Self complementary oligonucleotides

We have investigated the reactions of the COs " radicals with double-stranded DNA by laser flash photolysis techniques [15]. In these time-re-solved experiments, the COs radicals were generated by one-electron oxidation of HCOs by sulfate radical anions, SO4 the latter were derived from the photodissociation of persulfate anions, S20s initiated by 308-nm XeCl excimer laser pulse excitation. In air-equilibrated buffer solution containing the self-complementary oligonucleotide duplex d(AACGCGAATTCGCGTT), 208 , and an excess of HCO3., the decay of the CO3 radical anion absorption band at 600 nm is associated with the concomitant formation of the characteristic narrow absorption band of the G(-H) radicals near 310 nm. 

Similarly, the longer, but still self-complementary oligonucleotide d(CGCGAATTCGCG) has been observed to form a duplex via the dimerization/association reaction... 

Dynamic Processes. The binding of the Hoechst molecule to the self-complementary oligonucleotide duplexes in a 1 1 ratio lifts the dyad symmetry of the duplexes so that two sets of DNA resonances are observed. This indicates that the drug is in slow exchange between the free and the bound forms. Close examination of the 2D NOE data, however, reveals the presence of chemical-ex-... 

Applications of cyclised oligonucleotides are varied. They have been used to produce artificial human telomeres by rolling circle DNA synthesis/as inhibitors of viral replication in influenza virus and as structural motifs for quadruplex formation.A further form of cyclic oligonucleotide figures in a recently described method in which a self-complementary oligonucleotide, e.g., a hairpin structure, is denatured and allowed to re-anneal in the presence of circular DNA such as a plasmid (7). The effect is that the short oligonucleotide traps the plasmid in what has been termed a padlock. Such structures have been successfully used to inhibit transcription elongation reactions based on triple helix formation of the padlock structure. 

Fig. 29. LC/ESI-MS analysis of the oxidation of a short double-stranded oligonucleotide by Mn-TMPyP/KHSOs. ODN I stands for the self complementary oligonucleotide 5 -CAGCTG. The oxidation was carried out in 50 mM Tris/HCl buffer pH = 7, NaCl 100 mM with the following concentrations of reactants duplex ODN I, Mn-TMPyP, KHSO5, 200 pM, 200 pM, 2mM, respectively. The reaction lasted 5 min at 0°C. A HPLC trace B in-line ESI-MS spectrum of ODN I (retention time, 44.5 min).

The synthesis of oligonucleotide duplexes containing site specific disulphide linkages has been reported. Self complementary oligonucleotides were synthesised to present 6-thioinosine (188) and 4-thiothymidine (189) opposite one another upon duplex formation. The synthesis of the latter compounds has been described previously. 6-Thioinosine was protected for DNA synthesis with a 2-cyanoethyl group. Aerial oxidation afforded the disulphide. 

Figure 22. (Bio)mesogens approaching pre-life states (7 a, 17, 18, 43] a) von Kiedrowski s and Orgel s minimal models of replication on the basis of self-complementary oligonucleotide DNA and RNA systems [44a-d, f-h] b) distant nucleic acid strand-analogs as matrix reaction models [7a, 18, 19, 39f-i] c) Rebek s self-replicational and evolutionary nucleoside analog model [45] d) von Kiedrowski s self-replicational amidinium-carboxylate model, being suggestive of exponential growth kinetics [44 e] e) Lehn s...

Synthetic, self-complementary oligonucleotide with restriction site-s... 

What are the structural features of a hairpin A priori, a hairpin requires a self-complementary oligonucleotide to form the double-helical stem and a variable number of nucleotides to form the loop. The stability and dynamics of a hairpin thus depend on contributions from the stem as well as the loop. Thermodynamic studies have shown that four or five bases are optimal to form a loop in DNA as well as in RNA (102). Among all possible hairpin structures, a tetranucleotide loop or tetraloop is the predominant species in 16S and 23S rRNAs (103), transcription terminators (104), and the phage T4 genome (105). About 70% of these tetraloops have the consensus loop sequences UNCG or GNRA (where N is A, C, G, or U), while the closing base pairs tend to be C G or less preferably G C. 

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