
| | - Sarah Norsworthy
- Forensic Technology Center of Excellence, RTI International, Research Triangle Park, NC, USA
| | | | - Mallory N McCormick
- Forensic Services Division, United States Secret Service, Washington, DC, USA
| | - Donia Slack
- Forensic Technology Center of Excellence, RTI International, Research Triangle Park, NC, USA
| | - Robert S Ramotowski
- Forensic Services Division, United States Secret Service, Washington, DC, USA
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6
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Wang M, Tsukamoto M, Sergeyev VG, Zinchenko A. Fluorescent Nanoparticles Synthesized from DNA, RNA, and Nucleotides. NANOMATERIALS 2021; 11:nano11092265. [PMID: 34578581 PMCID: PMC8471148 DOI: 10.3390/nano11092265] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/23/2021] [Accepted: 08/30/2021] [Indexed: 12/24/2022]
Abstract
Ubiquitous on Earth, DNA and other nucleic acids are being increasingly considered as promising biomass resources. Due to their unique chemical structure, which is different from that of more common carbohydrate biomass polymers, materials based on nucleic acids may exhibit new, attractive characteristics. In this study, fluorescent nanoparticles (biodots) were prepared by a hydrothermal (HT) method from various nucleic acids (DNA, RNA, nucleotides, and nucleosides) to establish the relationship between the structure of precursors and fluorescent properties of biodots and to optimize conditions for preparation of the most fluorescent product. HT treatment of nucleic acids results in decomposition of sugar moieties and depurination/depyrimidation of nucleobases, while their consequent condensation and polymerization gives fluorescent nanoparticles. Fluorescent properties of DNA and RNA biodots are drastically different from biodots synthesized from individual nucleotides. In particular, biodots synthesized from purine-containing nucleotides or nucleosides show up to 50-fold higher fluorescence compared to analogous pyrimidine-derived biodots. The polymeric nature of a precursor disfavors formation of a bright fluorescent product. The reported effect of the structure of the nucleic acid precursor on the fluorescence properties of biodots should help designing and synthesizing brighter fluorescent nanomaterials with broader specification for bioimaging, sensing, and other applications.
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Affiliation(s)
- Maofei Wang
- Graduate School of Environmental Studies, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan;
| | - Masaki Tsukamoto
- Graduate School of Informatics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan;
| | - Vladimir G. Sergeyev
- Department of Chemistry, M.V. Lomonosov Moscow State University, 119899 Moscow, Russia;
| | - Anatoly Zinchenko
- Graduate School of Environmental Studies, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan;
- Correspondence: ; Tel.: +81-52-789-4771
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7
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Glynn CL. Potential applications of microRNA profiling to forensic investigations. RNA (NEW YORK, N.Y.) 2020; 26:1-9. [PMID: 31658993 PMCID: PMC6913128 DOI: 10.1261/rna.072173.119] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Within the forensic science community, there is a continued push to develop novel tools to aid in criminal investigations. microRNA (miRNA) analysis has been the focus of many researcher's attention in the biomedical field since its discovery in 1993; however, the forensic application of miRNA analysis has only been suggested within the last 10 years and has been gaining considerable traction recently. The primary focus of the forensic application of miRNA analysis has been on body fluid identification to provide confirmatory universal analysis of unknown biological stains obtained from crime scenes or evidence items. There are, however, other forensic applications of miRNA profiling that have shown potential, yet are largely understudied, and warrant further investigation such as organ tissue identification, donor age estimation, and more. This review paper aims to evaluate the current literature and future potential of miRNA analysis within the forensic science field.
