Approaching real-time molecular diagnostics: single-pair fluorescence resonance energy transfer (spFRET) detection for the analysis of low abundant point mutations in K-ras oncogenes

The aim of this study was to develop new strategies for analyzing molecular signatures of disease states approaching real-time using single pair fluorescence resonance energy transfer (spFRET) to rapidly detect point mutations in unamplified genomic DNA. In addition, the detection process was required to discriminate between normal and mutant (minority) DNAs in heterogeneous populations. The discrimination was carried out using allele-specific primers, which flanked the point mutation in the target gene and were ligated using a thermostable ligase enzyme only when the genomic DNA carried this mutation. The allele-specific primers also carried complementary stem structures with end-labels (donor/acceptor fluorescent dyes, Cy5/Cy5.5, respectively), which formed a molecular beacon following ligation. We coupled ligase detection reaction (LDR) with spFRET to identify a single base mutation in codon 12 of a K-ras oncogene that has high diagnostic value for colorectal cancers. A simple diode laser-based fluorescence system capable of interrogating single fluorescent molecules undergoing FRET was used to detect photon bursts generated from the molecular beacon probes formed upon ligation. LDR-spFRET provided the necessary specificity and sensitivity to detect single-point mutations in as little as 600 copies of human genomic DNA directly without PCR at a level of 1 mutant per 1000 wild type sequences using 20 LDR thermal cycles. We also demonstrate the ability to rapidly discriminate single base differences in the K-ras gene in less than 5 min at a frequency of 1 mutant DNA per 10 normals using only a single LDR thermal cycle of genomic DNA (600 copies). Real-time LDR-spFRET detection of point mutations in the K-ras gene was accomplished in PMMA microfluidic devices using sheath flows.     

Use of Raman and Raman optical activity for the structural characterization of a therapeutic monoclonal antibody formulation subjected to heat stress

Structural complexity of biological drug products presents an analytical challenge in terms of early detection of aggregation and/or degradation. In the present study, Raman and Raman optical activity (ROA) were evaluated for their sensitivity to detect heat‐induced molecular instability in an Immunoglobulin G4 subclass therapeutic monoclonal antibody present in its formulation matrix. The therapeutic antibody was subjected to heat stress at 50 °C and was analyzed at various time points up to 1 month. The current results suggest that Raman and ROA are sensitive to early‐stage detection of heat‐induced instability of the antibody, in which significant changes could be observed at 1 week of stress. ROA could provide early detection of the subtle differences at the tertiary structure level in a heat‐stressed monoclonal antibody and Raman/ROA spectra could provide early detection in secondary structural changes as well. Copyright © 2015 John Wiley & Sons, Ltd.     

Single molecule detection of double-stranded DNA in poly(methylmethacrylate) and polycarbonate microfluidic devices.

Single photon burst techniques were used to detect double-stranded DNA molecules in poly(methylmethacrylate) (PM MA) and polycarbonate (PC) microfluidic devices. A confocal epi-illumination detection system was constructed to monitor the fluorescence signature from single DNA molecules that were multiply labeled with the mono-intercalating dye, TOPRO-5, which possessed an absorption maximum at 765 nm allowing excitation with a solid-state diode laser and fluorescence monitoring in the near-infrared (IR). Near-IR excitation minimized autofluorescence produced from the polymer substrate, which was found to be significantly greater when excitation was provided in the visible range (488 nm). A solution containing lambda-DNA (48.5 kbp) was electrokinetically transported through the microfluidic devices at different applied voltages and solution pH values to investigate the effects of polymer substrate on the transport rate and detection efficiency of single molecular events. By applying an autocorrelation analysis to the data, we were able to obtain the molecular transit time of the individual molecules as they passed through the 7 microm laser beam. It was observed that the applied voltage for both devices affected the transport rate. However, solution pH did not alter the transit time for PM MA-based devices since the electroosmotic flow of PMMA was independent of solution pH. In addition, efforts were directed toward optimizing the sampling efficiency (number of molecules passing through the probe volume) by using either hydrodynamically focused flows from a sheath generated by electrokinetic pumping from side channels or reducing the channel width of the microfluidic device. Due to the low electroosmotic flows generated by both PMMA and PC, tight focusing of the sample stream was not possible. However, in PMMA devices, flow gating was observed by applying field strengths > -120 V/cm to the sheath flow channels. By narrowing the microchannel width, the number of molecular events detected per unit time was found to be four times higher in channels with 10 microm widths compared to those of 50 microm, indicating improved sampling efficiency for the narrower channels without significantly deteriorating detection efficiency. Attempts were made to do single molecule sizing of lambda-DNA, M13 (7.2 kbp) and pUC19 (2.7 kbp) using photon burst detection. While the average number of photons for each DNA type were different, the standard deviations were large due to the Gaussian intensity profile of the excitation beam. To demonstrate the sensitivity of single molecule analysis in the near-IR using polymer microfluidic devices, the near-IR chromophore, NN382, wasanalyzed using ourconfocal imager. A detection efficiency of 94% for single NN382 molecules was observed in the PC devices.     

