Competition for DNA binding sites using Promega DNA IQ™ paramagnetic beads

Recovery of DNA from acetaminophen exploring physical state and sampling methods

Research into the recovery of DNA from illicit drug samples has shown it is possible to get forensically useful profiles from such substrates. However, it is not yet known if the different physical states that drugs can be found in influences the quantity and quality of DNA that can be recovered or what is the best sampling method to adopt for powdered samples. This research used acetaminophen in four different states - large crystalline, powder, in solution, or residue - to determine the efficacy of current DNA technology in recovery and analysis of the resulting sample. Five replicates of each were prepared. Human blood was deposited on or mixed with the drug and left for 1 hour. The surface of the drug was sampled by wet/dry swabbing (where appropriate), or the entire sample was deposited in a tube, and the DNA then extracted using DNA-IQ™. The amount of DNA recovered (ng), degradation index, number of PCR cycles (Ct) required for the IPC to reach threshold, number of alleles in the DNA profile and average peak height (APH) were assessed. All samples, irrespective of the physical state they were collected from, returned full DNA profiles that corresponded to the DNA profile of the blood donor, with no degradation or inhibition detected. It was also found the wet/dry swabbing method returned higher levels of DNA than inclusion of the entire sample into the tube for powdered acetaminophen and the appropriate method to use will be dependent on casework circumstances. The findings of this research further develops our understanding of the recovery of DNA from drugs, and supports the need for further investigation to understand under what conditions DNA can be recovered from illicit substances.

Comparison of three DNA extraction methods tested on illicit drug-related powders

The detection of human DNA on and within illicit drug preparations is novel and a focus of current research. Previous studies have indicated that certain drug-related powders present in illicit drug preparations can interfere with downstream DNA analysis when directly added to the PCR. Therefore, it is important to determine if these drug-related powders are effectively removed during the DNA extraction or whether traces of powder remain to interfere with DNA processing. Three extraction methods were selected to assess their efficiency at removing drug-related powders for downstream processes using DNA from both saliva and touch depositions. This is the first study to compare efficiencies of DNA extraction methods from drug-related powders. The extraction methods compared were the DNA IQ™ System, the QIAamp® DNA Investigator Kit and the combination of a simple lysis step followed by use of the Microcon® DNA Fast Flow device. Saliva was added to dimethylsulfone (DMS), nitrostyrene and PROSOLV® tablet mixture to determine the effect of powder type (based on solubility). Saliva was also added to 0, 50, 200 and 400 mg of DMS to determine the effect of an increase in DMS quantity. Trace DNA was deposited onto DMS using a worn glove approach. These samples were re-tested six months post-DNA deposition and profiled for further comparisons. Ten replicates were conducted for each condition with five replicates of saliva positive controls per method (n = 255 samples). A subset of samples was chemically analysed to determine if DMS was present in the final DNA eluant. The readily soluble DMS did not interfere with any of the extraction methods at lower amounts, however increasing the DMS to 400 mg reduced the relative DNA yields using the Microcon® and Investigator methods. The tablet mixture reduced the relative DNA yield of all three methods, however the nitrostyrene (which was relatively insoluble) only reduced the relative DNA yield of the DNA IQ™. The Investigator method performed the best with the trace samples, followed by the Microcon® method and then the DNA IQ™. DMS was detected in all extracts chemically analysed from the DNA IQ™ and Microcon®, whereas only one sample tested from the Investigator kit contained DMS in the extract and was in a relatively low amount compared to the other samples. Not one kit outperformed the others in all comparisons, however the Investigator kit was the most efficient overall at optimising the DNA yield whilst also removing the powders more effectively.

Comparative analysis of two Rapid DNA technologies for the processing of blood and saliva-based samples