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Affiliation(s)
- Claire L Glynn
- Department of Forensic Science, Henry C. Lee College of Criminal Justice and Forensic Sciences, University of New Haven, West Haven, Connecticut 06516, USA
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8
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San Pietro D, Tagliaro F, Adamowicz MS. A preliminary assessment of the effect of PreCR™ DNA repair treatment on mixture ratios in two person mixtures. Sci Justice 2018; 58:308-314. [PMID: 30193656 DOI: 10.1016/j.scijus.2018.04.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 04/03/2018] [Accepted: 04/13/2018] [Indexed: 11/19/2022]
Abstract
In this study, DNA extracted from known buccal samples was combined into two component mixture samples. These were subjected to UV exposure prior to their amplification with the Promega PowerPlex® 16HS amplification kit, and subsequent capillary electrophoresis on the ABI 3130xl instrument. Damaged samples were subjected to enzymatic repair treatment and retested to assess the amount of repair. Data showed that there is fidelity associated with the application with profile concordance after its use, and a corresponding increase in the amount of recovered alleles post damage. Results also showed changes in the stochastic relationship between mixture components that appear to be induced by the repair process itself. The mixture ratios of DNA samples were altered from an approximate original 1:3 ratio, to a ratio of 1:2 or greater. This variation can have a significant effect regarding the ability to reliably de-convolute DNA mixtures that have been subjected to the repair process.
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Affiliation(s)
- David San Pietro
- Lee College, University of New Haven, 300 Boston Post Road, West Haven, CT 06516, United States.
| | - Franco Tagliaro
- Department of Diagnostics and Public Health - Section of Forensic Medicine, University of Verona, Verona, Italy
| | - Michael S Adamowicz
- College of Agricultural Sciences & Natural Resources, University of Nebraska-Lincoln, 103 Agriculture Hall, Lincoln, NE 68583-0702, United States
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9
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Muller R, Betsou F, Barnes MG, Harding K, Bonnet J, Kofanova O, Crowe JH. Preservation of Biospecimens at Ambient Temperature: Special Focus on Nucleic Acids and Opportunities for the Biobanking Community. Biopreserv Biobank 2016; 14:89-98. [DOI: 10.1089/bio.2015.0022] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
| | - Fay Betsou
- Integrated Biobank of Luxembourg, Luxembourg, Luxembourg
| | | | - Keith Harding
- Damar Research Scientists, Damar, Cupar Muir, United Kingdom
| | - Jacques Bonnet
- Imagene, Genopole Campus 1, Evry, France
- Université de Bordeaux Segalen, Institut Bergonié, Bordeaux, France
| | - Olga Kofanova
- Integrated Biobank of Luxembourg, Luxembourg, Luxembourg
| | - John H. Crowe
- Department of Molecular and Cellular Biology, University of California, Davis, California
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10
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Clermont D, Santoni S, Saker S, Gomard M, Gardais E, Bizet C. Assessment of DNA encapsulation, a new room-temperature DNA storage method. Biopreserv Biobank 2015; 12:176-83. [PMID: 24955733 DOI: 10.1089/bio.2013.0082] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A new procedure for room-temperature storage of DNA was evaluated whereby DNA samples from human tissue, bacteria, and plants were stored under an anoxic and anhydrous atmosphere in small glass vials fitted in stainless-steel, laser-sealed capsules (DNAshells(®)). Samples were stored in DNAshells(®) at room temperature for various periods of time to assess any degradation and compare it to frozen control samples and those stored in GenTegra™ tubes. The study included analysis of the effect of accelerated aging by using a high temperature (76°C) at 50% relative humidity. No detectable DNA degradation was seen in samples stored in DNAshells(®) at room temperature for 18 months. Polymerase chain reaction experiments, pulsed field gel electrophoresis, and amplified fragment length polymorphism analyses also demonstrated that the protective properties of DNAshells(®) are not affected by storage under extreme conditions (76°C, 50% humidity) for 30 hours, guaranteeing 100 years without DNA sample degradation. However, after 30 hours of storage at 76°C, it was necessary to include adjustments to the process in order to avoid DNA loss. Successful protection of DNA was obtained for 1 week and even 1 month of storage at high temperature by adding trehalose, which provides a protective matrix. This study demonstrates the many advantages of using DNAshells(®) for room-temperature storage, particularly in terms of long-term stability, safety, transport, and applications for molecular biology research.