Plasmonics nanoprobes: detection of single-nucleotide polymorphisms in the breast cancer BRCA1 gene

This paper describes the application of plasmonics-based nanoprobes that combine the modulation of the plasmonics effect to change the surface-enhanced Raman scattering (SERS) of a Raman label and the specificity of a DNA hairpin loop sequence to recognize and discriminate a variety of molecular target sequences. Hybridization with target DNA opens the hairpin and physically separates the Raman label from the metal nanoparticle thus reducing the plasmonics effect and quenching the SERS signal of the label. We have successfully demonstrated the specificity and selectivity of the nanoprobes in the detection of a single-nucleotide polymorphism (SNP) in the breast cancer BRCA1 gene in a homogenous solution at room temperature. In addition, the potential application of plasmonics nanoprobes for quantitative DNA diagnostic testing is discussed.     

Content uniformity determination of pharmaceutical tablets using five near-infrared reflectance spectrometers: a process analytical technology (PAT) approach using robust multivariate calibration transfer algorithms

Near-infrared calibration models were developed for the determination of content uniformity of pharmaceutical tablets containing 29.4% drug load for two dosage strengths (X and Y). Both dosage strengths have a circular geometry and the only difference is the size and weight. Strength X samples weigh approximately 425 mg with a diameter of 12 mm while strength Y samples, weigh approximately 1700 mg with a diameter of 20 mm. Data used in this study were acquired from five NIR instruments manufactured by two different vendors. One of these spectrometers is a dispersive-based NIR system while the other four were Fourier transform (FT) based. The transferability of the optimized partial least-squares (PLS) calibration models developed on the primary instrument (A) located in a research facility was evaluated using spectral data acquired from secondary instruments B, C, D and E. Instruments B and E were located in the same research facility as spectrometer A while instruments C and D were located in a production facility 35 miles away. The same set of tablet samples were used to acquire spectral data from all instruments. This scenario mimics the conventional pharmaceutical technology transfer from research and development to production. Direct cross-instrument prediction without standardization was performed between the primary and each secondary instrument to evaluate the robustness of the primary instrument calibration model. For the strength Y samples, this approach was successful for data acquired on instruments B, C, and D producing root mean square error of prediction (RMSEP) of 1.05, 1.05, and 1.22%, respectively. However for instrument E data, this approach was not successful producing an RMSEP value of 3.40%. A similar deterioration was observed for the strength X samples, with RMSEP values of 2.78, 5.54, 3.40, and 5.78% corresponding to spectral data acquired on instruments B, C, D, and E, respectively. To minimize the effect of instrument variability, calibration transfer techniques such as piecewise direct standardization (PDS) and wavelet hybrid direct standardization (WHDS) were used. The PDS approach, the RMSEP values for strength X samples were lowered to 1.22, 1.12, 1.19, and 1.08% for instruments B, C, D, and E, respectively. Similar improvements were obtained using the WHDS approach with RMSEP values of 1.36, 1.42, 1.36, and 0.98% corresponding to instruments B, C, D, and E, respectively.