Rapid DNA technologies recently gained significant momentum as a means to generate DNA profiles faster than with standard laboratory workflows. Initially developed for the analysis of buccal reference samples, applications are being considered for other types of forensic samples. In this study, an identical set of 150 blood and saliva-based samples was processed using two different Rapid DNA technologies, the Applied BioSystems™ RapidHIT™ ID System using the RapidINTEL™ sample cartridge and the ANDE™ 6C Rapid DNA Analysis™ System using the I-Chip. A subset of samples were subjected to alternative collection methods or sample pre-treatments to determine the optimal strategy for each instrument. An equivalent sample set was also processed using a conventional DNA analysis workflow. The sensitivity range of the two Rapid DNA technologies was comparable based on blood and saliva dilution series, with both technologies able to generate full profiles from samples typically yielding 5-10 ng of DNA when processed using conventional DNA analysis. The brand of cotton swabs used for Rapid DNA analysis had an impact on the results for both systems. Differences were observed in success rate between the two systems when processing blood (on fabrics, FTA paper or hard surfaces) and saliva-based samples (drink containers, FTA paper, chewing gum, cigarette butt filter paper) and depended on the sample type. Importantly, deviating from the manufacturer's instructions for sample collection and pre-treatment was more detrimental to the ANDE 6C results. The quality of DNA profiles, as assessed using heterozygote peak height ratios, interloci balance and artifact presence, confirmed the results to be reliable and acceptable for single source samples. Profiling results were obtained when samples were reprocessed using the same Rapid DNA technology or conventional DNA analysis. Secondary analysis using a substitute software (GeneMapper ID-X v1.5) to recover additional genetic information was shown to be feasible. Finally, a comparison between the Applied Biosystems™ RapidHIT™ ID System Software v1.3.1 and v1.3.2 was also performed. Findings of this study could assist those interested in using Rapid DNA technology for blood or saliva-based samples, in various settings and for different applications.

Persistence of touch DNA on commonly encountered substrates in different storage conditions

The persistence of touch DNA deposited after realistic handling of items typically encountered in forensic investigations has been the subject of few studies. Understanding the long-term persistence of touch DNA on different substrates in varying conditions can be central to the effective triage of samples for further processing. As the time between an alleged incident and collection of evidence may vary from a few days to years after an alleged event, this study assessed three different common substrates for the persistence of touch DNA over a time span up to 9 months. These substrates included fabric, steel, and rubber, each of which were handled in a way to imitate what may happen during a criminal act. The three substrates were exposed to two different environments for up to 9 months: inside a dark cupboard with no traffic to act as a control and an outside semi-exposed environment. Ten replicates from each of the 3 substrates were tested at 5 time points to create 300 samples. All samples were processed using a standard operating workflow to provide genotype data after exposure to different environments. It was found that the fabric samples produced informative STR profiles (defined here as 12 or more alleles) up to the 9 month timepoint for either environment. The rubber and steel substrates for the inside condition produced informative STR profiles up to the 9 month timepoint, but only generated informative STR profiles for the outside condition up to 3 and 6 months, respectively. These data add to our understanding of the external factors that affect DNA persistence.

Sequence-specific eDNA extraction using hydrophobic magnetic ionic liquids attached with oligonucleotide strand

Isolation of high-purity nucleic acids, especially sequence-specific DNA, from complex samples is critical to the downstream nucleic acid analysis. In this work, an oligonucleotide strand-attached magnetic ionic liquid (OSMIL) was designed and prepared for DNA extraction. The attached oligonucleotide strand has a sequence complementary to that of a specific DNA to be extracted. The OSMIL has good hydrophobicity and magnetic response properties. At the extraction temperature, OSMIL was in a liquid state, which was favorable for maximizing the adsorption of DNA; while at the separation temperature, OSMIL was in a solid state (with an average particle size of 897 nm) and could be attracted by an external magnet in 3s, which was favorable for the separation and recovery of DNA. The sequence-specific DNA extraction process with OSMIL is simple and fast. After extraction, the DNA-enriched OSMILs were quickly attracted and separated by an external magnetic field. The extracted DNA was evaluated by a NanoDrop (wavelength detection at 260-280 nm) and the OSMIL can be recycled and reused. The enrichment factor was 0.81. Through single-factor experimental analysis, the effects of OSMIL extraction volume, thermal excitation temperature, thermal excitation time, pH, and other factors on the DNA extraction process were systematically investigated. The RSD of repeatability experiment was 1.19% (n = 3), showing the method has good repeatability. The extraction method presented here has been shown to extract DNA with specific sequences from mixtures containing DNA of different sequences and from mixtures containing proteins, respectively. In addition, the OSMIL has been applied to extract target environmental DNA with specific sequences from different water environments with high extraction efficiency. In the long run, OSMIL has great potential for identifying existing organisms in environmental samples or exploring unknown organisms.

Manual Silica-Based DNA Extractions

There are several silica-based extraction methods that utilize silica-packed columns or silica-coated paramagnetic resin and are suitable for the needs of forensic DNA analysis and/or human identification. These rely on the use of chaotropic salts to alter the affinity of DNA such that it binds strongly to silica. A variety of samples can be successfully processed with these procedures, including buccal swabs, dried or liquid blood, saliva, semen, and other typical forensic-type samples. This chapter will describe the manual extraction process for Promega's DNA™ IQ System, as well as Qiagen's QIAamp® DNA Blood Mini Kit, QIAamp® DNA Mini Kit, and QIAamp® DNA Investigator Kit.