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Affiliation(s)
- Dominique Clermont
- 1 Institut Pasteur, Collection de l'Institut Pasteur , Département de Microbiologie, Paris, France
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11
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Robertson JM, Dineen SM, Scott KA, Lucyshyn J, Saeed M, Murphy DL, Schweighardt AJ, Meiklejohn KA. Assessing PreCR™ repair enzymes for restoration of STR profiles from artificially degraded DNA for human identification. Forensic Sci Int Genet 2014; 12:168-80. [PMID: 24997322 DOI: 10.1016/j.fsigen.2014.05.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 04/08/2014] [Accepted: 05/21/2014] [Indexed: 11/28/2022]
Abstract
Forensic scientists have used several approaches to obtain short tandem repeat (STR) profiles from compromised DNA samples, including supplementing the polymerase chain reaction (PCR) with enhancers and using procedures yielding reduced-length amplicons. For degraded DNA, the peak intensities of the alleles separated by electrophoresis generally decrease as the length of the allele increases. When the intensities of the alleles decrease below an established threshold, they are described as drop-outs, thus contributing to a partial STR profile. This work assesses the use of repair enzymes to improve the STR profiles from artificially degraded DNA. The commercial PreCR™ repair kit of DNA repair enzymes was tested on both purified DNA and native DNA in body fluids exposed to oxidizing agents, hydrolytic conditions, ultraviolet (UV) and ionizing radiation, and desiccation. The strategy was to restrict the level of DNA damage to that which yields partial STR profiles in order to test for allele restoration as opposed to simple allele enhancement. Two protocols were investigated for allele restoration: a sequential protocol using the manufacturer's repair procedure and a modified protocol reportedly designed for optimal STR analysis of forensic samples. Allele restoration was obtained with both protocols, but the peak height appeared to be higher for the modified protocol (determined by Mann-Kendall Trend Test). The success of the approach using the PreCR™ repair enzymes was sporadic; it led to allele restoration as well as allele drop-out. Additionally, allele restoration with the PreCR™ enzymes was compared with restoration by alternative, but commonly implemented approaches using Restorase™, PCRBoost™, bovine serum albumin (BSA) and the Minifiler™ STR system. The alternative methods were also successful in improving the STR profile, but their success also depended on the quality of the template encountered. Our results indicate the PreCR™ repair kit may be useful for restoring STR profiles from damaged DNA, but further work is required to develop a generalized approach.
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Affiliation(s)
- James M Robertson
- Counterterrorism and Forensic Science Research Unit, Federal Bureau of Investigation Laboratory Division, 2501 Investigation Parkway, Quantico, VA 22135, United States.
