DNA Base Pairing Principle

The Base Pairing Principle is: Complementary base pairs are: adenine and thymine (A - T )
guanine and cytosine (G - C)

The base pairing is called complementary because there are specific geometry requirements in the formation of hydrogen bonds between the heterocylic amines. Heterocyclic amine base pairing is an application of the hydrogen bonding principle. In the structures for the complementary base pairs given in the graphic on the left, notice that the thymine - adenine pair interacts through two hydrogen bonds represented as (T=A) and that the cytosine-guanine pair interacts through three hydrogen bonds represented as (C=G).

Although other base pairing-hydrogen bonding combinations may be possible, they are not utilized because the bond distances do not correspond to those given by the base pairs already cited. The diameter of the helix is 20 Angstroms.

http://www.elmhurst.edu/%7Echm/vchembook/582dnadoublehelix.html

DNA Quadruplex structures

Structure of a DNA quadruplex formed by telomere repeats. The conformation of the DNA backbone diverges significantly from the typical helical structure^[31]

Quadruplex structures

Further information: G-quadruplex

At the ends of the linear chromosomes are specialized regions of DNA called telomeres. The main function of these regions is to allow the cell to replicate chromosome ends using the enzyme telomerase, as the enzymes that normally replicate DNA cannot copy the extreme 3′ ends of chromosomes.^[32] These specialized chromosome caps also help protect the DNA ends, and stop the DNA repair systems in the cell from treating them as damage to be corrected.^[33] In human cells, telomeres are usually lengths of single-stranded DNA containing several thousand repeats of a simple TTAGGG sequence.^[34]

These guanine-rich sequences may stabilize chromosome ends by forming structures of stacked sets of four-base units, rather than the usual base pairs found in other DNA molecules. Here, four guanine bases form a flat plate and these flat four-base units then stack on top of each other, to form a stable G-quadruplex structure.^[35] These structures are stabilized by hydrogen bonding between the edges of the bases and chelation of a metal ion in the centre of each four-base unit.^[36] Other structures can also be formed, with the central set of four bases coming from either a single strand folded around the bases, or several different parallel strands, each contributing one base to the central structure.

In addition to these stacked structures, telomeres also form large loop structures called telomere loops, or T-loops. Here, the single-stranded DNA curls around in a long circle stabilized by telomere-binding proteins.^[37] At the very end of the T-loop, the single-stranded telomere DNA is held onto a region of double-stranded DNA by the telomere strand disrupting the double-helical DNA and base pairing to one of the two strands. This triple-stranded structure is called a displacement loop or D-loop.^[35]

http://en.wikipedia.org/wiki/DNA

DNA - Double Helix

The secondary structure of DNA is actually very similar to the secondary structure of proteins. The protein single alpha helix structure held together by hydrogen bonds was discovered with the aid of X-ray diffraction studies. The X-ray diffraction patterns for DNA show somewhat similar patterns.

In addition, chemical studies by E. Chargaff indicate several important clues about the structure of DNA. In the DNA of all organisms:
a) The concentration of adenine equals that of thymine.
b) The concentration of guanine equals that of cytosine.

Chargaff's findings clearly indicate that some type of heterocyclic amine base pairing exists in the DNA structure. X-ray diffraction data shows that a repeating helical pattern occurs every 34 Angstrom units with 10 subunits per turn. Each subunit occupies 3.4 Angstrom units which is the same amount of space occupied by a single nucleotide unit. Using Chargaff's information and the X-ray data in conjunction with building actual molecular models, Watson and Crick developed the double helix as a model for DNA.

The double helix in DNA consists of two right-handed polynucleotide chains that are coiled about the same axis. The heterocyclic amine bases project inward toward the center so that the base of one strand interacts or pairs with a base of the other strand. According to the chemical and X-ray data and model building exercises, only specific heterocyclic amine bases may be paired.

http://www.elmhurst.edu/~chm/vchembook/582dnadoublehelix.html

Alternative double-helical structures

Further information: Mechanical properties of DNA

DNA exists in many possible conformations.^[8] However, only A-DNA, B-DNA, and Z-DNA have been observed in organisms. Which conformation DNA adopts depends on the sequence of the DNA, the amount and direction of supercoiling, chemical modifications of the bases and also solution conditions, such as the concentration of metal ions and polyamines.^[25] Of these three conformations, the "B" form described above is most common under the conditions found in cells.^[26] The two alternative double-helical forms of DNA differ in their geometry and dimensions.

