An enzyme-based DNA preparation method for application to forensic biological samples and degraded stains

Lounsbury, Jenny A.; Coult, Natalie; Miranian, Daniel C.; Cronk, Stephen M.; Haverstick, Doris M.; Kinnon, Paul; Saul, David; Landers, James P.

doi:10.1016/j.fsigen.2012.01.011

Cited by 36 publications

(40 citation statements)

References 27 publications

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“…Its broad lysis specificity and protein-degrading properties are very useful for NA preparation. Other proteases, such as the temperature-stable proteinase EA1, may also be useful in NA preparations (22 ). Most proteases are too specific in their cleavage sites and not useful for NA preparations or are too difficult to produce in production quantities.…”

Section: A History Of Nucleic Acid Preparation Toolsmentioning

confidence: 99%

DNA/RNA Preparation for Molecular Detection

Thatcher

2015

Clinical Chemistry

107

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BACKGROUND Effective upstream preparation of nucleic acid (NA) is important for molecular techniques that detect unique DNA or RNA sequences. The isolated NA should be extracted efficiently and purified away from inhibitors of a downstream molecular assay. CONTENT Many NA sample preparation techniques and commercial kits are available. Techniques for cell lysis and isolation or purification of NA were discovered in early NA characterization studies, evolved in the 20th century with molecular techniques, and still serve as the foundation for current methods. Advances in solid phase extraction methods with nonhazardous chemicals and automated systems have changed the way NA is prepared. Factors to consider when selecting NA preparation methods for molecular detection include lysis (from sources as diverse as human cells, viruses, bacterial spores, or protozoan oocysts), DNA vs RNA, sample background, appropriate preparation chemicals, and required detection limits. Methods are also selected on the basis of requirements for a particular application, such as sample volume or removal of inhibitors. Sometimes tradeoffs are made. SUMMARY Good automated and manual methods are available to effectively prepare NA for molecular detection in under an hour. Numerous systems are available for various applications, including techniques that are flexible for multiple sample types, are capable of processing large batches, can be performed in <10 min, or that can yield high-purity NA. When methods are selected using the most applicable combination of lysis isolation efficiency and concentration, NA preparation can be very effective, even for molecular detection of multiple targets from the same sample.

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Section: A History Of Nucleic Acid Preparation Toolsmentioning

confidence: 99%

DNA/RNA Preparation for Molecular Detection

Thatcher

2015

Clinical Chemistry

107

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“…This is driven by highly selective assays, using fluorescence-based detection, which have been demonstrated successful at detecting a base change in the presence of 50 nM [22] and even 10 nM of target DNA [23]. A number of label-free methods for SPM detection have also been reported, including resonator arrays [24], silicon nanowires [12,[25][26][27][28] and colorimetric detection with gold nanoparticles , and these have been associated with limits of detection (LOD's) of 1.95 nM, 1 nM and 50 fM, respectively. However, these assays involve relatively lengthy assay times, cumbersome instrumentation, and/or specialized fabrication techniques.…”

Section: Discussionmentioning

confidence: 99%

“…EA1 is a neutral proteinase, isolated from Bacillus sp. EA1, and has been shown to rapidly liberate DNA with high yield [26]. To minimize non-specific amplification, a new direct-PCR master mix was devised using EA1 in addition to traditional PCR reagents.…”

Section: Polymerase Performance With Ea1mentioning

confidence: 99%

Development and Application of Sequence Specific DNA Detection through Hybridization-induced Aggregation

Strachan

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ii AcknowledgementsFew things in life are truly accomplished alone, and this is not one of them. I am here not because of who I am but due to those that got me here. Dr Landers, I cannot express the profound influence your guidance, energy and vision have had on me. For making me the scientist I am I will forever be grateful and appreciative to have worked with you. Our group is a family; we will do anything for each other to bring success whether that be a 2 am coffee run or knowing how to stop frustration tears. To Carmen and Dan, thank you for molding my young analytical mind, enabling me to go it alone. To my amazing undergraduate Daniel, without whom this work would not have been accomplished. Of particular note is the bear family. Brother, Baby and Koala, you made this an experience that I never want to end. You were all there for me when life was hard and science was slow. My best moments were the ones spent with you. My roommate Amanda: you have been a wonderful person to me over this very stressful year, for that I am forever grateful. Then there is Jenny, who was a mentor, a friend, a sister. It's not an exaggeration to say that this would not have been possible without you. To Kristin, without whom I would not be here at all. Infinityillions, always pumpkin. Finally, to my family who were always there even though they are far across the pond. We were raised to believe that we can do anything if we put our minds to it and Russell you are the embodiment of that philosophy. To my Granddad, who's generosity made all of this possible and to Frank for always being there. Finally, to my Mum, my best friend, whom I love more each day.I promise, no more degrees.iii AbstractThe interrogation of genomic DNA for the presence of specific sequences is paramount for most biological assays, including clinical diagnostics, functional genomics, food safety and forensic DNA analysis. Here we present a new detection modality, based on hybridization of the target sequence to probes bound to paramagnetic particles. When hybridization occurs, the particles aggregate together in a visual manner, confirming the presence target DNA with a limit of detection of 100 fM for ssDNA. A systematic study into the effect sequence length alterations have on detection sensitivity is demonstrated. The specificity of HIA enables the detection of 1, 2 or 3 single point mutations in the target DNA, working towards applying HIA to future mutation detection. HIA was adapted for the detection of dsDNA, enabling the label-free detection of Salmonella enterica, bacteriophage for the diagnosis of multi-drug resistant tuberculosis and for the detection of thyroid peroxidase (TPOX) for human identification. Furthermore, HIA is interfaced with PCR on a plastic integrated microdevice, where multiplexed IR-PCR is demonstrated for the first time. The microdevice combines low cost and minimal hardware to provide an easy to use system capable of PCR and HIA detection in 30 minutes. In addition, a direct-PCR protocol from whole blood was developed to aid i...

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“…The biggest advantage of the method is there is minimal chance of cross contamination due to lack of multiple transfer steps and the simple protocol makes it amenable for automation [79].…”

Section: B5 Thermostable Proteinasesmentioning

confidence: 99%

“…The effect of pressure treatment at 45000 psi on DNA recovery from a mixture in the presence of TCEP and DTT indicates a 13% increase in yields compared to TCEP treatment alone. No increase in yield was observed when the number of pressure cycles was increased to 99 cycles..……………………….………………..…... 79 25. The effect of various treatments on DNA recovery from a swab with pressure treatment at 45000 psi for 60 cycles indicates that the best yields and selective recovery of sperm DNA was observed with a buffer containing TCEP and DTT although the overall yields dropped due to inefficient sample recovery from a cotton swab…………………………………………………………………………………...…82 31.…”

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confidence: 99%

A Novel Method for Rapid and Selective Extraction of Male DNA from Rape Kits using Alkaline Lysis and Pressure Cycling Technology (PCT)

Nori¹

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An enzyme-based DNA preparation method for application to forensic biological samples and degraded stains

Cited by 36 publications

References 27 publications

DNA/RNA Preparation for Molecular Detection

DNA/RNA Preparation for Molecular Detection

Development and Application of Sequence Specific DNA Detection through Hybridization-induced Aggregation

A Novel Method for Rapid and Selective Extraction of Male DNA from Rape Kits using Alkaline Lysis and Pressure Cycling Technology (PCT)

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