Nucleic acid sequencing short forms

A selective method of preventing the expression of adhesion molecules or cytokines is the use of antisense oligonucleotides. These oligonucleotides are short sequences of nucleic acids complementary to mRNA sequences of specific proteins of interest. If delivered to the cytoplasmic compartment of cells these oligonucleotides are able to form a complex with their target mRNA. In this way the translation of mRNA into protein by ribosomes is inhibited. The subsequent mRNA degradation by RNAse H results in reduced expression of the protein (see also Chapter 5 for a description of antisense ohgonucleotides as therapeutic modalities). 

The principle that sequences of monomeric subunits are rich in information emerges most fully in the discussion of nucleic acids (Chapter 8). However, proteins and some short polymers of sugars (oligosaccharides) are also information-rich molecules. The amino acid sequence is a form of information that directs the folding of the protein into its unique three-dimensional structure, and ultimately determines the function of the protein. Some oligosaccharides also have unique sequences and three-dimensional structures that are recognized by other macromolecules. 

The Z-DNA form is adopted by short oligonucleotides that have sequences of alternating pyrimidines and purines. High salt concentrations are required to reduce electrostatic repulsion between the backbone phosphates, which are closer to one another than in A- and B-DNA, Under physiological conditions, most DNA is in the B form. Nonetheless, protein domains have been discovered that bind nucleic acids specifically in the Z-form, This observation strongly suggests that such structures are present in cells and perform specific functions. The properties of A-, B-, and Z-DNA are compared in Table 28.1. 

Extraction of DNA from biological samples can be accomplished by precipitation or affinity methods [15]. Amplification of the amount of DNA is also needed before any sequence detection can be done. This can be done by a method known as polymerase chain reaction or PCR in short. This process is depicted in Figure 8.6. Briefly, original double stranded DNA molecules, shown as black rectangles, are heated to more than 90°C for separation. Afterward, DNA primers, shown as squares, as well as nucleic acids are added to the solution to initiate the DNA synthesis, forming two pairs of double stranded DNA at the end of the first cycle. The process is repeated for more than 30 times, doubling the amount of DNA at each step [16]. RNA can also be amplified using a similar process known as reverse transcription-polymerase chain reaction (RT-PCR) [17]. 

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