A Portal for Three-dimensional Structural Information about Nucleic Acids
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An Introduction to Nucleic Acids: DNA

Deoxyribonucleic acid (DNA) is the basic hereditary material found in the nucleus of most cells. This genetic information is passed on from one generation to the next and is required for protein synthesis. This important life information is packaged in the nucleus in a highly structured and organised manner. DNA is tightly wrapped around proteins called histones and this complex structure is the nucleosome. Nucleosomes are the structural and functional units of a chromatin. These are then folded and looped over other proteins and this chromatin is further compressed into the chromatid of a chromosome.

DNA is a linear polymer that is made up of nucleotide units. The nucleotide unit consists of a base, a deoxyribose sugar, and a phosphate. There are four types of bases: adenine (A), thymine (T), guanine (G), and cytosine (C). Each base is connected to a sugar via a ß glycosyl linkage. The nucleotide units are connected via the O3' and O5' atoms forming phosphodiester linkages.In normal DNA, the bases form pairs: A to T and G to C. This is called complementarity. A duplex of DNA is formed by two complementary chains that are arranged in an anti-parallel manner.


NDB ID: BD0002
Throughtout the site, in all DNA nucleotide block models, adenine is red, thymine is blue, cytosine is yellow, guanine is green.

DNA can have several conformations. The most common one is called B-DNA. B-DNA is a right-handed double helix with a wide and narrow groove. The bases are perpendicular to the helix axis. DNA can also be found in the A form in which the major groove is very deep and the minor groove is quite shallow. A-DNA is also a right-handed double helix. A very unusual form of DNA is the left-handed Z-DNA. In this DNA, the basic building block consists of two nucleotides, each with different conformations. Z-DNA forms excellent crystals.

 


An Introduction to Nucleic Acids: RNA

Ribonucleic acid (RNA) is present in several forms - messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). Each of these RNA forms is involved in different steps of protein synthesis. mRNA is generated from DNA and is the template for protein synthesis. tRNA is critical to the translation of the mRNA sequence into protein sequence. rRNA are components of the ribosomes which are the sites of protein synthesis.

The mRNA once produced, comes out of the nucleus and meets with the ribosome. The smaller and bigger subunits of the robosome locks on to the mRNA and reads the information from the mRNA. The ribosomes pick the appropriate t-RNA which has brought the corresponding aminoacid to the three letter code found on the mRNA to make the protein. This last step is repeated until the stop codon is reached and the protein synthesis is completed.

RNA is a polymer that contains ribose sugar instead of the deoxyribose sugars found in DNA.

The normal base composition is adenine, uracil, guanine, and cytosine.

NDB ID: AR0003 Throughtout the site, in all RNA nucleotide block models, adenine is red, cytosine is yellow, guanine is green, and uracil is cyan.

RNA can form double stranded duplexes. These duplexes are in the A conformation because the 2'OH precludes the B conformation. More commonly, RNA is single stranded and can form complexes and unusual shapes. One example is tRNA which contains about 70 bases that are folded such that there are base paired stems and open loops. The completely folded tRNA is L shaped. Another very interesting type of RNA is called a ribozyme, which is an RNA that has a catalytic activity.