INTRODUCTION TO NUCLEIC ACIDS

Nucleic acids are the main information-carrying molecules of the cell, and, by directing the process of protein synthesis, they determine the inherited characteristics of every living thing. Nucleic acids are the carriers of genetic information. The two main classes of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).

DNA is the master blueprint for life and constitutes the genetic material in all free-living organisms and most viruses. RNA is the genetic material of certain viruses, but it is also found in all living cells, where it plays an important role in certain processes such as the making of proteins.

NUCLEOTIDES

Nucleotides are the building blocks of nucleic acids: they are the monomers which, repeated many times, form the polymers DNA and RNA.  Each nucleotide consists of a nitrogen-containing aromatic base attached to a pentose (five-carbon) sugar, which is in turn attached to a phosphate group. Figure 1 shows the structure of the nucleotides making up nucleic acids.

Figure 1:  The chemical structure of nucleotides. A nucleotide comprises a five-carbon sugar molecule: deoxyribose in DNA (A) and ribose in RNA (B). The carbon atoms on the sugar molecule are numbered in red. Deoxyribose (A) is different from ribose (B) in that it lacks an –OH group at carbon 2’. The 5’-carbon atom is attached to a phosphate group (here a monophosphate in orange) and the 1’-carbon is attached to a base (blue).

The main difference between nucleotides from DNA and those from RNA is the nature of the sugar. Nucleotides making up RNA (Figure 1B) contain ribose, making them ribonucleotides. In DNA, however, the sugar lacks an -OH group at the 2’-carbon, making it deoxyribose and the corresponding nucleotides deoxyribonuleotides.

A nucleotide may contain more than one phosphate at its 5’-carbon, for instance the nucleotide adenosine triphosphate has three, as shown in Figure 2. When there is no phosphate group, the molecule is no longer called a nucleotide, but a nucleoside.

Figure 2

Bases in nucleic acids

Each nucleic acid contains four of five possible nitrogen-containing bases: adenine (A), guanine (G), cytosine (C), thymine (T), and uracil (U) [Figure 3].

A and G are categorized as purines, and C, T, and U are collectively called pyrimidines. All nucleic acids contain the bases A, C, and G; T, however, is found only in DNA, while U is found in RNA. The pentose sugar in DNA (2′-deoxyribose) differs from the sugar in RNA (ribose) by the absence of a hydroxyl group (-OH) on the 2′ carbon of the sugar ring. Without an attached phosphate group, the sugar attached to one of the bases is known as a nucleoside. The phosphate group connects successive sugar residues by bridging the 5′-hydroxyl group on one sugar to the 3′-hydroxyl group of the next sugar in the chain. These nucleoside linkages are called phosphodiester bonds and are the same in RNA and DNA.

Figure 3: Different bases of nucleic acid. The ‘R’ represents the deoxyribose covalently attached to the base to form the nucleoside named in the third row.

Deoxyribonucleic acid (DNA)

DNA is a polymer of the four nucleotides A, C, G, and T, which are joined through a backbone of alternating phosphate and deoxyribose sugar residues. These nitrogen-containing bases occur in complementary pairs as determined by their ability to form hydrogen bonds between them. A always pairs with T through two hydrogen bonds, and G always pairs with C through three hydrogen bonds. The spans of A:T and G:C hydrogen-bonded pairs are nearly identical, allowing them to bridge the sugar-phosphate chains uniformly. This structure, along with the molecule’s chemical stability, makes DNA the ideal genetic material. The bonding between complementary bases also provides a mechanism for the replication of DNA and the transmission of genetic information.

Chemical structure

In 1953 James D. Watson and Francis H.C. Crick proposed a three-dimensional structure for DNA based on low-resolution X-ray crystallographic data and on Erwin Chargaff’s observation that, in naturally occurring DNA, the amount of T equals the amount of A and the amount of G equals the amount of C. Watson and Crick, who shared a Nobel Prize in 1962 for their efforts, postulated that two strands of polynucleotides coil around each other, forming a double helix. The two strands, though identical, run in opposite directions as determined by the orientation of the 5′ to 3′ phosphodiester bond. The sugar-phosphate chains run along the outside of the helix, and the bases lie on the inside, where they are linked to complementary bases on the other strand through hydrogen bonds.

