Nucleic acid sequencing purine

Genetic code The sequence of triplets of the nucleic acid bases (purines and pyrimidines) that specifies the individual amino acids. 

The anticodon region consists of seven nucleotides, and it recognizes the three-letter codon in mRNA (Figure 38-2). The sequence read from the 3 to 5 direction in that anticodon loop consists of a variable base-modified purine-XYZ-pyrimidine-pyrimidine-5h Note that this direction of reading the anticodon is 3 " to 5 whereas the genetic code in Table 38—1 is read 5 to 3 since the codon and the anticodon loop of the mRNA and tRNA molecules, respectively, are antipar-allel in their complementarity just like all other inter-molecular interactions between nucleic acid strands. 

The formation of three-stranded nucleic acid complexes was first demonstrated over five decades ago [56] but the possible biological role of an extended triplex was expanded by the discovery of the H-DNA structure in natural DNA samples [57-59]. H-DNA is an intermolecular triplex that is generally of the pyrimidine-purine x pyrimidine type ( dot -Watson-Crick pairing and cross Hoogsteen base paring) and can be formed at mirror repeat sequences in supercoiled plasmids [59]. 

Very recently the trans- [Pt(NH3)2Cl2] isomer has been shown to promote the formation of some highly unusual multiple strand nucleic acid structures (28). A parallel-stranded DNA duplex, psPtDNA, has been prepared which incorporates a frarcs-Pt(NH3)2+ crosslink. The pla-tinated strands were synthesized through the series of reactions illustrated in Fig. 3. The initial mono-functional G N7 adduct is formed at pH 3.5 by addition of rans-[Pt(NH3)2(H20)Cl]+ to the pyrimidine-rich sequence 5 -d(T4CT4G). After the pH is increased, normal anti-parallel duplex formation occurs upon addition of the complementary purine-rich strand, 5 -d(A4GA4G). This intermediate anti-parallel stranded... 

Nucleic Acid. A nucleic acid is a natural polynucleotide. It is a sugar-phosphate chain with purine and pyrimidine bases attached to it, as shown in Chart 10. If the sugar is deoxyribose and the pyrimidine bases are cytosine and thymine, the nucleic acid is deoxyribonucleic acid, DNA if the sugar is ribose, and the pyrimidine bases are (mostly) cytosine and uracil, the nucleic acid is ribonucleic acid, RNA. The sequence of bases may appear arbitrary and random, but it constitutes a meaningful code (see Code Word). In double-stranded nucleic acids,... 

Interestingly, the emission of [Pt(tpy)(OH)]+ is quenched in water, but is restored upon intercalation with double-stranded nucleic acids [poly(dA-dT)]2 and [poly(dI-dC)]2 [73]. Although intercalation can also occur at G-C-rich sequences - and indeed it does so more strongly than for A-T - emission is then quenched by electron-transfer from guanine, the most readily oxidized of the nucleobases. The initial intercalative interactions are probably followed by covalent platination of the DNA, most likely by purine-N7 displacing the OH ligand, reminiscent of cisplatin. The absorption... 

As much of the terminology used in molecular biology may be unfamiliar to some readers, it is appropriate to define some of the vocabulary and this is given in an appendix to this chapter. There are two types of nucleic acids, the ribonucleic acids (RNA) and the deoxyribonucleic acids (DNA). Genetic information is carried in the linear sequence of nucleotides in DNA. Each molecule of DNA contains two complementary strands of deoxyribonucleotides which contain the purine bases, adenine and guanine and the pyrimidines, cytosine and thymine. RNA is single-stranded, being composed of a linear sequence of ribonucleotides the bases are the same as in DNA with the exception that thymine is replaced by the closely related base uracil. DNA replication occurs by the polymerisation of a new complementary strand on to each of the old strands. 

With a small adjustment to this procedure, using thiophosphoryl chloride (PSCI3) in place of phosphoryl chloride (POCI3), the nucleoside 5 -(l-thio)triphosphates can be easily synthesized.7 These compounds have been used extensively for applications inter alia for site-directed mutagenesis, sequencing of nucleic acids and investigation of enzyme mechanisms.16 Phosphorylation with thiophosphoryl chloride is generally slower than with phosphoryl chloride but still occurs at a reasonable rate for purine nucleosides. However, for pyrimidine nucleosides, it is necessary to add 2,4,6-collidine as a catalyst, which forms a reactive intermediate with the thiophosphoryl chloride in situ. 

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