Hybrid duplexes

If DNA from two different species are mixed, denatured, and allowed to cool slowly so that reannealing can occur, artificial hybrid duplexes may form, provided the DNA from one species is similar in nucleotide sequence to the DNA of the other. The degree of hybridization is a measure of the sequence similarity or relatedness between the two species. Depending on the conditions of the experiment, about 25% of the DNA from a human forms hybrids with mouse DNA, implying that some of the nucleotide sequences (genes) in humans are very similar to those in mice. Mixed RNA DNA hybrids can be created in vitro if single-stranded DNA is allowed to anneal with RNA copies of itself, such as those formed when genes are transcribed into mRNA molecules. 

Fig. 4 Flavin amino acids FI and F2 used for the preparation of DNA PNA hybrid duplexes. These duplexes possess the flavin in the PNA strand and the backbone opened dimer in the DNA strand. a Indicates unstructured melting. M.p.= melting points of the constructs...

Incorporation of an artificial flavin nucleobase and of a cyclobutane pyrimidine dimer building block into DNA DNA double strands, DNArPNA hybrid duplexes, and DNA-hairpins, provided compelling evidence that an excess electron can hop through DNA to initiate dimer repair even at a remote site. The maximum excess electron transfer distance realised so far in these defined Donor-DNA-Acceptor systems is 24 A. New experiments are now in progress to clarify whether even larger transfer distances can be achieved. 

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. 

This report was the first of its type to show the ability of such a large covalently linked carbohydrate (neomycin) to aid in RNA-DNA hybrid complex-ation. N-Neo-conjugate and a 7-base-long RNA sequence present in a-sarcin loop can form a stable hybrid duplex. The stability of a hybrid duplex with addition of one neomycin equivalent is comparable to the stability of a hybrid duplex where the DNA has a covalent bond to neomycin. The presence of a single mismatch decreases the melting temperature of both neomycin-conjugated... 

Denatured single-stranded DNAs from two species can form a hybrid duplex, the degree of hybridization depending on the extent of sequence similarity. Hybridization is the basis for important techniques used to study and isolate specific genes and RNAs. 

RNA-DNA double helix, estimated to be 8 bp long (Fig. 26-la). The RNA in this hybrid duplex peels off shortly after its formation, and the DNA duplex re-forms. 

Local variations in the sequence of nucleotides affect the conformation of a DNA molecule and it is clear that the helix is not uniformly coiled throughout the entire length.80 103,124 129 134 While most helix segments probably have a right-handed twist others may be left-handed. Most DNA is probably in the B form but there are segments in the A form. These may arise from formation of hybrid duplexes with RNA, which assume the A conformation and are also favored by certain base sequences. Rules for predicting the DNA conformation from the nucleotide sequence have been proposed.116135 In the simplest case135 we consider each pair of adjacent nucleotides in the double helix. 

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... 

As the polymerase traverses the DNA, it must continually cause a melting or strand separation of the DNA so that a single DNA template strand is available at the active site of the enzyme. During elongation, one base pair re-forms behind the active site for every base pair opened in front of it. The short transient RNA-DNA hybrid duplex that forms between the newly synthesized RNA and the unpaired region of the DNA helps to hold the RNA to the elongating complex. 

What happens if two nucleic acids are partly complementary and partly different In this case, some stretches of the two strands may form base pairs while others don t. The two molecules can be manipulated so that they form a hybrid or separate. The conditions favoring the formation of duplex nucleic acid are low temperature (below the Tm), high salt, and the absence of organic solvents. The latter two conditions raise the Tm of the hybrid duplex so that the DNA would remain more double-stranded. On the other hand, higher temperatures (closer to the Tm of the hybrid) lower salt, and the presence of organic solvents would tend to push the two strands of the DNA apart. 

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