Sequencing, oligonucleotide

This group was developed for terminal protection of an oligonucleotide sequence for purposes of monitoring the purification by HPLC after a synthesis. It shows characteristic UV maxima at 365 and 380 nm. The group is prepared from the chloride in pyridine and can be bound directly to the support-bound oligonucleotide. ... 

Genomics—the analysis of the entire oligonucleotide sequence of an organism s complete genetic material—has provided further enhancements. 

Recombinant DNA technology can also be used to create modified proteins that are readily purified by affinity chromatography. The gene of interest is Unked to an oligonucleotide sequence that encodes a carboxyl or amino terminal extension to the encoded protein. The... 

Primers The primers are short (15-30) oligonucleotide sequences designed to base pair or anneal to complementary sequences that flank the DNA target sequence to be amplified. The primers are added at 0.1-1 qM in the assay. 

Critical to the success of this procedure was the development of a suitable temporary ligand that is sufficiently inert to conditions of oligonucleotide deprotection (typically aqueous ammonia, 6h at 50° C) and can subsequently be replaced by chloride. The nucleobase derivative 1-cyclohexamethyl-thymine 41 was found to satisfy these criteria and can be converted to the trans-Pt-Cl species by treatment with dilute HC1 (pH 2.3, 40°C, 48 h). This last step restricts the range of possible oligonucleotide sequences to those that are not susceptible to depurination, but clearly establishes a prototype system for future development. 

Figure 12 Split-probe oligonucleotide sequencing using DELFIA.

In order to facilitate analysis of FeBABE produced fragments, the prey protein or biomolecule is labeled at one end with a tag that can be detected after electrophoresis, usually in a transfer blot. The tag can be a fusion tag, such as 6X His, or any other group that can be targeted with an antibody and detected. Alternatively, radiolabels and fluorescent labels have been used with prey molecules, including the use of end-labeled DNA to study where DNA binding proteins dock onto the oligonucleotide sequence. 

Figure 4.2 Generalized outline of a gene chip. In this example, short oligonucleotide sequences are attached to the anchoring surface (only the outer rows are shown). Each probe displays a different nucleotide sequence, and the sequences used are usually based upon genome sequence information. The sequence of one such probe is shown as AGGCA. By incubating the chip with, for example, total cellular mRNA under appropriate conditions, any mRNA with a complementary sequence (UCCGU in the case of the probe sequence shown) will hybridize with the probes. In reality, probes will have longer sequences than the one shown above...

Table 2 Oligonucleotide sequences used as templates for the formation of silver clusters...

I believe that the bottom-up approach to the origin of life will enjoy a considerable boost, when conditions are found for the prebiotic synthesis of many identical copies of long (>30) co-oligopeptide or co-oligonucleotide sequences. This would at least show that the prebiotic synthesis of enzymes and/or RNA is in principle possible. This remains the main problem with the prebiotic RNA world. 

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