Basic Chemical Structure

Content of Nucleic Acid Synthesis
» Nucleic Acids
» Structure and Function of Nucleic Acids
    » Basic Chemical Structure
    » Base Pairing in Nucleic Acids: Double Helical Structure of Dna
    » Size, Structure, Organization, and Complexity of Genomes
    » Information Storage, Processing, and Transfer
    » Chromosomal Dna Compaction and Its Implications in Replication and Transcription
    » DNA Sequence and Chromosome Organization
    » Repetitive Sequences: Selfish DNA
    » Chromatin Remodeling and Histone Acetylation
» Nucleic Acid Syntheses
    » Similarity of DNA and RNA Synthesis
    » DNA Replication Vs Transcription: Enzymatic Processes
    » Multiplicity of DNA and RNA Polymerases
» DNA Replication and Its Regulation
    » DNA Replication
    » Regulation of DNA Replication
    » Regulation of Bacterial DNA Replication at the Level of Initiation
    » DNA Chain Elongation and Termination in Prokaryotes
    » General Features of Eukaryotic DNA Replication
    » Licensing of Eukaryotic Genome Replication
    » Fidelity of DNA Replication
    » Replication of Telomeres—The End Game
    » Telomere Shortening: Linkage Between Telomere Length and Limited Life Span
» Maintenance of Genome Integrity
» DNA Manipulations and their Applications
» Transcriptional Processes
    » Recognition of Prokaryotic Promoters and Role of S-Factors
    » Regulation of Transcription in Bacteria
    » Eukaryotic Transcription
    » RNA Splicing in Metazoans
    » Regulation of Transcription in Eukaryotes
    » Fidelity of Transcription (RNA Editing)
» Chemical Synthesis of Nucleic Acids (Oligonucleotides)
» Bibliography of Nucleic Acid Synthesis
The basic information for all activities in living systems, at least on our planet, is stored ultimately in nucleic acids, namely, deoxyribonucleic (DNA) and ribonucleic (RNA) acids. Except for certain viruses, DNA is the universal genetic material (Fig. 1). The chemical structures of basic units of RNA and DNA have been elucidated, and both types of nucleic acids are linear polymers of monomeric units called nucleotides. A nucleotide consists of a purine or pyrimidine base linked to C´-1 of a pentose (furanose) via an NC glycosyl bond and contains a phosphate residue attached to the sugar via an ester bond with a CH2OH group at the 5´ position. The linear polymer in both RNA and DNA is generated by a C´-3 ester linkage of 5´ nucleotides generating a 3´-5´ phosphodiester linkage (Fig. 1B).

There are several differences in the chemical structures of DNA and RNA. First is the nature of the pentose ring in these macromolecules, i.e., ribofuranose for RNA and 2-deoxyribofuranose for DNA (Fig. 1A). Because of the presence of deoxyribose in DNA, the monomeric unit is called a deoxyribonucleotide or simply a deoxynucleotide, while the RNA monomer unit is called a ribonucleotide. The term “nucleotide” is used generically for both RNA and DNA units. The absence of a 2-OH group in DNA prevents alkali-mediated cleavage of the 3´-5´ phosphodiester cleavage observed in RNA and thus makes DNA more resistant to hydrolysis. Both RNA and DNA contain two types of purines, adenine (A) and guanine (G), and two types of pyrimidine bases (Fig. 1C). The second key difference between RNA and DNA is that while cytosine (C) is present in both RNA and DNA, RNA normally contains uracil (U), while DNA contains 5-methyluracil, called thymine (T), as the other pyrimidine base. The difference in chemical structure is reflected in the intrinsic chemical stability of these nucleic acids. The purine Nglycosyl bond in DNA is more unstable than in RNA, and as a result, purines are released much more easily from DNA by acid catalysis. Furthermore, cytosine deamination to produce U also occurs at a finite rate in DNA. Various processes have evolved to maintain the genomic integrity, as discussed later.

Finally, two other critical differences betweenDNAand RNA are in the length and structure of the polymer chains. DNA polymers, as elaborated later, usually exist as a helix consisting of two intertwining chains, while RNA is present mostly as a single chain. Furthermore, DNA could contain up to several billion deoxynucleotide monomeric units in the genomes of higher organisms, although the genomes of smaller self-replicating units such as viruses contain only a few thousand deoxynucleotides. In contrast, RNA chains are never more than a few thousand nucleotides long.