Forensic applicability of multi‐allelic InDels with mononucleotide homopolymer structures

Insertion/deletion polymorphisms (InDels), which possess the characteristics of low mutation rates and a short amplicon size, have been regarded as promising markers for forensic DNA analysis. InDels can be classified as bi‐allelic or multi‐allelic, depending on the number of alleles. Many studies have explored the use of bi‐allelic InDels in forensic applications, such as individual identification and ancestry inference. However, multi‐allelic InDels have received relatively little attention. In this study, InDels with 2–6 alleles and a minor allele frequency ≥0.01, in Chinese Southern Han (CHS), were retrieved from the 1000 Genomes Project Phase III. Based on the structural analysis of all retrieved InDels, 17 multi‐allelic markers with mononucleotide homopolymer structures were selected and combined in one multiplex PCR reaction system. Sensitivity, species specificity and applicability in forensic case work of the multiplex were analyzed. A total of 218 unrelated individuals from a Chinese Han population were genotyped. The combined discriminatory power (CDP), the combined match probability (CMP) and the cumulative probability of exclusion (CPE) were 0.9999999999609, 3.91E‐13 and 0.9956, respectively. The results demonstrated that this InDel multiplex panel was highly informative in the investigated population and most of the 26 populations of the 1000 Genomes Project. The data also suggested that multi‐allelic InDel markers with monomeric base pair expansions are useful for forensic applications.     

Verification of protein biomarker specificity for the identification of biological stains by quadrupole time‐of‐flight mass spectrometry

Advances in proteomics technology over the past decade offer forensic serologists a greatly improved opportunity to accurately characterize the tissue source from which a DNA profile has been developed. Such information can provide critical context to evidence and can help to prioritize downstream DNA analyses. Previous proteome studies compiled panels of “candidate biomarkers” specific to each of five body fluids (i.e ., peripheral blood, vaginal/menstrual fluid, seminal fluid, urine, and saliva). Here, a multiplex quadrupole time‐of‐flight mass spectrometry assay has been developed in order to verify the tissue/body fluid specificity the 23 protein biomarkers that comprise these panels and the consistency with which they can be detected across a sample population of 50 humans. Single‐source samples of these human body fluids were accurately identified by the detection of one or more high‐specificity biomarkers. Recovery of body fluid samples from a variety of substrates did not impede accurate characterization and, of the potential inhibitors assayed, only chewing tobacco juice appeared to preclude the identification of a target body fluid. Using a series of 2‐component mixtures of human body fluids, the multiplex assay accurately identified both components in a single‐pass. Only in the case of saliva and peripheral blood did matrix effects appear to impede the detection of salivary proteins.     

DNA Dangling‐End‐Induced Colloidal Stabilization of Gold Nanoparticles for Colorimetric Single‐Nucleotide Polymorphism Genotyping

A single‐nucleotide polymorphism (SNP) detection method was developed by combining single‐base primer extension and salt‐induced aggregation of gold nanoparticles densely functionalized with double‐stranded DNA (dsDNA‐AuNP). The dsDNA‐AuNPs undergo rapid aggregation in a medium of high ionic strength, whereas particles having a single‐base protrusion at the outermost surface disperse stably, allowing detection of a single‐base difference in length by color changes. When SNP typing primers are used as analytes to hybridize to the single‐stranded DNA on the AuNP surface, the resulting dsDNA‐AuNP works as a visual indicator of single‐base extension. A set of four extension reaction mixtures is prepared using each of ddNTPs and subsequently subjected to the aggregation assay. Three mixtures involving ddNTP that is not complementary to the SNP site in the target produce the aggregates that exhibit a purple color. In contrast, one mixture with the complementary ddNTP generates the single‐base protrusion and appears red. This method could potentially be used in clinical diagnostics for personalized medicine.     

