Oligo ureas

Intramolecular hydrogen bonds were also incorporated into aromatic oligo-(ureas) [73]. For example, NMR studies showed that tetramer 20 adopted a crescent conformation. Cyclic tetramer 21 was prepared in high yield... 

The deprotected oligonucleotide synthetic product is precipitated twice in ethanol, and a 0.5 fig/fd solution in water is prepared (concentration is measured from a UV absorption spectrum). One microliter of the oligo-deoxynucleotide solution is mixed with 2 fd of 10X PL, 5 fd of [y-32P]ATP (or [y-35S]ATP), 1 fd of T4 polynucleotide kinase, and 11 fd water. After incubation at 37 ° (for 45 min with [y-32P]ATP or for 2 hr with [y-35S]ATP), the reaction is stopped by the addition of 150 [A of 5 M ammonium acetate, pH 5.5, and 130 fd water and 10 fd of the yeast tRNA solution are added to the mixture before precipitation with 1 ml ethanol. After chilling at —70° for at least 15 min, the precipitate is collected by centrifugation (12,000 g, 15 min), redissolved, and submitted to two additional cycles of precipitation-redissolution. Finally, the precipitate is redissolved in 20 fd of gel loading mix and the mixture analyzed on a 8% acrylamide-7 Af urea slab gel in IX electrophoresis buffer, until the bromphenol blue has reached the middle of the gel. 

FIGURE 9.14 (a) Scheme of oligo-guanidinium 15. (b) Scheme of oligo-aromatic urea 16. (c) Top view of x-ray crystal structure of 16. (d) Side view. 

FIGURE 9.15 (a) Modified oligo-aromatic urea 17 and its x-ray crystal structure as triple helix with phosphate anion and nickel(II) cation, (b) Side view, (c) Bottom view. 

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