A Non-Watson–Crick Motif of Base-pairing on Surfaces for Untethered Oligonucleotides

Sensors for DNA detection: theoretical investigation of the conformational properties of immobilized single-strand DNA

“…The Brownian motion and translational degrees of freedom are reduced upon immobilization but the flexibility of the strand and its interaction with the support functional groups can lead to adsorption of the whole chain. DNA-surface adsorption and conformational arrangement of the fragment on the interface are very similar to the ones already observed by Wong and co-workers 18 even though from their investigations it appeared that the untethered fragment was more strongly bound to the surface due to the highly positive charge density of the layer. In the case of a neutral interface and a cross-linked strand, the adsorption, which is mainly due to the attractive forces between the base oxygens or the oxygens of the negatively charged backbone phosphates and the positively charged hydrogens of the propylamine headgroups of the surface, is reversible.…”

“…These simulations cannot provide asymptotic time averages of the various properties of the selected systems but can provide an adequate description of their dynamical structure. Indeed, as demonstrated by other authors 15,18,19,57 simulation times lower than 50 ns were sufficient to obtain a realistic picture of ssDNA dynamics in solution and satisfactory results in line with the experimental findings. In order to check if the systems were equilibrated, rms deviation of the sampled configurations from the starting structures were examined in detail.…”

“…Many experimental and theoretical studies aimed at a more comprehensive understanding of the various aspect connected to DNA microarrays design and performance have been carried out over the years. [6][7][8][9][10][11][12][13][14][15][16][17][18] All of these investigations provided important information regarding surface characteristics and coverage, DNA spatial distribution and folding. They were able to identifying various factors influencing microarray performance such as the choice of the sequence (base composition), length, and concentration of both probe and target molecules; the spacer length, and the temperature.…”

“…In a previous work 18 the authors studied the adsorption of a 12-base B-DNA single strand on a positively charged glass surface functionalized with an ammonium monolayer in salt water using all-atom MD simulations. Two different starting configurations were considered and after relaxation, production MD simulations were run for about 10 ns.…”

Design of microarray probes for virus identification and detection of emerging viruses at the genus level

“…For example, to investigate the JEV cross-hybridization issue in Figure 4B, we performed BLASTN alignments for the crosshybridizing virus probe sequences with the sequence of JEV, and found that none of the probe sequences had significant sequence similarity with JEV. Thus, the sequence complementarity guidelines do not explain why the JEV viral sample cross-hybridized to the other three non-target probes -this might instead be attributable to non-Watson-Crick base pairing [17][18][19][20].…”