Oligonucleotide linkers

Figure 1. DNA sequence and translation product of 14-1 cDNA clone. The EcoRI sites at the 5 and 3 ends were generated by oligonucleotide linkers.

Outline how restriction enzymes and DNA ligase have enabled recombinant DNA technology. Explain the roles of oligonucleotide linkers and polynucleotide kinase in creating recombinant molecules. 

Oligonucleotide linkers can be used for many applications, such as, as a physical spacer or for the attachment of other groups or molecules. A three carbon spacer, for example, has been used as a surrogate for an abasic site. A C3 spacer has also been incorporated into a cyclic DNA dumbbell and binding sites for topoisomerase I, and the resultant dumbbell was shown to be an inhibitor of the enzyme. Fluorophores have been... 

Both phosphoramidate and phosphate triester derivatives have been used as linkers to attach reporter groups to oligonucleotides. These derivatives are not entirely resistant to nucleases and they possess a chiral center. They have not been widely iavestigated as antisense dmgs. 

Recent developments in DNA/RNA chemical synthesis have allowed us to attach some functional groups covalently to nucleic acids, thus permitting the introduction of a functionality or properties not normally present in the native biomolecule The use of non-nucleosidic linkers is probably the most popular approach for the 5 -terminal modification of chemically synthesized nucleic acid oligonucleotides and a number of such linkers are commercially available. The linker shown in Fig. 2 is designed as a phosphoramidate derivative so that it can be incorporated into the 5 -terminus of the sequence as the last... 

Preliminary results of DNA sequence detection using the OFRR are thoroughly described by Suter, et al.32 The experimental setup described above for tracking the resonant mode shift is used. An OFRR with RI sensitivity of about 7 nm/RIU was produced and used for these experiments. The OFRR surface was functionalized with 3APS and then DMA was used as an amine-amine crosslinker. The single-stranded oligonucleotide capture probe was synthesized with an amine functional group connected to the 5 end by a 6-carbon linker, and has a 25 base-pair sequence. ... 

Silyl linkers (Tab. 3.5) have successfully been used for the synthesis of natural products [96, 97], oligosaccharides [98], oligonucleotides [99] and in peptide synthesis [100]. 

---