Double‐Stranded RNA‐Specific Templated Reaction with Triplex Forming PNA

RNA, originally perceived as a simple information transfer biopolymer, is emerging as an important regulator in cellular processes. A number of non‐coding RNAs are double‐stranded and there is a need for technologies to reliably detect and image such RNAs for biological and biomedical research. Herein we report double‐stranded RNA‐specific templated reaction resulting from PNA‐reagent conjugates that are brought within reactive distance through the formation of sequence‐specific triplexes onto double‐stranded RNA. The reaction makes use of a ruthenium‐based photocatalyst that reduces a pyridinium‐based immolative linker, unmasking a profluorophore. The reaction was shown to proceed with signal amplification and to be selective for double‐stranded RNA over DNA as well as single‐stranded RNA. The generality of the triplex formation was enabled by non‐canonical nucleobases that extend the Hoogsteen base‐pairing repertoire. The technology was applied to a templated reaction using pre‐microRNA 31.     

Quantitative analysis of single‐nucleotide polymorphisms by pyrosequencing with di‐base addition

We have developed and validated a novel method for quantitative detection of SNPs by using pyrosequencing with di‐base addition (PDBA). Based on the principle that the signal intensity is proportional to the template concentration within a linear concentration range, linear formula (Y = AX + B ) for each genotype is established, and the relationship between two genotypes of a single SNP can be resolved by corresponding linear formulas. Here, PDBA assays were developed to detect variants rs6717546 and rs4148324, and the linear formulas for each genotype of rs6717546 and rs4148324 were established. The method allowed to quantitatively determine each genotype and showed 100% accordant results against a panel of defined mixtures. A set of 24 template fragments containing variants rs6717546 or rs4148324 was tested to evaluate the method. Our results showed that allele frequency of each genotype was accurately quantified, with results comparable to those of conventional pyrosequencing. Furthermore, this method was capable of detecting alleles with frequencies as low as 3%, which was more sensitive than ∼5 to ∼7% level detected by conventional pyrosequencing. This method offers high sensitivity, reproducibility, and relatively low costs, and thus could provide a much‐needed approach for quantitative analysis of SNPs in clinical samples.     

Studies on structure and conformational stability of free canonical 2′‐deoxyribonucleosides: Approximate SCC‐DFTB and LMP2 methods

The molecular structure of free canonical 2′‐deoxyribonucleosides have been studied by applying the electron‐correlated local second‐order Møller–Plesset perturbation theory (LMP2) and self‐consistent‐charge density‐functional tight‐binding (SCC‐DFTB) methods. The variation of structural parameters for C2, C3 endo and exo conformations, and anti, syn orientation of the base unit with furanose ring have been discussed. The relative energies have been calculated for the anti and syn conformations of dT, dC, dG, and dA. Conformational analysis has been performed using the results of the LMP2 and SCC‐DFTB methods. Chemical hardness and chemical potential have been used to study the conformational stability of the conformers. The maximum hardness principle is obeyed for the furanose ring conformations and not for the nucleosides. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

Self‐Assembled Aptamer‐Based Drug Carriers for Bispecific Cytotoxicity to Cancer Cells

Monovalent aptamers can deliver drugs to target cells by specific recognition. However, different cancer subtypes are distinguished by heterogeneous biomarkers and one single aptamer is unable to recognize all clinical samples from different patients with even the same type of cancers. To address heterogeneity among cancer subtypes for targeted drug delivery, as a model, we developed a drug carrier with a broader recognition range of cancer subtypes. This carrier, sgc8c‐sgd5a (SD), was self‐assembled from two modified monovalent aptamers. It showed bispecific recognition abilities to target cells in cell mixtures; thus broadening the recognition capabilities of its parent aptamers. The self‐assembly of SD simultaneously formed multiple drug loading sites for the anticancer drug doxorubicin (Dox). The Dox‐loaded SD (SD–Dox) also showed bispecific abilities for target cell binding and drug delivery. Most importantly, SD–Dox induced bispecific cytotoxicity in target cells in cell mixtures. Therefore, by broadening the otherwise limited recognition capabilities of monovalent aptamers, bispecific aptamer‐based drug carriers would facilitate aptamer applications for clinically heterogeneous cancer subtypes that respond to the same cancer therapy.     

