An Oligo-Library-Based Approach for Mapping DNA-DNA Triplex Interactions In Vitro

We present Triplex-seq, a deep-sequencing method that systematically maps the interaction space between an oligo library of ssDNA triplex-forming oligos (TFOs) and a particular dsDNA triplex target site (TTS). We demonstrate the method using a randomized oligo library comprising 67 million variants, with five TTSs that differ in guanine (G) content, at two different buffer conditions, denoted pH 5 and pH 7. Our results show that G-rich triplexes form at both pH 5 and pH 7, with the pH 5 set being more stable, indicating that there is a subset of TFOs that form triplexes only at pH 5. In addition, using information analysis, we identify triplex-forming motifs (TFMs), which correspond to minimal functional TFO sequences. We demonstrate, in single-variant verification experiments, that TFOs with these TFMs indeed form a triplex with G-rich TTSs, and that a single mutation in the TFM motif can alleviate binding. Our results show that deep-sequencing platforms can substantially expand our understanding of triplex binding rules and aid in refining the DNA triplex code.

Critical Detection of Agglomeration of Magnetic Nanoparticles by Magnetic Orientational Linear Dichroism

Magnetic orientational linear dichroism (MOLD) spectroscopy was found to be useful for detecting the initiation of the agglomeration process of COOH-modified iron-oxide magnetic nanoparticles (MNPs) in water, which was produced by the addition of a small amount of a cationic surfactant or a metal ion. The critical association of MNPs leading to agglomeration was detected from the increase of the maximum MOLD value as well as from the shift of the maximum wavelength of the MOLD spectrum. The magnetic field dependence of MOLD was analyzed by the Langevin equation, and the apparent association numbers of MNPs in the agglomerates were obtained.

Optomagnetic Detection of Rolling Circle Amplification Products

Rolling circle amplification (RCA) of a synthetic nucleic acid target is detected using magnetic nanoparticles (MNPs) combined with an optomagnetic (OM) readout. Two RCA assays are developed with on-chip detection of rolling circle products (RCPs) either at end-point where MNPs are mixed with the sample after completion of RCA or in real time where MNPs are mixed with the sample during RCA. The plastic chip acts as a cuvette, which is positioned in a setup integrated with temperature control and simultaneous detection of four parallel DNA hybridization reactions between functionalized MNPs and products of DNA amplification. The OM technique probes the small-angle rotation of MNPs bearing oligonucleotide probes complementary to the repeated nucleotide sequence of the RCPs. This rotation is restricted when MNPs bind to RCPs, which can be observed as a turn-off of the signal from MNPs that are free to rotate. The amount of MNPs bound to RCPs is found to increase in response to the amplification time as well as in response to the synthetic DNA target concentration (2-40 pM dynamic range). We report OM real-time results obtained with MNPs present during RCA and compare to relevant end-point OM results for RCPs generated for different RCA times. The real-time approach avoids opening of tubes post-RCA and thus reduces risk of lab contamination with amplification products without compromising the sensitivity and dynamic range of the assay.

Magnetic Orientational Linear Dichroism Spectra of Magnetic Nanoparticles as a Probe of the Dispersion State

Magnetic orientational linear dichroism (MOLD) spectra of magnetic nanoparticles (MNPs) in the UV-Vis wavelength region were found to be useful as a probe to detect changes of the dispersion state due to a restriction of the rotational Brownian motion of MNPs; a change of the medium from liquid to resin and the formation of agglomerates in solution. The magnetic-field dependence of MOLD was analyzed by using the Langevin equation, which gave information about the magnetic moment of MNPs.

Time-Gated FRET and DNA-Based Photonic Molecular Logic Gates: AND, OR, NAND, and NOR

Molecular logic devices (MLDs) constructed from DNA are promising for applications in bioanalysis, computing, and other applications requiring Boolean logic. These MLDs accept oligonucleotide inputs and generate fluorescence output through changes in structure. Although fluorescent dyes are most common in MLD designs, nontraditional luminescent materials with unique optical properties can potentially enhance MLD capabilities. In this context, luminescent lanthanide complexes (LLCs) have been largely overlooked. Here, we demonstrate a set of high-contrast DNA photonic logic gates based on toehold-mediated strand displacement and time-gated FRET. The gates include NAND, NOR, OR, and AND designs that accept two unlabeled target oligonucleotide sequences as inputs. Bright "true" output states utilize time-gated, FRET-sensitized emission from an Alexa Fluor 546 (A546) dye acceptor paired with a luminescent terbium cryptate (Tb) donor. Dark "false" output states are generated through either displacement of the A546, or through competitive and sequential quenching of the Tb or A546 by a dark quencher. Time-gated FRET and the long luminescence lifetime and spectrally narrow emission lines of the Tb donor enable 4-10-fold contrast between Boolean outputs, ≤10% signal variation for a common output, multicolor implementation of two logic gates in parallel, and effective performance in buffer and serum. These metrics exceed those reported for many other logic gate designs with only fluorescent dyes and with other non-LLC materials. Preliminary three-input AND and NAND gates are also demonstrated. The powerful combination of an LLC FRET donor with DNA-based logic gates is anticipated to have many future applications in bioanalysis.

Sequence-specific validation of LAMP amplicons in real-time optomagnetic detection of Dengue serotype 2 synthetic DNA

Loop-targeting detection probes are used to discriminate true positive from spurious DNA amplicons in a real-time optomagnetic LAMP nanobead assay.