The A form is a wider right-handed spiral, with a shallow, wide minor groove and a narrower, deeper major groove. The A form occurs under non-physiological conditions in dehydrated samples of DNA, while in the cell it may be produced in hybrid pairings of DNA and RNA strands, as well as in enzyme-DNA complexes.^[27][28] Segments of DNA where the bases have been chemically-modified by methylation may undergo a larger change in conformation and adopt the Z form. Here, the strands turn about the helical axis in a left-handed spiral, the opposite of the more common B form.^[29] These unusual structures can be recognized by specific Z-DNA binding proteins and may be involved in the regulation of transcription.^[30]

From left to right, the structures of A, B and Z DNA

http://en.wikipedia.org/wiki/DNA

DNA genetic material

	We All Share the Same Building Blocks
		DNA is a winning formula for packaging genetic material. Therefore almost all organisms – bacteria, plants, yeast and animals – carry genetic information encapsulated as DNA. One exception is some viruses that use RNA instead. Different species need different amounts of DNA. Therefore the copying of the DNA that precedes cell division differs between organisms. For example, the DNA in E. coli bacteria is made up of 4 million base pairs and the whole genome is thus one millimeter long. The single-cell bacterium can copy its genome and divide into two cells once every 20 minutes. The DNA of humans, on the other hand, is composed of approximately 3 billion base pairs, making up a total of almost a meter-long stretch of DNA in every cell in our bodies. In order to fit, the DNA must be packaged in a very compact form. In E. coli the single circular DNA molecule is curled up in a condensed fashion, whereas the human DNA is packaged in 23 distinct chromosome pairs. Here the genetic material is tightly rolled up on structures called histones.
		A New Biological Era
		This knowledge of how genetic material is stored and copied has given rise to a new way of looking at and manipulating biological processes, called molecular biology. With the help of so-called restriction enzymes, molecules that cut the DNA at particular stretches, pieces of DNA can be cut out or inserted at different places. In basic science, where you want to understand the role of all the different genes in humans and animals, new techniques have been developed. For one thing, it is now possible to make mice that are genetically modified and lack particular genes. By studying these animals scientists try to figure out what that gene may be used for in normal mice. This is called the knockout technique, since stretches of DNA have been taken away, or knocked out. Scientists have also been able to insert new bits of DNA into cells that lack particular pieces of genes or whole genes. With this new DNA, the cell becomes capable of producing gene products it could not make before. The hope is that, in the future, diseases that arise due to the lack of a particular protein could be treated by this kind of gene therapy.
		Was Franklin Nominated?
Rosalind Franklin. Photo: Cold Spring Harbor Laboratory Archives		Many voices have argued that the Nobel Prize should also have been awarded to Rosalind Franklin, since her experimental data provided a very important piece of evidence leading to the solving of the DNA structure. In a recent interview in the magazine Scientific American, Watson himself suggested that it might have been a good idea to give Wilkins and Franklin the Nobel Prize in Chemistry, and him and Crick the Nobel Prize in Physiology or Medicine – in that way all four would have been honored. Rosalind Franklin died in 1958. As a rule only living persons can be nominated for the the Nobel Prize, so the 1962 Prize was out of the question. But she may have been a nominee while she was still alive. The Nobel archives, that among other things contain the nominations connected to the prizes, are held closed. But 50 years after a particular prize had been awarded, the archives concerning the nominees are released. Therefore, in 2008 it will be possible to see whether Rosalind Franklin was ever a nominee for the Nobel Prize concerning the DNA helix.
		The DNA-Helix
The sugar-phosphate backbone is on the outside and the four different bases are on the inside of the DNA molecule.		The two strands of the double helix are anti-parallel, which means that they run in opposite directions. The sugar-phosphate backbone is on the outside of the helix, and the bases are on the inside. The backbone can be thought of as the sides of a ladder, whereas the bases in the middle form the rungs of the ladder. Each rung is composed of two base pairs. Either an adenine-thymine pair that form a two-hydrogen bond together, or a cytosine-guanine pair that form a three-hydrogen bond. The base pairing is thus restricted. This restriction is essential when the DNA is being copied: the DNA-helix is first "unzipped" in two long stretches of sugar-phosphate backbone with a line of free bases sticking up from it, like the teeth of a comb. Each half will then be the template for a new, complementary strand. Biological machines inside the cell put the corresponding free bases onto the split molecule and also "proof-read" the result to find and correct any mistakes. After the doubling, this gives rise to two exact copies of the original DNA molecule. The coding regions in the DNA strand, the genes, make up only a fraction of the total amount of DNA. The stretches that flank the coding regions are called introns, and consist of non-coding DNA. Introns were looked upon as junk in the early days. Today, biologists and geneticists believe that this non-coding DNA may be essential in order to expose the coding regions and to regulate how the genes are expressed.

http://nobelprize.org/educational_games/medicine/dna_double_helix/readmore.html