Electrochemical Genoassay Design for Allele‐Specific Detection of Toll‐Like Receptor‐2 Gene Polymorphism

An allele‐specific voltammetric genoassay for the detection of allele‐specific toll‐like receptor‐2 gene arg753gln polymorphism (TLR‐2) from polymerase chain reaction (PCR) amplified real samples was described in this study. Meldola blue (MDB), an intercalator molecule, was used as hybridization label. The wild‐type and mutant type oligonucleotide probes were immobilized onto disposable graphite electrode surfaces by covalent attachment method. The extent of hybridization between probe and target sequences was determined by using differential pulse voltammetry (DPV). As a result of the interaction between MDB and DNA at electrode surface, the MDB signal observed from probe sequence before hybridization and after hybridization with MM sequence is lower than that observed after hybridization with complementary sequence. The differences between the MDB reduction peaks obtained from probe modified, hybrid modified and MM modified electrode were used to detect TLR‐2 from PCR amplified real samples. The discrimination of homozygous and heterozygous alleles was also established by comparing the peak currents of MDB reduction signals. Numerous factors affecting the target hybridization and indicator binding reactions are optimized to maximize the sensitivity.     

Sequencing 5‐Hydroxymethyluracil at Single‐Base Resolution

5‐hydroxymethyluracil (5hmU) is formed through oxidation of thymine both enzymatically and non‐enzymatically in various biological systems. Although 5hmU has been reported to affect biological processes such as protein–DNA interactions, the consequences of 5hmU formation in genomes have not been yet fully explored. Herein, we report a method to sequence 5hmU at single‐base resolution. We employ chemical oxidation to transform 5hmU to 5‐formyluracil (5fU), followed by the polymerase extension to induce T‐to‐C base changes owing to the inherent ability of 5fU to form 5fU:G base pairing. In combination with the Illumina next generation sequencing technology, we developed polymerase chain reaction (PCR) conditions to amplify the T‐to‐C base changes and demonstrate the method in three different synthetic oligonucleotide models as well as part of the genome of a 5hmU‐rich eukaryotic pathogen. Our method has the potential capability to map 5hmU in genomic DNA and thus will contribute to promote the understanding of this modified base.     

Remarkable Regioisomer Control in the Hydrogel Formation from a Two‐Component Mixture of Pyridine‐End Oligo(p‐phenylenevinylene)s and N‐Decanoyl‐L‐alanine

N‐Decanoyl‐L ‐alanine (DA) was mixed with either colorless 4,4′‐bipyridine (BP) or various derivatives such as chromogenic oligo(p‐phenylenevinylene) (OPV) functionalized with isomeric pyridine termini in specific molar ratios. This mixtures form salt‐type gels in a water/ethanol (2:1, v/v) mixture. The gelation properties of these two‐component mixtures could be modulated by variation of the position of the ′′N′′ atom of the end pyridyl groups in OPVs. The presence of acid–base interactions in the self‐assembly of these two‐component systems leading to gelation was probed in detail by using stoichiometry‐dependent UV/Vis and FTIR spectroscopy. Furthermore, temperature‐dependent UV/Vis and fluorescence spectroscopy clearly demonstrated a J‐type aggregation mode of these gelator molecules during the sol‐to‐gel transition process. Morphological features and the arrangement of the molecules in the gels were examined by using scanning electron microscopy (SEM), atomic force microscopy (AFM), and X‐ray diffraction (XRD) techniques. Calculation of the length of each molecular system by energy minimization in its extended conformation and comparison with the XRD patterns revealed that this class of gelator molecules adopts lamellar organizations. Rheological properties of these two‐component systems provided clear evidence that the flow behavior could be modulated by varying the acid/amine ratio. Polarized optical microscopy (POM), differential scanning calorimetry (DSC), and XRD results revealed that the solid‐phase behavior of such two‐component mixtures (acid/base=2:1) varied significantly upon changing the proton‐acceptor part from BP to OPV. Interestingly, the XRD pattern of these acid/base mixtures after annealing at their associated isotropic temperature was significantly different from that of their xerogels.     

