Polynucleotide specificity

Smith M, Rammler DH, Goldberg IH, Khorana HG. Studies on polynucleotides. Specific synthesis of the C3 -C5 interribonucleotide linkage. J Am Chem Soc 84 430-440, 1962. 

In 1953, James Watson and Francis Crick made their classic proposal for the secondary structure of DNA. According to the Watson-Crick model, DNA under physiological conditions consists of two polynucleotide strands, running in opposite directions and coiled around each other in a double helix like the handrails on a spiral staircase. The two strands are complementary rather than identical and are held together by hydrogen bonds between specific pairs of... 

Signal The end product observed when a specific sequence of DNA or RNA is detected by autoradiography or some other method. Hybridization with a complementary radioactive polynucleotide (eg, by Southern or Northern blotting) is commonly used to generate the signal. 

The process by which cells take up large molecules is called endocytosis. Some of these molecules (eg, polysaccharides, proteins, and polynucleotides), when hydrolyzed inside the cell, yield nutrients. Endocytosis provides a mechanism for regulating the content of certain membrane components, hormone receptors being a case in point. Endocytosis can be used to learn more about how cells function. DNA from one cell type can be used to transfect a different cell and alter the latter s function or phenotype. A specific gene is often employed in these experiments, and this provides a unique way to smdy and analyze the regulation of that gene. DNA transfection depends upon endocytosis endocy-... 

The nature of the target to be attacked by any drug obviously depends on the specific application. Many cytotoxic metal complexes target DNA because of its importance in replication and cell viability. Coordination compounds offer many binding modes to polynucleotides, including outer-sphere noncovalent binding, metal coordination to nucleobase and phosphate backbone... 

Base Specificity of Physical Binding. To determine whether the physical binding of hydrocarbon metabolites to DNA exhibits base specificity, the binding of trans-7,8-dihydroxy-7,8,9,10-tetrahy-dro-BP was examined using fluorescence and absorption techniques (9). A comparison was also made of the varying degrees to which different synthetic polynucleotides are able to solubilize BPT... 

In this method the single-stranded DNA fragment to be sequenced is end-labelled by treatment with alkaline phosphatase to remove the 5 phosphate, followed by reaction with 32P-labelled ATP in the presence of polynucleotide kinase, which attaches 32P to the 5 terminal. The labelled DNA fragment is then divided into four aliquots, each of which is treated with a reagent which modifies a specific base as follows. 

Separation and Quantitation.—The specific radioactivity of [y-32P]ATP of very high activity (up to 240 Ci per millimole) may be measured by using it to phosphorylate [dT(pT)10] quantitatively, using polynucleotide kinase, isolating the labelled undecanucleotide, and measuring its activity.170 Isotope dilution is used to confirm the values. An alternative method of measuring specific radioactivities of ribo-nucleoside triphosphates utilizes a 3H-labelled nucleoside triphosphate (e.g. UTP) of unknown specific activity, a 14C-labelled nucleoside (e.g. ATP), a suitable primer in... 

All organisms synthesize carbohydrates, lipids, proteins, and polynucleotides, although the details of their molecular structures can be somewhat species specific. These basic classes of macromolecules have changed little over geologic time. The secondary metabolites are more species specific and have also changed little over geologic time. Many are resistant to degradation, and those provide excellent biomarkers that have been preserved in ancient marine sediments and petroleum deposits. 

Transfer RNAs are small, single-stranded polynucleotides (70-90 bases long). The tRNA molecule is linked to its specific amino acid in a reaction that is catalysed by the enzyme tRNA-aminoacyl synthetase. It occurs in two stages ... 

In addition to the enzymes that catalyse the formation of nucleotides and polynucleotides, a large number of catabolic systems exist which operate at all levels of the internucleotide pathways. The ribonucleases and deoxyribonucleases that degrade polynucleotides are probably not significantly involved in purine analogue metabolism, but the enzymes which dephosphorylate nucleoside 5 -monophosphates are known to attack analogue nucleotides and may be of some importance to their in vivo activity. Phosphatases of low specificity are abundant in many tissues [38], particularly the intestine [29]. Purified mammalian 5-nucleotidases hydrolyse only the nucleoside 5 monophosphates [28] and... 

A tRNA molecule is specific for a particular amino acid, though there may be several different forms for each amino acid. Although relatively small, the polynucleotide chain may show several loops or arms because of base pairing along the chain. One arm always ends in the sequence cytosine-cytosine-adenosine. The 3 -hydroxyl of this terminal adenosine unit is used to attach the amino acid via an ester linkage. However, it is now a section of the nucleotide sequence that identifies the tRNA-amino acid combination, and not the amino acid itself. A loop in the RNA molecule contains a specific sequence of bases, termed an anticodon, and this sequence allows the tRNA to bind to a complementary sequence of bases, a codon, on mRNA. The synthesis of a protein from the message carried in mRNA is called translation, and a simplified representation of the process as characterized in the bacterium Escherichia coli is shown below. 

Any enzyme that catalyzes breakage of a phosphodiester linkage at one or the other end of a polynucleotide chain, resulting in the release of single nucleotides or small oligonucleotides. See specific exonuclease... 

The techniques called mobility shift or gel shift assay can be considered a first step in this direction. These are widely used in molecular biology to detect interactions between regulatory proteins for gene expression and specific sequences of polynucleotides (21-23). 

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