November 2001 Molecule of the Month by David Goodsell
Keywords: double helix, base pairing, A-DNA, B-DNA, Z-DNA, oligonucleotides, DNA bending
Each of the cells in your body carries about 1.5 gigabytes of genetic information, an amount of information that would fill two CD ROMs or a small hard disk drive. Surprisingly, when placed in an appropriate egg cell, this amount of information is enough to build an entire living, breathing, thinking human being. Through the efforts of the international human genome sequencing projects, you can now read this information. Along with most of the biological research community, you can marvel at the complexity of this information and try to understand what it means. At the same time, you can wonder at the simplicity of this information when compared to the intricacy of the human body.
DNA is read-only memory, archived safely inside cells. Genetic information is stored in an orderly manner in strands of DNA. DNA is composed of a long linear strand of millions of nucleotides, and is most often found paired with a partner strand. These strands wrap around one another in the familiar double helix, as shown here. The code is quite easy to read: you simply step down the strand of DNA one nucleotide at a time and read off the bases: A, T, C or G. This is exactly what your cells do: they scan down a messenger RNA (copied from the DNA), and use ribosomes to build proteins based on the code that is read. This is also how researchers determine the sequence of a DNA strand: they clip off one nucleotide at a time to see what it is.
Your genetic information, inherited from your parents, is your most precious possession. It guided the construction of your body in the first nine months of your life and it continues to control all of the basic functions of living. Each of your cells is constantly using this information, asking questions about how to control blood sugar levels and body temperature, how to digest different foods and how to deal with new environmental challenges, and thousands of other important questions. The answers are held in the DNA. Hundreds of different proteins are built to interact with this information: to read it and use it to build new proteins, to copy it when the cell divides, to store and protect it when it is not actively being used, and to repair the information when it becomes corrupted by chemicals or radiation.
A Central Icon
DNA is arguably one of the most beautiful molecules in living cells. Its graceful helix is pleasing to the eye. DNA is also one of the most familiar molecules, the central icon of molecular biology, easily recognized by everyone. To some, it may carry a negative connotation, being a pervasive symbol for activists against genetically engineered produce. To others, it may bring to mind advances in forensics such as the DNA fingerprinting used in many recent high-profile trials. Some may have seen it in science fiction, modified to build dinosaurs or store cryptic messages from aliens. To all it is a pervasive symbol of our growing understanding of the human body and our close kinship with the rest of the biosphere, and the moral and ethical issues that must be addressed in the face of that knowledge.
DNA is perfect for the storage and readout of information. It is laden with information. Every surface and edge of the molecule carries information. The basic mechanism by which DNA stores and transmits genetic information was discovered in the 1950's by Watson and Crick. This basic information is stored in the way that the bases match one another on opposite sides of the double helix--adenine with thymine, guanine with cytosine--forming a set of complementary hydrogen bonds. These are shown in the diagram with red arrows.
Additional 'extragenetic' information is read from the surfaces that are left exposed in the double helix. In the major groove (the wider of the two grooves in the structure on the left), the different base pairs have a characteristic pattern of chemical groups that carry information, shown by green arrows in the close-up diagrams on the right. These include hydrogen bond donors (D) and acceptors (A) as well as a site with a large, bulky group in adenine-thymine base pairs (large asterisk) or a small group in guanine-cytosine base pairs (small asterisk). In the minor groove, there is a different arrangement of chemical groups that carry additional information, indicated with blue arrows in the diagram on the right and the blue letters in the structure on the left. As revealed in hundreds of structures in the PDB, this extragenetic information is used by proteins to read the genetic code in DNA without unwinding the double helix. It is also targeted by a number of toxins and drugs that attack DNA.
Variations on a Theme
DNA adopts the familiar smooth double helix, termed a B-helix, under the typical conditions found in living cells. An example is shown in the center, exemplified by the crystal structure in PDB entry 1bna, shown at the top superimposed over the idealized version of the B-helix. Under other conditions, however, DNA can form other structures, as revealed in two early crystal structures: PDB entries 1ana on the left and 2dcg on the right. The one on the left, with tipped bases and a deep major groove, is termed A-DNA. It is formed under dehydrating conditions. Also, RNA most often shows this form, because its extra hydroxyl group on the sugar gets in the way, making the B-form unstable (look, for instance, at the A-helical structure of transfer RNA shown in a previous Molecule of the Month). The form on the right, which winds in the opposite direction from A-DNA and B- DNA, is termed Z-DNA. It is found under high salt conditions and requires a special type of base sequence, with many alternating cytosine-guanine and guanine-cytosine base pairs.
Exploring the Structure
We often think of DNA as a perfect, smooth double helix. In reality, DNA has a lot of local structure. The small piece of DNA shown here, from PDB entry 1bna, shows some of the common variations. At the top, the helix is bent to the left, distorted by the way that the helices are packed into the crystal. At the bottom, two of the bases are strongly propeller twisted--they are not in one perfect plane. This improves the way that the bases stack on top of one another along each strand, stabilizing the whole double helix. As more and more structures of DNA are studied, it is becoming clear that DNA is a dynamic molecule, quite flexible on its own, which is bent, kinked, knotted and unknotted, unwound and rewound by the proteins that interact with it.
This illustration was created with RasMol. You can create similar illustrations by clicking on the PDB accession code above and then picking one of the options under View Structure.
To locate DNA structures in the PDB using the Advanced Search interface, in the "Contains Chain Type" section select DNA-YES and all others NO. A list of all DNA structures in the PDB as of November, 2001 is available here.
For information about DNA, click here.
Further information about DNA
Richard E. Dickerson (1983) The DNA Helix and How it is Read. Scientific American 249 (December), pp. 94-111.
Wolfram Saenger (1994) Principles of Nucleic Acid Structure (Springer-Verlag, New York).
The Nucleic Acid Database, http://ndbserver.rutgers.edu/
© 2015 David Goodsell & RCSB Protein Data Bank