DNA/RNA hybrids duplex

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... 

CD and UV melting profiles in the presence of the ligands were carried ont to confirm the presence of a DNA-RNA hybrid duplex in the presence of the ligands. The addition of 2.2 tiM of neomycin and ethidium bromide results in a increase of 12°C, whereas the addition of 6 resnlts in a increase of 20°C. Increased concentration of 6 caused a gradual increase in the hybrid melting temperature. As the concentration of NM was increased from 0 p.M to 3 p.M, the melting temperature of the hybrid increases from 48.9°C to 70.1°C, a 21.2°C increase overall. 

Both DNA hybrids and DNA-RNA hybrid duplexes are very important to present day genetic research.560 562 Molecules of mRNA that represent transcripts of a particular gene will hybridize only with one of the two separated strands of DNA for that gene. 

DNA-RNA Hybrid Duplexes Suggest That RNA Carries the DNA Sequences... 

DNA-RNA hybrid duplexes are substrates for RNase H and reverse transcriptase. The crystal structure of a hybrid deoxy-polypyrimidine with polypurine RNA has been solved. The structure showed an A-form duplex, and the terminal base pair abuts the minor groove of another duplex creating a bend. RNase H is believed to interact through the minor groove but of an intermediate width between an A- and B-form duplex. The present structure did not exhibit an intermediate width of minor groove. A crystal structure of the chimeric ODN d(CCACTAGTG)rG shows that the presence of the 3 -ribonucleotide induces a... 

The difficulties arising from the first two problems can be treated reliably, but new experimental methods are needed for the last two. To deal effectively with conformational averaging, newer computational procedures are required. Approaches to these problems are described, and illustrated with an example of a DNA.RNA hybrid duplex. 

Lesnik, E.A. and Freier, S.M., Relative thermodynamic stability of DNA, RNA, and DNA RNA hybrid duplexes relationship with base composition and structure. Biochemistry, 34, 10807, 1995. 

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