Oligomer, single-stranded

Lee et al. [60] investigated the adhesion of a single pair of DNA strands. They identified two types of forces interchain forces associated with Watson-Crick base pairing between complementary strands, and intrachain forces associated with the elasticity of single strands. For studying interchain interactions, complementary oligomers (ACTG)s and... 

Single stranded oligomers exhibit a completely different behavior than double strands. As shown in Fig. 6, the increase of the number n of thymine bases in the bridge between the electron donor guanine and the enol ether radical cation as electron acceptor influence the rate of the electron transfer only slightly. This can be explained by the flexibility of the single strand, which levels out the distance between donor and acceptor [13]. 

The complementary strands are mixed in 1 1 ratio and annealed by heating to 80 C followed by slow cooling (Protocol 15.2). The annealed double-stranded oligomer can be further purified by ion-exchange chromatography (Protocol 15.3) to remove single strands. Protocols 15.1 and 15.3 are modified from the methods described by Aggarwal (1990) and Joachimiak et al. (1987). 

This section examines the synthesis of nucleosides that contain seven-membered sugar analogues in place of the deoxyribose component. Nucleosides from the last group have been further incorporated into ONs via solid-phase DNA synthesis. A physical and biochemical investigation of the oligomers thus prepared continues in the next section. The study under review culminated in the assessment of the ability of the oligomers to complex with single-stranded RNA and for the heteroduplexes so formed to serve as substrates of RNAseH. 

Oxepanyl oligomers oA15 and oA15 were also evaluated for their ability to hybridize with single-stranded deoxyribosyl or ribosyl oligomers. Binding studies,... 

Hjerde, T., Smidsrad, O., Christensen, B.E. (1998b). Acid hydrolysis of k- and i-carra-geenan in the disordered and ordered conformations characterization of partially hydrolyzed samples and single-stranded oligomers released from the ordered structures. Macromolecules, 31, 1842-1851. 

An elegant study of the kinetics has been performed on single-stranded biosynthetic polymers (58), prepared by the method of Bollum et al. (59). Three polymers were used (1) d([3H]pA)B(pA)r2e, (2) d([3H]pA)5(pA)uo ([2- C]pA) - and (3) d([3H]PT)t(PA)in. The digestion was carried out in the presence of Mg2+ and allowed to proceed in a pH stat until 10% of internucleotide bonds were hydrolyzed. The reaction was stopped by heating on a steam bath. The size of the products in the digestion mixture was determined by means of chromatography on a column of Bio-Gel P-60 previously calibrated with oligomers. 

In an attempt to design a protocell, a Los Alamos group proposed a system essentially composed of non-enzymatic template replication coupled to micelle growth [55,56]. The micelle aggregate is assumed to incorporate from the medium precursors of lipids and template building blocks (monomers or oligomers). The authors assume that for this particular construct PNAs [57] would serve better because of their hydrophobic nature. It is assumed that single-stranded molecules face the hydrophilic anterior whereas double-stranded molecules immerse into the hydrophobic interior of the micelles. Alternation between these two states is assumed to facilitate replication. 

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