The initial proposal of the structure of DNA by James Watson and Francis Crick, which was accompanied by a suggestion on the means of replication.

Several structural variants of DNA are also known. The double helical structure of normal DNA takes a right-handed form called the B-helix. The helix makes one complete turn approximately every 10 base pairs. B-DNA has two principal grooves, a wide major groove and a narrow minor groove. Many proteins interact in the space of the major groove, where they make sequence-specific contacts with the bases. In addition, a few proteins are known to make contacts via the minor groove.

In A-DNA, which forms under conditions of high salt concentration and minimal water, the base pairs are tilted and displaced toward the minor groove. Left-handed Z-DNA forms most readily in strands that contain sequences with alternating purines and pyrimidines. DNA can form triple helices when two strands containing runs of pyrimidines interact with a third strand containing a run of purines.

Ribonucleic acid (RNA)

RNA is a single-stranded nucleic acid polymer of the four nucleotides A, C, G, and U joined through a backbone of alternating phosphate and ribose sugar residues. It is the first intermediate in converting the information from DNA into proteins essential for the working of a cell. Some RNAs also serve direct roles in cellular metabolism. RNA is made by copying the base sequence of a section of double-stranded DNA, called a gene, into a piece of single-stranded nucleic acid. This process, called transcription is catalyzed by an enzyme called RNA polymerase.

Chemical structure

Whereas DNA provides the genetic information for the cell and is inherently quite stable, RNA has many roles and is much more reactive chemically. RNA is sensitive to oxidizing agents such as periodate that lead to opening of the 3′-terminal ribose ring. The 2′-hydroxyl group on the ribose ring is a major cause of instability in RNA, because the presence of alkali leads to rapid cleavage of the phosphodiester bond linking ribose and phosphate groups. In general, this instability is not a significant problem for the cell, because RNA is constantly being synthesized and degraded.

Interactions between the nitrogen-containing bases differ in DNA and RNA. In DNA, which is usually double-stranded, the bases in one strand pair with complementary bases in a second DNA strand. In RNA, which is usually single-stranded, the bases pair with other bases within the same molecule, leading to complex three-dimensional structures. Single-stranded RNAs are flexible molecules that form a variety of structures through internal base pairing and additional non-base pair interactions. They can form hairpin loops such as those found in transfer RNA (tRNA), as well as longer-range interactions involving both the bases and the phosphate residues of two or more nucleotides. This leads to compact three-dimensional structures.

Types of RNA

Messenger RNA (mRNA)

Messenger RNA (mRNA) delivers the information encoded in one or more genes from the DNA to the ribosome, a specialized structure, or organelle, where that information is decoded into a protein. In prokaryotes, mRNAs contain an exact transcribed copy of the original DNA sequence with a terminal 5′-triphosphate group and a 3′-hydroxyl residue. In eukaryotes the mRNA molecules are more elaborate. The 5′-triphosphate residue is further esterified, forming a structure called a cap. At the 3′ ends, eukaryotic mRNAs typically contain long runs of adenosine residues (polyA) that are not encoded in the DNA but are added enzymatically after transcription. Eukaryotic mRNA molecules are usually composed of small segments of the original gene and are generated by a process of cleavage and rejoining from an original precursor RNA (pre-mRNA) molecule, which is an exact copy of the gene. In general, prokaryotic mRNAs are degraded very rapidly, whereas the cap structure and the polyA tail of eukaryotic mRNAs greatly enhance their stability.

Ribosomal RNA (rRNA)

Ribosomal RNA (rRNA) molecules are the structural components of the ribosome. The rRNAs form extensive secondary structures and play an active role in recognizing conserved portions of mRNAs and tRNAs. They also assist with the catalysis of protein synthesis.

Transfer RNA (tRNA)

Transfer RNA (tRNA) carries individual amino acids into the ribosome for assembly into the growing polypeptide chain. The tRNA molecules contain 70 to 80 nucleotides and fold into a characteristic cloverleaf structure. Specialized tRNAs exist for each of the 20 amino acids needed for protein synthesis, and in many cases more than one tRNA for each amino acid is present. The nucleotide sequence is converted into a protein sequence by translating each three-base sequence (called a codon) with a specific protein.