Differential Extraction with Purification via Organic/Microcon® and Promega DNA IQ™ Methods

The differential extraction method allows for the separation of sperm cell DNA from non-sperm cell DNA by incorporating two separate lysis steps. This is crucial in forensic casework, as sexual assault samples frequently deal with a mixture of seminal fluid and other body fluids. After performing a differential lysis, DNA extraction can be completed through a variety of methods. In addition to the differential lysis, two methods will be described in this chapter for DNA purification: Organic (Phenol)/Microcon® purification and purification with the Promega DNA IQ™ System.

Guanidinium Hydrophobic Magnetic Ionic Liquid-Based Dispersive Droplet Extraction for the Selective Extraction of DNA

Six hydrophobic magnetic guanidinium ionic liquids (HMILs) were designed and prepared for the extraction of DNA. The physical and thermal properties of the HMILs were characterized using vibrating sample magnetometry, density meter, rotational rheometer, Karl Fischer moisture, Fourier transform infrared spectrometry, and thermogravimetric analysis. Single-stranded DNA and duplex DNA extracted by HMILs can be rapidly collected by a magnet. Three assisted extraction methods, including vortex extraction, mechanical shaking extraction, and ultrasonic extraction, were introduced to extract DNA with HMILs and the extraction efficiencies were evaluated using NanoDrop. Influencing factors of the DNA extraction were comprehensively evaluated, involving the HMIL volume, extraction time, pH, and extraction temperature. The HMIL-based extraction method can well extract DNA from complex matrices and Escherichia coli cell lysates.

Evaluation of DNA Extraction Methods for Processing Fingerprint Powder-Coated Forensic Evidence

In unison, fingerprinting and DNA analysis have played a pivotal role in forensic investigations. Fingerprint powders that are available on the market can come in a range of colors and with specific properties. This study evaluated the efficiency of DNA extraction from samples coated with 3 brands of fingerprint powders: Lightning, Sirchie, and SupraNano, covering a range of colors and properties. A total of 23 fingerprint powders were tested using the Chelex, Promega DNA IQ™, and Applied Biosystems™ PrepFiler™ DNA extraction protocols. The DNA IQ™ and PrepFiler™ methods extracted higher yields of DNA in comparison to Chelex, which also accounted for better quality of PowerPlex x00AE; 21 DNA profiles recovered. There were no signs of degradation or inhibition in the quantification data, indicating that samples returning low DNA yield was due to interference during DNA extraction and not PCR inhibition. DNA profiles were recovered from the majority of fingerprint powders with only a single powder, Sirchie Magnetic Silver, failing to produce a profile using any of the methods tested. A link was observed between the DNA extraction chemistry, fingerprint powder property, that is, nonmagnetic, magnetic and aqueous, and the brand of fingerprint powder. Overall, the DNA IQ™ method was favorable for nonmagnetic fingerprint powders, while magnetic fingerprint powders produced more DNA profiles when extracted with the PrepFiler™ chemistry. This study highlights the importance of screening DNA extraction chemistries for the type of fingerprint powder used, as there is not a single DNA extraction method that suits all fingerprint powder brands and properties.

Persistence of DNA in the Singapore context

The relevance and not merely the presence of one's DNA at a crime scene has become the emerging issue in courtrooms all over the world today. By studying the length of time DNA is likely to persist in an environment until detection, a more holistic assessment of DNA evidence in the context of a case can be made. The current study looks at the persistence of DNA from blood, keratinocytes, and several types of mock exhibits under various conditions, in the tropical rainforest climate of Singapore. While DNA on articles left outdoors showed highly variable persistence subject to the presence of rainfall, DNA from items placed indoors at ambient temperature and under controlled temperature and humidity is comparatively stable. The information gathered from this study, while not exhaustive, serves to provide investigators and the courts with a better understanding of the relevance of DNA recovered from crime scenes of different environmental conditions.

Extraction of DNA by magnetic ionic liquids: tunable solvents for rapid and selective DNA analysis

