Nucleic acid hybridization renaturation

Before cloning and routine sequence analysis, DNA renaturation provided the only method for comparing nucleic acid sequences. Naturally, for a time, the importance of this approach decreased as the newer methods became routine. However, the availability of oligonucleotides for use as hybridization probes and PCR primers has reinvigorated the usefulness of nucleic acid hybridization as a complement to DNA sequence analysis. 

With the advent of nucleic acid hybridization as a pivotal technique in recombinant DNA technology, the theoretical and practical aspects of nucleic acid denaturation—renaturation have received renewed, more rigorous attention (11). How does a smaU piece of DNA (or RNA) find its complementary sequence from among often astronomical numbers of similar sequences Finding a 1000 base stretch in the human genome would be like finding a needle in a 2-ton haystack. 

The manufacture and processing of the protein microarray should be conducted in such a manner that the arrayed proteins remain in their native and active state. For most proteins, this usually means the hydrated state in order to avoid surface denaturation. For antibody arrays which are perhaps more forgiving than other proteins, it has been our experience that while these could be stored cold and dry, it is most important to rehydrate them prior to use. This process is in sharp contrast to the preparation of nucleic acid arrays in which strand melting or denaturahon is necessary to achieve optimal binding to the solid support. While the hybridization process is well understood and can be controlled under thermodynamic principles, the folding and renaturation of proteins on planar (microarray) surfaces is under study. 

Double-stranded DNA denatures into single strands as the temperature rises but renatures into a double-stranded structure as the temperature falls. Any two single-stranded nucleic acid molecules can form double-stranded structures (hybridize) provided that they have sufficient complementary nucleotide sequence to make the resulting hybrid stable under the reaction conditions. 

Hybridization can occur between complementary strands of nucleic acids derived from different sources. The double stranded nucleic acid that forms is a heteroduplex and the extent of heteroduplexes indicates homology between the two nucleic acid sources. For example, humans and mice mix with a very small fraction of the DNA renaturing but humans and chimpanzees give greater than 98% homology. DNA and RNA can also hybridize with one another to form heteroduplexes. 

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