A microfluidic chip‐based fluorescent biosensor for the sensitive and specific detection of label‐free single‐base mismatch via magnetic beads‐based “sandwich” hybridization strategy

A novel microfluidic chip‐based fluorescent DNA biosensor, which utilized the electrophoretic driving mode and magnetic beads‐based “sandwich” hybridization strategy, was developed for the sensitive and ultra‐specific detection of single‐base mismatch DNA in this study. In comparison with previous biosensors, the proposed DNA biosensor has much more robust resistibility to the complex matrix of real saliva and serum samples, shorter analysis time, and much higher discrimination ability for the detection of single‐base mismatch. These features, as well as its easiness of fabrication, operation convenience, stability, better reusability, and low cost, make it a promising alternative to the SNPs genotyping/detection in clinical diagnosis. By using the biosensor, we have successfully determined oral cancer‐related DNA in saliva and serum samples without sample labeling and any preseparation or dilution with a detection limit of 5.6 × 10^?11 M, a RSD (n = 5) < 5% and a discrimination factor of 3.58–4.54 for one‐base mismatch.     

Analysis of tetrahydrocannabinol derivative from cannabis‐infused chocolate by QuEChERS‐thin layer chromatography‐desorption electrospray ionization mass spectrometry

Recently in Canada and some states of the United States, marijuana (cannabis) has become fully legalized and regulated, for both medical and recreational purposes. This fact is going to make cannabis products such as edibles even more popular than ever before. Therefore, it is assumed that there will be a high demand for analytical methods, which are accurate and sensitive enough to be used in different forensic and pharmaceutical cannabis–related applications. Cannabis derivatives have an extreme range and number of constituents with possible interactions with one another. Thus, this characteristic leads to their vast and highly complex chemistry, which requires robust analytical tools to be able to precisely and accurately quantify and qualify them. We developed and validated an analytical method using desorption electrospray ionization (DESI)–mass spectrometry (MS) to accurately detect, characterize, and quantify cannabinoids and also offer an easy, cost‐effective, and reliable technique, which can be performed in a short time for infused edibles in complex matrices such as chocolate. We evaluated a quantitative analysis of tetrahydrocannabinol (THC) in cannabis‐infused chocolate with thin‐layer chromatography (TLC)–DESI‐MS and QuEChERS extraction method. Both techniques of TLC and QuEChERS are cost‐effective and can be run in short time.     

Non‐hybridization single nucleotide polymorphism detection and genotyping assay through direct discrimination of single base mutation by capillary electrophoretic separation of single‐stranded DNA

The significant demands for single nucleotide polymorphism detection and genotyping assays have grown. Most common assays are based on the recognition of the target sequence by the hybridization with its specific probe having the complementary sequence of the target. Herein, a simple, label‐free, and economical non‐hybridization assay was developed for single nucleotide polymorphism detection and genotyping, based on the direct discrimination of single base mutation by simple capillary electrophoresis separation for single‐stranded DNA in an acidic electrophoretic buffer solution containing urea. Capillary electrophoresis separation of single‐base sequential isomers of DNA was achieved due to charge differences resulting from the different protonation properties of the DNA bases. Single nucleotide polymorphism detection and genotyping were achieved by discriminating the electropherogram pattern change, that is, peak number in the electropherogram, obtained by the proposed method. The successful practical application of the proposed method was demonstrated through single nucleotide polymorphism detection and genotyping on a known gene region of 84‐mer, in which guanine to adenine single‐base mutation is commonly observed, using a human hair sample in combination with genomic DNA extraction, polymerase chain reaction amplification, DNA purification from polymerase chain reaction products, and capillary electrophoresis separation.     