DNA extraction represents a significant bottleneck in nucleic acid analysis. In this study, hydrophobic magnetic ionic liquids (MILs) were synthesized and employed as solvents for the rapid and efficient extraction of DNA from aqueous solution. The DNA-enriched microdroplets were manipulated by application of a magnetic field. The three MILs examined in this study exhibited unique DNA extraction capabilities when applied toward a variety of DNA samples and matrices. High extraction efficiencies were obtained for smaller single-stranded and double-stranded DNA using the benzyltrioctylammonium bromotrichloroferrate(III) ([(C8)3BnN(+)][FeCl3Br(-)]) MIL, while the dicationic 1,12-di(3-hexadecylbenzimidazolium)dodecane bis[(trifluoromethyl)sulfonyl]imide bromotrichloroferrate(III) ([(C16BnIM)2C12(2+)][NTf2(-), FeCl3Br(-)]) MIL produced higher extraction efficiencies for larger DNA molecules. The MIL-based method was also employed for the extraction of DNA from a complex matrix containing albumin, revealing a competitive extraction behavior for the trihexyl(tetradecyl)phosphonium tetrachloroferrate(III) ([P6,6,6,14(+)][FeCl4(-)]) MIL in contrast to the [(C8)3BnN(+)][FeCl3Br(-)] MIL, which resulted in significantly less coextraction of albumin. The MIL-DNA method was employed for the extraction of plasmid DNA from bacterial cell lysate. DNA of sufficient quality and quantity for polymerase chain reaction (PCR) amplification was recovered from the MIL extraction phase, demonstrating the feasibility of MIL-based DNA sample preparation prior to downstream analysis.

Magnetic ionic liquids as PCR-compatible solvents for DNA extraction from biological samples

A novel strategy for the rapid detection of bacterial plasmid DNA preconcentrated by hydrophobic magnetic ionic liquids (MILs) is described.

DNA capture and next-generation sequencing can recover whole mitochondrial genomes from highly degraded samples for human identification

Background

Mitochondrial DNA (mtDNA) typing can be a useful aid for identifying people from compromised samples when nuclear DNA is too damaged, degraded or below detection thresholds for routine short tandem repeat (STR)-based analysis. Standard mtDNA typing, focused on PCR amplicon sequencing of the control region (HVS I and HVS II), is limited by the resolving power of this short sequence, which misses up to 70% of the variation present in the mtDNA genome.

Methods

We used in-solution hybridisation-based DNA capture (using DNA capture probes prepared from modern human mtDNA) to recover mtDNA from post-mortem human remains in which the majority of DNA is both highly fragmented (<100 base pairs in length) and chemically damaged. The method ‘immortalises’ the finite quantities of DNA in valuable extracts as DNA libraries, which is followed by the targeted enrichment of endogenous mtDNA sequences and characterisation by next-generation sequencing (NGS).

Results

We sequenced whole mitochondrial genomes for human identification from samples where standard nuclear STR typing produced only partial profiles or demonstrably failed and/or where standard mtDNA hypervariable region sequences lacked resolving power. Multiple rounds of enrichment can substantially improve coverage and sequencing depth of mtDNA genomes from highly degraded samples. The application of this method has led to the reliable mitochondrial sequencing of human skeletal remains from unidentified World War Two (WWII) casualties approximately 70 years old and from archaeological remains (up to 2,500 years old).

Conclusions

This approach has potential applications in forensic science, historical human identification cases, archived medical samples, kinship analysis and population studies. In particular the methodology can be applied to any case, involving human or non-human species, where whole mitochondrial genome sequences are required to provide the highest level of maternal lineage discrimination. Multiple rounds of in-solution hybridisation-based DNA capture can retrieve whole mitochondrial genome sequences from even the most challenging samples.

Development of a fast PCR protocol enabling rapid generation of AmpFℓSTR® Identifiler® profiles for genotyping of human DNA

Background

Traditional PCR methods for forensic STR genotyping require approximately 2.5 to 4 hours to complete, contributing a significant portion of the time required to process forensic DNA samples. The purpose of this study was to develop and validate a fast PCR protocol that enabled amplification of the 16 loci targeted by the AmpFℓSTR^® Identifiler^® primer set, allowing decreased cycling times.

Methods

Fast PCR conditions were achieved by substituting the traditional Taq polymerase for SpeedSTAR™ HS DNA polymerase which is designed for fast PCR, by upgrading to a thermal cycler with faster temperature ramping rates and by modifying cycling parameters (less time at each temperature) and adopting a two-step PCR approach.

Results

The total time required for the optimized protocol is 26 min. A total of 147 forensically relevant DNA samples were amplified using the fast PCR protocol for Identifiler. Heterozygote peak height ratios were not affected by fast PCR conditions, and full profiles were generated for single-source DNA amounts between 0.125 ng and 2.0 ng. Individual loci in profiles produced with the fast PCR protocol exhibited average n-4 stutter percentages ranging from 2.5 ± 0.9% (THO1) to 9.9 ± 2.7% (D2S1338). No increase in non-adenylation or other amplification artefacts was observed. Minor contributor alleles in two-person DNA mixtures were reliably discerned. Low level cross-reactivity (monomorphic peaks) was observed with some domestic animal DNA.

Conclusions

The fast PCR protocol presented offers a feasible alternative to current amplification methods and could aid in reducing the overall time in STR profile production or could be incorporated into a fast STR genotyping procedure for time-sensitive situations.