RNA-DNA hybrid triplexes

RR duplexes and the derived triplexes. This could be a consequence of stable duplex structures which need more energy to become distorted to accommodate the third strand. The stability order of various RNA-DNA hybrid triplexes indicates that duplexes with DNA in the purine strand readily bind to either RNA or DNA to form triplexes. In contrast, a purine RNA duplex binds only RNA on a third strand. It was recently shown that RNA cannot be a part of a triplex with the R RY motif [92c]. These studies point to the fundamental role of sugars in controlling nucleic acid recognition through conformational switches. Since RNA-DNA hybrids are cellular targets for a number of... 

Figure 36 Relative stabilities of RNA-DNA hybrid triplexes in the Y RY motif,...

Complementary base pairs are joined by hydrogen bonds and are best represented by a centered dot dA-dT and dG-dC are the canonical pairings in double-stranded DNA, although alternate pairings, DNA-RNA hybrids, triplexes, and other variations may occur. 

The application of absorption and circular dichroism spectra to the study of nucleic acids is discussed by Gray et al. [3]. Examples of the advantages of circular dichroism spectra over absorption spectra in analysis of the stoichiometry and structure of DNA, RNA, and hybrid duplexes and triplexes are given. 

The CD spectra of three triplexes are given in Fig. 7A. Two interesting conclusions were drawn from the spectra. First, the CD spectrum of the DNA triplex was much different from those of the RNA triplex and the one hybrid triplex that could be formed under the conditions (see legend to Fig. 4). This was consistent with molecular mechanics calculations that showed that DNA helices with alternating C" - G-C and T-A-T base triples can have predominately C2 -endo sugars, except for cytidines in the third strand. Second, the CD spectra of the other two triplexes were similar and A-like, indicating that the conformation of the hybrid triplex was close to that of the RNA triplex. The hybrid triplex had a d(AG),2... 

Previous work has suggested that aminoglycoside specificity may occur in nucleic acid forms that display features characteristic of an A-type conformation (RNA triplex, DNA-RNA hybrid duplex,RNA duplex, DNA triplex, A-form DNA duplex, and DNA tetraplex ), rather than in naturally occurring RNA. However, conflicting results have been reported regarding the conformation of the triplex and of the Watson-Crick duplex within these triplexes. Both... 

Figure 2 Most common DNA/RNA binding modes. Left Strand invasion of homopyrimidine PNA into duplex DNA yields a PNA2-DNA triplex. Right Hybridization of mixed sequence PNA with complementary DNA or RNA produces Watson-Crick base-paired duplex structures.

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