Double-stranded complexes

Fig. 11 a,b Schematic representation for the formation of PEO-PEI-dexy-CD networks, a A supramolecular network is formed via the double-strand complex between y-CD and double strands of the PEO-PEI chains. The double-strand complexes are either of the parallel or antiparallel type, b a-CD and y-CD include single and double strands of PEI, respectively. Stoichiometric ratios of a-CD or y-CD to the repeating unit of PEI are 1 2 and 1 4, respectively [84]... 

Fig. 12 a-c Proposed structures of supramolecular networks under different conditions, a PEO-PEI-dex-y-CD network is formed with a full double-strand complex at pH 10. b The Ml doublestand complex of PEO-PEI-dex-y-CD network is transformed to a partial double-stand complex at pH 4 owing to protonation of the PEI chains, c PEO-PEI-dex-a-CD networks do not form any double-strand complex at pH 10 [84]... 

Several unique properties of the nucleic acids (e.g., absorpdon of UV light at specific wavelengths and their tendency to reversibly form double-stranded complexes) are exploited in nucleic acid research. Several applications of these properties are briefly discussed. 

DNA arrays, like more traditional hybridization techniques such as Southern and Northern blotting, make use of the fact that single-stranded nucleic acid species (DNA and RNA) that possess sequences complementary to each other will hybridize together with exquisite specificity to form double-stranded complexes. In the traditional approaches, the samples to be analyzed are distributed according to size by gel electrophoresis, transferred to and immobilized on solid membrane supports, and probed with specific, labeled complementary nucleic acid sequences. 

To probe the photophysical properties of the double-stranded complexes, the corresponding zinc derivatives were also made. The assembly technique allows the production of freebase and zinc derivatives within the one com-... 

Nucleic acid hybridization tests are based on the ability of complementary nucleic acid strands to specifically align and associate to form stable double-stranded complexes (1). The Gen-Probe PACE 2 system uses an acridinium labeled, single-stranded DNA probe that is complementary to the ribosomal RNA of N. gonorrhoeae. After the ribosomal RNA is released from the test organism, the labeled... 

The preferential initiation site on the "minus" strand might result from a particular sequence at the 3 eud of the complementary RNA, or the conformation of the double-stranded complex so formed may be such that the 3 end of the "minus" strand becomes the only possible initiation site (Figure 4> C an D). 

In each section double stranded complexes are shown first, followed by triple stranded complexes. Strands 1 and 2 are considered to be Watson-Crick hydrogenbonded and thus anti-parallel, except otherwise indicated. In the triple-strand case the Hoogsteen bound strand is strand 3 and thus parallel to strand 1. In the homopolymer complexes the strands are generally parallel. 

Several additional results have arisen from these studies. Polynucleotides can not only form Watson-Crick helical double-stranded complexes but may also form helical structures between themselves which can have more than two strands, as well as non-Watson-Crick base pairs, like the complex poly(l) poly(A)-poly(l). Furthermore, numerous polymers of base and sugar analogues have been prepared and studied. 

In contrast, immunochemical techniques which have already shown a sensitivity sufficient to distinguish single from double-stranded complexes and two-stranded hehces from triple-stranded complexes may be extremely useful in such studies. Indeed, recent work using spontaneous antibodies such as those found in systemic lupus erythematosus (SLE) sera, as well as experimentally induced antibodies, has demonstrated immunochemical differences between different double-stranded hehcal complexes and it is clear that development of this approach will be extremely fruitful. 

In aqueous solution the two homopolynucleotides poly I and poly C readily associate to give a double hehcal complex poly I poly C (Davies and Rich, 1958). The stoichiometry of this complex has been estabUshed by a variety of techniques and at pH 7 only the double-stranded complex is obtained. No triple-stranded structure has been demonstrated under these conditions. The stabihty of the complex is a function of salt concentration and in 0.15 MNa+, pH 7.0, the temperature of dissociation of the two strands is about 60°. The complex is a right-handed hehx and appears to have a geometry similar to that of the A form of RNA. 

In fact, all of the heterologous double-stranded complexes which have been tested react to different extents with anti-poly A poly U antibodies. Among these complexes, poly rG poly rC precipitates the smallest amount of antibodies and the reactivity differs not only from that of poly rl poly rC but also from that of the equivalent double-helical polydeoxyribonucleotide complex containing guanine and cytosine residues, poly dG - poly dC (Fig. 5). Thus the homologous antigen precipitates 219.7 [xg/ml of antibodies (expressed as N), poly rl poly rC precipitates almost the same amount, 209.5 (J-g/ml, and poly rG poly rC precipitates only 20.3 [xg/ml, whereas poly dG poly dC shows an intermediate reactivity and precipitates 77.8 (xg/ml of antibodies of the same anti-poly A poly U serum. 

Apparently this difference in reactivity of the various double-stranded complexes can be assigned to differences in their stereochemical structure orientation and distance of the bases in the interior of the double-helix, inclination of base pairs to the helix axis, and relative sizes of the large and small grooves, all of which characters can modify the external geometry of the polyribose phosphate chains. 

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