Single nucleotide polymorphisms of mitochondrial DNA HVS‐I and HVS‐II in Chinese Bai ethnic group

For forensic and population genetic purposes, a total of 125 unrelated volunteers’ blood samples were collected from Chinese Bai ethnic minority group to analyze sequence variation of two hypervariable segments (HVS‐I and HVS‐II) in the mitochondrial DNA control region. Comparing the HVS‐I and HVS‐II sequences of the 125 Chinese Bais to the Anderson reference sequence, we found 86 polymorphic loci in HVS‐I and 40 in HVS‐II in mitochondrial DNA sequences of the Chinese Bai ethnic minority group, which defined 93 and 53 different haplotypes, respectively. Haplotype diversity and the mean pairwise differences were 0.992 ± 0.003 and 6.553 in HVS‐I, and 0.877 ± 0.027 and 2.407 in HVS‐II, respectively. We defined four macrohaplogroups R, M, N and D with the proportions ranging from 9.6% to 40.0%. With the analysis of the hypervariable domain from nucleotide 16 180–16 193 in HVS‐I, our study revealed new haplotypes of sequence variations. In addition, the Fst metric, phylogenetic tree, and principal component analysis demonstrated a close genetic relationship between the Bai group and Chinese Han populations from South China, Changsha, and Guangdong. The results support that the Bai group is a multiorigin ethnic minority that has merged with the Chinese Han population.     

A new set of DIP‐SNP markers for detection of unbalanced and degraded DNA mixtures

Unbalanced and degraded mixtures (UDM) are frequently encountered during forensic DNA analysis. For example, forensic DNA units regularly encounter DNA mixture signal where the DNA signal from the alleged offender is masked or swamped by high quantities of DNA from the victim. Our previous data presented a new kind of DNA markers that composed of a deletion/insertion polymorphism (DIP) and a SNP and we termed this new kind of microhaplotypes DIP‐SNP (combination of DIP and SNP). Since such markers could be designed short enough for degraded DNA amplification, we hypothesized that DIP‐SNP markers are applicable for typing of UDM. In this study, we developed a new set of DIP‐SNPs with short amplicons which were complement to our prior developed system. The multiplex PCR and SNaPshot assay were established for 20 DIP‐SNPs in a Chinese Han population. The DIP‐SNPs were capable of detecting the minor contributor's allele in home‐made DNA mixture with sensitivities from 1:100 to 1:1000 with a total of 1 –10 ng input DNA. Moreover, this system successfully typed the degraded DNA whether it came from the single source or mixture samples. In Chinese population, the system showed an average informative value of 0.293 and combined informative value of 0.998363862. Our results demonstrated that DIP‐SNPs may serve as a valuable tool in detection of UDM in forensic medicine.     

Applications of MALDI‐TOF MS to large‐scale human mtDNA population‐based studies

Analysis of the mitochondrial DNA variation in populations is commonly carried out in many fields of biomedical research. We propose the analysis of mitochondrial DNA coding region SNP (mtSNP) variation to a high level of phylogenetic resolution based on MALDI‐TOF MS. The African phylogeny has been chosen to test the applicability of the technique but any other part of the worldwide phylogeny (or any other mtSNP panel) could be equally suitable for MALDI‐TOF MS genotyping. SNP selection thus aimed to fully cover all the mtSNPs defining major and minor branches of the known African tree, including, macro‐haplogroup L, and haplogroups M1, and U6. A total of 230 mtSNPs were finally selected. We used tests samples collected from two different African locations, namely, Mozambique and Chad Basin. Different internal genotyping controls and other indirect approaches (e.g. phylogenetic checking coupled with automatic sequencing) were used in order to evaluate the reproducibility of the technique, which resulted to be 100% using samples previously subjected to whole genome amplification. The advantages of the MALDI‐TOF MS are also discussed in comparison with other popular methods such as minisequencing, highlighting its high‐throughput nature, which is particularly suitable for case–control medical studies, forensic databasing or population and anthropological studies.     

