Detection Sequence

The simplest detection scheme is to use a single probe to detect the target, with either the target or the probe being labeled. This 

Using the single-probe method, a 30-base sequence common to five strains of coli could be detected using the latex-based labels, with detection limits of 25 fM (silver nanoparticles on hollow capsules) [105] and 0.5 fM (gold nanoparticles on latex) [131], as shown in Fig. 8.18. The lower detection limit for the second method 

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The effect of the bite angle has been reviewed.243,244 The 103Rh chemical shifts of a series of hydridorhodiumbis(carbonyl)diphosphine compounds containing chelating bidentate P-ligands have been obtained by inverse HMQC detection sequences.245... 

Users of any NMR instrument are well aware of the extensive employment of what is known as pulse sequences. The roots of the term go back to the early days of pulsed NMR when multiple, precisely spaced RF excitation pulses had been invented (17,98-110) and employed to overcome instrumental imperfections such as magnetic field inhomogeneity (Hahn echo) or receiver dead time (solid echo), monitor relaxation phenomena (saturationrrecovery, inversion recovery, CPMG), excite and/or isolate specific components of NMR signals (stimulated echo, quadrupole echo), etc. Later on, employment of pulse sequences of increasing complexity, combined with the so-called phase-cycling technique, has revolutionized FT-NMR spectroscopy, a field where hundreds of useful excitation and detection sequences (111,112) are at present routinely used to acquire qualitatively distinct ID, 2D, and 3D NMR... 

The relatively long timescales of the ionization, isolation, thermalization, reaction, and detection sequences associated with low-pressure FTICR experiments are generally thought to preclude the use of this technique as a means of examining the unimolecular dissociation of conventional metastable ions occurring on the microsecond to millisecond timescale. Nonetheless, as just demonstrated (Section IIIC), intermediates with this order of magnitude of lifetime are routinely formed in the bimolecular reactions of gaseous ions with neutral molecules at low pressures in the FTICR cell, as in Equation (13). 

Additionally, the cellular location at which the resultant polypeptide will function often cannot be predicted from RNA detection/sequences nor can detailed information regarding how the polypeptide product s functional activity will be regulated (e.g. via post-translational mechanisms such as phosphorylation, partial proteolysis, etc.). Therefore, protein-based drug leads/targets are often more successfully identified by direct examination of the expressed protein complement of the cell, i.e. its proteome. Like the transcriptome (total cellular RNA content) and in contrast to the genome, the proteome is not static with changes in cellular... 

When two genes share readily detectable sequence similarities (nucleotide sequence in DNA or amino acid sequence in the proteins they encode), their sequences... 

The four-Pulse PELDOR pulse sequence is in principle a pump-probe experiment that selects from all contributions to the EPR spectrum dominantly the dipolar coupling between the two unpaired electrons. The detection sequence 7i/2-T1-7i-T1-echo1-T2-7i (Fig. 16.IB) applied at a microwave frequency vA creates at time t2 after the last n-pulse a refocused echo (RE) for the spins being in resonance with vA. The position in time of... 

At X-band and for nitroxides, the experiment is performed by applying the pump pulse on the maximum of the nitroxides spectrum (Fig. 16.5A) at the center of the cavity. At this position the pump pulse selects all orientations (Fig. 16.5B). The frequency of the detection sequence is applied at 90 MHz higher frequency than the pump pulse frequency. At this frequency the pulses excite the low-field edge of the nitroxides field sweep spectrum, which is the Azz component of the hyperfine tensor (Fig. 16.5C). Stepping the frequency offset in 10 MHz steps down to 40 MHz (each frequency offset is an independent PELDOR experiment that is set up as described... 

Reliably Called Difficult to Detect/Sequence Stops Sequencing... 

The most notable feature of the process described above is that ions are not destroyed by the detection process. Therefore ions can be further manipulated after detection. The simplest example is the remeasurement of ions (i.e., repeating the excite and/or detect sequence to obtain another mass spectrum of the same group of ions). More complex manipulations include multiple stages of MS/MS. The facts that ions are detected nondestructively and that they are trapped in a region of space mean that very complex sequences of ion manipulations are possible, making FT-ICR instruments the most versatile of all mass spectrometers. 

Matrix-assisted laser-desorption ionization time-of-fiight (MALDI-TOF) mass spectrometry can be used to detect sequence polymorphisms. With mass spectroscopy, no label is necessary because the alleles differ in mass. After... 

The reference sequences used for our pharmacogenetic studies are as follows KRAS (NM 004985 and M54968), EGFR (NM 005228.3.), CKIT (NM 000222.2), PDGFRA (NM 006206), and BRAF (NM 004333) mRNA sequences from GeneBank (http //www.ncbi.nlm.nih.gov). To compare all detected sequence variants we previously identified the most widely used mutations Internet databases listed in Table 3. 

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