Isometric artifacts from polymerase chain reaction-massively parallel sequencing analysis of short tandem repeat loci: An emerging issue from a new technology?

The recent introduction of polymerase chain reaction (PCR)-massively parallel sequencing (MPS) technologies in forensics has changed the approach to allelic short tandem repeat (STR) typing because sequencing cloned PCR fragments enables alleles with identical molecular weights to be distinguished based on their nucleotide sequences. Therefore, because PCR fidelity mainly depends on template integrity, new technical issues could arise in the interpretation of the results obtained from the degraded samples. In this work, a set of DNA samples degraded in vitro was used to investigate whether PCR-MPS could generate “isometric drop-ins” (IDIs; i.e., molecular products having the same length as the original allele but with a different nucleotide sequence within the repeated units). The Precision ID GlobalFiler NGS STR panel kit was used to analyze 0.5 and 1 ng of mock samples in duplicate tests (for a total of 16 PCR-MPS analyses). As expected, several well-known PCR artifacts (such as allelic dropout, stutters above the threshold) were scored; 95 IDIs with an average occurrence of 5.9 IDIs per test (min: 1, max: 11) were scored as well. In total, IDIs represented one of the most frequent artifacts. The coverage of these IDIs reached up to 981 reads (median: 239 reads), and the ratios with the coverage of the original allele ranged from 0.069 to 7.285 (median: 0.221). In addition, approximately 5.2% of the IDIs showed coverage higher than that of the original allele. Molecular analysis of these artifacts showed that they were generated in 96.8% of cases through a single nucleotide change event, with the C > T transition being the most frequent (85.7%). Thus, in a forensic evaluation of evidence, IDIs may represent an actual issue, particularly when DNA mixtures need to be interpreted because they could mislead the operator regarding the number of contributors. Overall, the molecular features of the IDIs described in this work, as well as the performance of duplicate tests, may be useful tools for managing this new class of artifacts otherwise not detected by capillary electrophoresis technology.     

Tuning Deazaflavins Towards Highly Potent Reducing Photocatalysts Guided by Mechanistic Understanding – Enhancement of the Key Step by the Internal Heavy Atom Effect

Deazaflavins are well suited for reductive chemistry acting via a consecutive photo-induced electron transfer, in which their triplet state and semiquinone – the latter is formed from the former after electron transfer from a sacrificial electron donor – are key intermediates. Guided by mechanistic investigations aiming to increase intersystem crossing by the internal heavy atom effect and optimising the concentration conditions to avoid unproductive excited singlet reactions, we synthesised 5-aryldeazaflavins with Br or Cl substituents on different structural positions via a three-component reaction. Bromination of the deazaisoalloxazine core leads to almost 100 % triplet yield but causes photo-instability and enhances unproductive side reactions. Bromine on the 5-phenyl group in ortho position does not affect the photostability, increases the triplet yield, and allows its efficient usage in the photocatalytic dehalogenation of bromo- and chloroarenes with electron-donating methoxy and alkyl groups even under aerobic conditions. Reductive powers comparable to lithium are achieved.     

Correction to: Aziridine-2-Carboxylic Acid Derivatives and Its Open-Ring Isomers as a Novel PDIA1 Inhibitors

Chemistry of Heterocyclic Compounds -     

Calculations of 1H NMR coupling constants for conformational studies of isomeric pentofuranosyl nucleosides

The SCF FPT method in the INDO approximation of molecular orbital theory is employed for calculations of ¹H NMR cisoidal coupling constants in model compounds. Obtained results are used for finding conformational states of α-xylo-, β-lyxo-, and α-2′-deoxyribonucleosides in solution.     

Metalloxide mit großer Oberfläche durch Tieftemperatur-Vorbehandlung ihrer Stammprodukte

Zusammenfassung Basisches Magnesiumcarbonat und basisches Zinkcarbonat erlangen nach Tieftemperaturbehandlung mit flüssiger Luft eine bedeutend größere Oberfläche, die auch bei den betr. oxidischen Abkömmlingen nach ihrer thermischen Beanspruchung bei 800° bestehen bleibt. Ebenfalls tieftemperatur-empfindlich ist das dunkelbraune röntgenamorphe Eisen(III)-hydroxid (Orthohydroxid), während das topochemische röntgenamorphe und ziegelfarbige Eisen(III)-hydroxid (Iso-Orthohydroxid) sowie ein daraus gewonnenes hellgelbes -FeOOH, die schon von sich aus oberflächengroß sind, sich in dieser Hinsicht als indifferent erwiesen. Die aus den verschiedenen Eisen(III)-hydroxiden bei 800° gewonnenen -Oxide hatten eine sehr differente scheinbare Dichte bzw. Oberfläche.     

Bacteriochlorin <Emphasis Type="Italic">e</Emphasis><Subscript>6</Subscript> as a sensitizer for photodynamic therapy

A simple scheme of modification of the native pigment bacteriochlorophyll a, extracted from the biomass of phototropic bacteria, for the purpose of obtaining a water-soluble derivative — bacteriochlorin e ₆ — which is similar in molecular structure to the effective sensitizer chlorin e ₆ and, in addition, has an intense longwave absorption band in the near-infrared region of the spectrum where biological tissues weakly absorb light — has been developed. The ease of production of bacteriochlorin e ₆ in combination with its physicochemical and spectral properties allow it to be considered as a promising sensitizer for photodynamic therapy.Translated from Zhurnal Prikladnoi Spektroskopii, Vol. 71, No. 6, pp. 745–748, November–December, 2004.This revised version was published online in April 2005 with a corrected cover date.