Hybrid DNA

Figure 10.19 Heterodimerization of leucine zipper proteins can alter their DNA-binding specificity. Leucine zipper homodimers bind to symmetric DNA sequences, as shown In the left-hand and center drawings. These two proteins recognize different DNA sequences, as indicated by the red and blue regions in the DNA. The two different monomers can combine to form a heterodimer that recognizes a hybrid DNA sequence, composed of one red and one blue region.

Recombinant DNA (r-DNA) The hybrid DNA produeed by joining pieees of DNA from different organisms together in vitro (i.e., in an artifieial apparatus). 

Unmodified PNAs have been introduced to cells by microinjection [33], electroporation [60, 62, 76], co-transfection with partially hybridized DNA oligos [43, 61,... 

Bifunctional adamantyl, as a hydrophobic central core, can be used to construct peptidic scaffolding [151], as shown in Fig. 27. This is the reason why adamantane is considered one of the best MBBs. This may be considered an effective and practical strategy to substitute different amino acids or DNA segments on the adamantane core (Fig. 28). In other words, one may exploit nucleic acid (DNA or RNA) sequences as linkers and DNA hybridization (DNA probe) to attach to these modules with an adamantane core. Thus a DNA-adamantane-amino acid nanostructure may be produced. 

Similar techniques can be used to devise (strept)avidin-biotin assay systems for detection of nucleic acid hybridization. DNA probes labeled with biotin can be detected after they bind... 

Guo W, Yuan J, Dong Q, Wang E (2010) Highly sequence-dependent formation of fluorescent silver nanoclusters in hybridized DNA duplexes for single nucleotide mutation identification. J Am Chem Soc 132 932-934... 

In contrast to DNA, which is quite generally found in a double-stranded structure, RNA is generally, but not always, found in nature as a single-stranded molecule. There are, as always, exceptions, one of which we note below. Double-stranded RNAs as well as hybrid DNA RNA double-stranded molecules are found. 

Keywords DNA diagnostics Impedimetric detection DNA hybridization DNA immobilization... 

Ho HA, Bera-Aberem M, Leclerc M. Optical sensors based on hybrid DNA/conjugated polymer complexes. Chemistry 2005 11 1718-1724. 

Fig. 1.38. Formation of homo- and heterodimeric transcription factors and the specificy of DNA-binding. Shown are two different helrx-loop-helix proteins, which bind as homodimers (a, b) to the each of their cognate palindromic DNA elements (drawn as arrows). The two homodimers display different DNA-binding specificity. The heterodimerization (c) of the two proteins creates a complex that recognizes a hybrid DNA element.

If one then adds DNA polymerase and sufficient amounts of all four deoxyri-bonucleotide triphosphates to a solution containing the hybridized DNA, the DNA polymerase will bind to the duplex region and start to synthesize new DNA that is complementary in sequence to the single-stranded region. The DNA polymerase synthesizes new DNA by stepwise attachment of the 5 phosphate of an incoming... 

In this double-strand break repair model for recombination, the 3 ends are used to initiate the genetic exchange. Once paired with the complementary strand on the intact homolog, a region of hybrid DNA is created that contains complementary strands from two different parent DNAs (the product of step (2)in Fig. 25-31a). Each of the 3 ends can then act as a primer for DNA replication. The structures thus formed, Holliday intermediates (Fig. 25 31b), are a feature of homologous genetic recombination pathways in all organisms. 

Recombinant DNA A hybrid DNA composed of DNA strands from different organisms. 

These bound water molecules, in turn, can bond to associated protein and to other atoms of the complex loops found in RNA molecules. The 2 -OH groups also act as ligands for divalent metal ions in some tRNAs and in some RNA catalytic sites. Transient hybrid DNA-RNA double helices also exist within cells and they too usually have the overall shape of A-DNA.55/307 309 However, the minor groove is intermediate in width between that expected for the A and B forms. 

Prepare and insert the foreign DNA fragment into the vehicle. This produces a recombinant or hybrid DNA molecule. 

Introduce the hybrid DNA into a host organism (usually a bacterial cell), where it can be replicated. This process is called transformation. 

Develop a method for identifying and screening the host cells that have accepted and are replicating the hybrid DNA. 

Restriction endonucleases catalyze the hydrolysis of specific phosphodi-ester bonds in double-stranded DNA. These enzymes are often used to linearize a circular plasmid for hybrid DNA construction. They have also found use in the analysis of DNA and the construction of restriction maps. In this experiment, students will incubate various restriction enzymes with plasmid or viral DNA and analyze the product DNA fragments by agarose gel electrophoresis. 

Chemically modified DNAs can also be used as hybridization probes, provided that the modification does not interfere with the formation of hybrid DNA molecules. A psoralen biotin label has also been developed. Psoralen is a photoactivable agent that can intercalates into single- or double-stranded nucleic acids. On irradiation at 365 nm, it will covalently bind to the probes. This labeling reaction is simple and straightforward. However, the reagents for labeling and detection are only available in a kit format. 

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