| | - Shauna M Dineen
- Counterterrorism and Forensic Science Research Unit, Visiting Scientist Program, Federal Bureau of Investigation Laboratory Division, 2501 Investigation Parkway, Quantico, VA 22135, United States
| | - Kristina A Scott
- Counterterrorism and Forensic Science Research Unit, Visiting Scientist Program, Federal Bureau of Investigation Laboratory Division, 2501 Investigation Parkway, Quantico, VA 22135, United States
| | - Jonathan Lucyshyn
- Counterterrorism and Forensic Science Research Unit, Visiting Scientist Program, Federal Bureau of Investigation Laboratory Division, 2501 Investigation Parkway, Quantico, VA 22135, United States; Armed Forces DNA Identification Laboratory, Armed Forces Medical Examiner System, 115 Purple Heart Ave., Dover Air Force Base, Dover, DE 19902, United States; American Registry of Pathology, P.O. Box 495, Dover, DE 19903, United States
| | - Maria Saeed
- Counterterrorism and Forensic Science Research Unit, Visiting Scientist Program, Federal Bureau of Investigation Laboratory Division, 2501 Investigation Parkway, Quantico, VA 22135, United States
| | - Devonie L Murphy
- Counterterrorism and Forensic Science Research Unit, Visiting Scientist Program, Federal Bureau of Investigation Laboratory Division, 2501 Investigation Parkway, Quantico, VA 22135, United States
| | - Andrew J Schweighardt
- Counterterrorism and Forensic Science Research Unit, Visiting Scientist Program, Federal Bureau of Investigation Laboratory Division, 2501 Investigation Parkway, Quantico, VA 22135, United States
| | - Kelly A Meiklejohn
- Counterterrorism and Forensic Science Research Unit, Visiting Scientist Program, Federal Bureau of Investigation Laboratory Division, 2501 Investigation Parkway, Quantico, VA 22135, United States
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12
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Colotte M, Coudy D, Tuffet S, Bonnet J. Adverse effect of air exposure on the stability of DNA stored at room temperature. Biopreserv Biobank 2014; 9:47-50. [PMID: 24850205 DOI: 10.1089/bio.2010.0028] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Marthe Colotte
- 1 Société Imagene, Plateforme de Production, Evry, France
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13
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Hall A, Sims LM, Ballantyne J. Assessment of DNA damage induced by terrestrial UV irradiation of dried bloodstains: forensic implications. Forensic Sci Int Genet 2013; 8:24-32. [PMID: 24315585 DOI: 10.1016/j.fsigen.2013.06.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 06/04/2013] [Accepted: 06/18/2013] [Indexed: 12/12/2022]
Abstract
Few publications have detailed the nature of DNA damage in contemporary (i.e. non-ancient) dried biological stains. The chief concern, from a forensic standpoint, is that the damage can inhibit polymerase-mediated primer extension, ultimately resulting in DNA typing failure. In the work described here, we analyzed the effects of UVA and UVB irradiation on cell-free solubilized DNA, cell-free dehydrated DNA and dehydrated cellular DNA (from bloodstains). After UV exposure ranging from 25 J cm(-2) to 1236 J cm(-2), we assayed for the presence of bipyrimidine photoproducts (BPPPs), oxidative lesions and strand breaks, correlating the damage with the inhibition of STR profiling. Subsequent to irradiation with either UVA and UVB, the incidence of BPPPs, oxidative products and strand breaks were observed in decreasing quantities as follows: cell-free solubilized DNA>cell-free dehydrated DNA>bloodstain DNA. UVA irradiation did not result in even the partial loss of a STR profile in any sample tested. Somewhat different results were observed after genetic analysis of UVB exposed samples, in that the ability to produce a complete STR profile was affected earliest in bloodstain DNA, next in cell-free solubilized DNA and not at all in cell-free dehydrated DNA. Therefore, it is likely that other types of damage contributed to allele-drop-out in these samples but remained undetected by our assays, whereby the endonucleases did not react with the lesions or the presence of the lesions was masked by strand breaks. Under the conditions of the study, strand breaks appeared to be the predominant types of damage that ultimately resulted in DNA typing failure from physiological stains, although some evidence suggested oxidative damage may have played a role as well.
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Affiliation(s)
- Ashley Hall
- University of Nebraska-Lincoln, P.O. Box 830816, Lincoln, NE 68583-0816, United States.
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14
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Material modifications for the alkaline differential extraction method for sexual assault evidence. Forensic Sci Int Genet 2013; 7:e104-5. [DOI: 10.1016/j.fsigen.2013.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 04/01/2013] [Accepted: 04/14/2013] [Indexed: 11/21/2022]
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15
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Affiliation(s)
- T. A. Brettell
- Department of Chemical and Physical Sciences, Cedar Crest College, 100 College Drive, Allentown, Pennsylvania 18104-6196, United States
| | - J. M. Butler
- Biochemical Science Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8312, United States
| | - J. R. Almirall
- Department of Chemistry and Biochemistry and International Forensic Research Institute, Florida International University, University Park, Miami, Florida 33199, United States
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