Sequence-specific analysis

Alike any other G-protein coupled receptors (GPCRs), mGlu receptors have seven transmembrane helices, also known as the heptahelical domain (Fig. 2). As observed for all GPCRs, the intracellular loops 2 and 3 as well as the C-terminal tail are the key determinants for the interaction with and activation of G-proteins. However, sequence similarity analysis as well as specific structural features make these mGlu receptors different from many other... 

Chen C., Wu B., Wie T, Egholm M., Strauss W. M. Unique chromosome identification and sequence-specific structural analysis with short PNA oligomers. Mamm. Genome 2000 11 384—391. 

Sequence-specific assignments were obtained by analysis of the NOESY and COSY spectra obtained under the similar conditions in H2O. The three important classes of NOE cross peaks for this purpose are designated d j, d j, and In... 

Saiki RK, Walsh PS, Levbnson CH., Erlich HA (1989) Genetic analysis of amplified DNA with immobilized sequence specific oligonucleotide probes. Proc. Natl Acad Sd USA 86 6230-6234. 

It should be possible to extend the DNA microarray-binding experiment to whole-genome analysis of transcription factor binding sites. The authors suggest that a microarray spotted with 12,000 one-kilobase sequences would span the entire Saccharomyces cerevisiae genome (Bulyk et al., 2001). Such an array could be used to characterize the sequence specificity of S. cerevisiae transcription factors. These experiments would be useful for predicting functions of previously uncharacterized transcription... 

To overcome this limitation, a series of images of an entire field of cells can be obtained, then the waves can be visualized when the images are played back in rapid sequence. Specific lines of analysis can then be chosen after the experiment is completed. The line is selected to be perpendicular to the wave front (that is, along the direction of propagation). As before, the lines are stacked on top of one another, yielding a reconstructed line scan that contains all the information of a true line scan. The leading edge of the Ca2+ wave appears on the line scan as a sharp line with a constant slope. Since the slope is distance/time, appropriate conversion factors allow true speeds to be obtained in jUm/s. 

ABC transporters involved in the uptake of siderophores, haem, and vitamin B]2 are widely conserved in bacteria and Archaea (see Figure 10). Very few species lack representatives of the siderophore family transporters. These species are mainly intracellular parasites whose metabolism is closely coupled to the metabolism of their hosts (e.g. mycoplasma), or bacteria with no need for iron (e.g. lactobacilli). In many cases, several systems of this transporter family can be detected in a single species, thus allowing the use of structurally different chelators. Most systems were exclusively identified by sequence data analysis, some were biochemically characterised, and their substrate specificity was determined. However, only very few systems have been studied in detail. At present, the best-characterised ABC transporters of this type are the fhuBCD and the btuCDF systems of E. coli, which might serve as model systems of the siderophore family. Therefore, in the following sections, this report will mainly focus on the components that mediate ferric hydroxamate uptake (fhu) and vitamin B12 uptake (htu). 

The peptide mixture on the MALDI target can be exposed to a chemical derivatization to confirm the identity of a peptide by the mass shift associated with the sequence-specific derivatization. A large number of possible derivatization reactions can be combined with the MALDI-TOF analysis. Their usefulness depends critically on the kinetics of the derivatization reaction, whether the reaction is complete with small amounts of peptides and whether only one product is generated. A visible MALDI signal can be generated from low atomole of peptide present under the laser beam (Vorm et al., 1994), but these amounts are often not sufficient... 

The easiest way to detect a protein modification seems to be the mass measurement of all peptides generated by enzymatic digestion. The comparison with the predicted peptide masses from the sequence of the protein identifies unmodified peptides and unexplained masses would give indications to modified peptides. Unfortunately, this is not a suitable approach in practice. In many peptide mapping experiments done with the MALDI mass mapping technique, up to 30% of the measured masses remain unexplained. This is probably due to protein contaminations from human keratins, chemical modifications introduced by gel electrophoresis and the digestion procedure, and other proteins present at low levels in the piece excised from the sodium dodecyl sulfate gel. The detection of a protein modification requires a more specific analysis. 

Automation Users can fuUy automate their systems from pre- and post-run programming to multi-method sequencing to meet specific analysis requirements. 

Hardenbol, P. and van Dyke, M.W. (1996) Sequence specificity of triplex DNA formation analysis by a combinatorial approach, restriction endonuclease protection selection and amplification. Proc. Natl. Acad. Sci. USA, 93, 2811-2816. 

The first scientific articles from the IKhPS were submitted for publication in the early 1960s, among them being Nikolay s reports on his work in the new field. His major project in nucleotide chemistry was specific chemical modifications of heterocyclic bases. Reactions of hydroxylamine with cytidine and uridine were studied in detail and a new reagent, O-methylhydroxylamine, was proposed for modification of cytidine. These investigations aimed at the development of efficient methods for sequencing and analysis of the secondary structure of polynucleotides. Later, a reaction of chloroacetaldehyde with adenosine and cytidine was discovered and used for preparation of fluorescent polynucleotide derivatives. 

Furthermore, the sequence-specific identification abilities of the hybridization step in IPCR-ELOSA allow for separation between different amplification products in multiplex analysis or individual detection of a marker and competitor DNA for internal standardization (see Section 2.3.6) [66]. 

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