In silico screening of ssDNA aptamer against Escherichia coli O157:H7: A machine learning and the Pseudo K-tuple nucleotide composition based approach.

This study was planned to in silico screening of ssDNA aptamer against Escherichia coli O157:H7 by combination of machine learning and the PseKNC approach. For this, firstly a total numbers of 47 validated ssDNA aptamers as well as 498 random DNA sequences were considered as positive and negative training data respectively. The sequences then converted to numerical vectors using PseKNC method through Pse-in-one 2.0 web server. After that, the numerical vectors were subjected to classification by the SVM, ANN and RF algorithms available in Orange 3.2.0 software. The performances of the tested models were evaluated using cross-validation, random sampling and ROC curve analyzes. The primary results demonstrated that the ANN and RF algorithms have appropriate performances for the data classification. To improve the performances of mentioned classifiers the positive training data was triplicated and re-training process was also performed. The results confirmed that data size improvement had significant effect on the accuracy of data classification especially about RF model. Subsequently, the RF algorithm with accuracy of 98% was selected for aptamer screening. The thermodynamics details of folding process as well as secondary structures of the screened aptamers were also considered as final evaluations. The results confirmed that the selected aptamers by the proposed method had appropriate structure properties and there is no thermodynamics limit for the aptamers folding.

Optimal Arrangement of Four Short DNA Strands for Delivery of Immunostimulatory Nucleic Acids to Immune Cells.

Nanosized DNA assemblies are useful for delivering immunostimulatory cytosine-phosphate-guanine (CpG) DNA to immune cells, but little is known about the optimal structure for such delivery. In this study, we designed three different DNA nanostructures using four 55-mer oligodeoxynucleotides (ODNs), that is, tetrapod-like structured DNA (tetrapodna), tetrahedral DNA (tetrahedron), and tetragonal DNA (tetragon), and compared their potencies. Electrophoresis showed that tetrapodna was obtained with high yield and purity, whereas tetrahedron formed multimers at high ODN concentrations. Atomic force microscopy revealed that all preparations were properly constructed under optimal conditions. The thermal stability of tetrapodna was higher than those of the others. Dynamic light scattering analysis showed that all of the assemblies were about 8 nm in diameter. Upon addition to mouse macrophage-like RAW264.7 cells, tetrahedron was most efficiently taken up by the cells. Then, a CpG DNA, a ligand for toll-like receptor 9, was linked to these DNA nanostructures and added to RAW264.7 cells. CpG tetrahedron induced the largest amount of tumor necrosis factor-α, followed by CpG tetrapodna. Similar results were obtained using human peripheral blood mononuclear cells. Taken together, these results indicate that tetrapodna is the best assembly with the highest yield and high immunostimulatory activity, and tetrahedron can be another useful assembly for cellular delivery if its preparation yield is improved.

Specificity of an Escherichia coli RNA polymerase-associated NTPase.

Standard preparations of Escherichia coli RNA polymerase harbor a 70 kDa protein with NTPase (beta-gamma cleavage) activity that is not a recognized polymerase subunit. The NTPase activity of this component, before and after separation from the polymerase, is strongly dependent on the presence of DNA; single-stranded polydeoxynucleotides are more effective than double-stranded. ATP and GTP are cleaved, the latter much less readily. The NTPase as it occurs with the polymerase displays cleavage preference for NTPs that are not complementary to the DNA, a fact that has led to proposals for involvement of the NTPase in transcriptional error prevention [Volloch, V. Z., Rits, L. & Tumerman, L. (1979) Nucleic Acids Res. 6, 1535-1546; Libby, R. T., Nelson, J. L., Calvo, J. M., & Gallant, J. A. (1989) EMBO J. 8, 3253-3158]. We find, however, that the lesser cleavage in the presence of complementary DNA results from competition for the NTP between the processes of incorporation by the polymerase and of cleavage by the NTPase, operating on the same substrate pool. The greater cleavage with noncomplementary DNA occurs because of the lack of incorporation by the polymerase, which then does not compete with the NTPase for the substrate pool. Thus, these findings indicate that the cleavage preference of the NTPase for noncomplementary NTPs is not part of a mechanism for error prevention during transcription.