Room‐Temperature Formation Pathway for CdTeSe Alloy Magic‐Size Clusters

Little is known about the pathway of room‐temperature formation of ternary CdTeSe magic‐size clusters (MSCs) obtained by mixing binary CdTe and CdSe induction period samples containing binary precursor compounds (PCs) of MSCs, monomers (Ms), and fragments (Fs). Also, unestablished are dispersion effects that occur when as‐mixed samples (without incubation) are placed in toluene (Tol) and octylamine (OTA) mixtures. The resulting ternary MSCs, exhibiting a sharp optical absorption peak at 399 nm, are labelled CdTeSe MSC‐399, and their PCs are referred to as CdTeSe PC‐399. When the amount of OTA is relatively small, single‐ensemble MSC‐399 evolved without either binary CdTe or CdSe MSCs. When the OTA amount is relatively large, CdTe MSC‐371 appeared initially and then disappeared, while single‐ensemble MSC‐399 developed more deliberately. The larger the OTA amount, the more slowly these changes proceeded. The substitution reaction of CdTe PC + CdSe M/F?CdTeSe PC‐399 + CdTe M/F is proposed to be rate‐determining for the MSC‐399 formation in a Tol and OTA mixture. This study provides further understanding of the transformation pathway between MSCs.     

Pluronics‐Stabilized Gold Nanoparticles: Investigation of the Structure of the Polymer–Particle Hybrid

Hybrid gold–polymer nanoparticles are obtained by self‐assembly of amphiphilic copolymers (Pluronics) in solutions containing preformed gold nanoparticles (diameter ca. 12 nm). Dynamic light scattering, TEM, cryo‐TEM, and small‐angle neutron scattering experiments with contrast variation are used to characterize the structure of the gold–polymer particles. Five Pluronics (F127, F68, F88, F108, P84) with different molecular weights and hydrophilic/hydrophobic balances are investigated. Gold nanoparticles are individually embedded within globules of polymer, even under conditions for which Pluronics micelles do not form in solution. The hybrid particles are several tens of nanometers in size (larger than micelles of the corresponding Pluronics), and the size can be tuned by changing the temperature.     

Development of a carbon‐nanoparticle‐coated stirrer for stir bar sorptive extraction by a simple carbon deposition in flame

Stir bar sorptive extraction is an environmentally friendly microextraction technique based on a stir bar with various sorbents. A commercial stirrer is a good support, but it has not been used in stir bar sorptive extraction due to difficult modification. A stirrer was modified with carbon nanoparticles by a simple carbon deposition process in flame and characterized by scanning electron microscopy and energy‐dispersive X‐ray spectrometry. A three‐dimensional porous coating was formed with carbon nanoparticles. In combination with high‐performance liquid chromatography, the stir bar was evaluated using five polycyclic aromatic hydrocarbons as model analytes. Conditions including extraction time and temperature, ionic strength, and desorption solvent were investigated by a factor‐by‐factor optimization method. The established method exhibited good linearity (0.01–10 μg/L) and low limits of quantification (0.01 μg/L). It was applied to detect model analytes in environmental water samples. No analyte was detected in river water, and five analytes were quantified in rain water. The recoveries of five analytes in two samples with spiked at 2 μg/L were in the range of 92.2–106% and 93.4–108%, respectively. The results indicated that the carbon nanoparticle‐coated stirrer was an efficient stir bar for extraction analysis of some polycyclic aromatic hydrocarbons.     

Differential pre‐amplification of STR loci for fragmented forensic DNA profiling

DNA profiling of short tandem repeats (STR) has been successfully used for the identification of individuals in forensic samples, accidents and natural disasters. However, STR profiling of DNA isolated from old crime scenes and damaged biological samples is difficult due to DNA degradation and fragmentation. Here, we show that pre‐amplification of STR loci using biotinylated primers for the STR loci is an efficient strategy to obtain STR profiling results from fragmented forensic samples. Analysis of STR loci with longer amplicon sizes is generally hampered, since these relatively long loci are vulnerable to DNA fragmentation. This problem was overcome by using reduced or increased primer concentrations for loci with shorter or longer amplicon sizes, respectively, in our pre‐amplification strategy. In addition, pre‐amplification of STR loci into two groups of short or long amplicon size increases the efficiency of STR profiling from highly fragmented forensic DNA samples. Therefore, differential pre‐amplification of STR loci is an effective way to obtain DNA profiling results from fragmented forensic samples.