Genetic information is carried and flows through polynucleotides in the form of DNA and RNA.
Polynucleotides [local]; long, slender polymeric molecules generally linked by phosphodiester (R1-3'OH . . .HO5'R2)
DNA is sensitive to acid conditions. Purine bases are selectively lost (depurination) by hydrolysis of the beta-riboside bonds.
RNA is sensitive to base hydrolysis, but DNA is not because it is lacking the 2'-OH. The 2'-OH in RNA participates in the hydrolysis by forming a 2',3'-cyclic-phosphate intermediate.
Chemical forces are important for polynucleotide structure and solubility
DNA Secondary Structure
The secondary structure of DNA is a double helix, with the phosphates out and the bases in. The classic Watson-Crick double helix is called the B-helix or B-DNA. This is a right-handed double helix that makes a complete turn about every 10 base pairs. The individual bases are in the anti-conformation and hydrogen bonding to the corresponding base takes place in the middle of the helix with the bases almost perpendicular to the helical axis. The major and minor grooves are quite distinct from one another.
Two sites with information and visuals about DNA structure: Site 1 [local], Site 2
If you have the Chime plug-in installed on your computer, you may want to view one of these tutorials on DNA structure.
Chime Tutorial 1, Chime Tutorial 2
Below are sites that contain PDB files for DNA structures that can be downloaded to your computer and viewed with software such as RasMol or Cn3D.
See jmol: DNA Duplex (B-DNA)
End on view of DNA is shown above.
Side view of DNA is shown above.
See jmol: Homeobox protein bound in groove (homeobox protein bound in the major groove)
See jmol: TATA Box Binding (shows a TATA box binding protein bound in the minor groove)
Is this what DNA looks like in the cell? That's a tough question to answer because structural information is usually obtained by hitting crystallized molecules with an X-ray beam, conditions not compatible with most living organisms. We currently like the B-DNA structure and like to think that most of the DNA in a cell is more or less in a conformation something like this.
Other forms of DNA have been found in crystals. A-DNA is a more compact right handed helix with about 11 base-pairs per turn and the pairing not along the central axis of the helix. The A-DNA probably doesn't exist in cells. Z-DNA is a left-handed helix in which the phosphate-sugar backbone is more irregular than in the right-handed helixes. Z-DNA (or something similar) may exist for short stretches in cellular DNA.
See jmol: DNA-RNA duplex (shows a DNA-RNA duplex in the form of A-DNA (see end view below). Notice that the base pairs are spaced farther from the central axis of the helix than in B-DNA.)
See jmol: Z-DNA
The DNA in cells is not inert. It is constantly moving and the bases are constantly pairing and unpairing. Sections of double helixes will occasionally come apart and 'breathe'. This is normal.
Denaturation of DNA
When DNA is in its double-helix structure, it is soluble. If the base-pairing between the two strands is disrupted, the DNA is said to be 'denatured', i.e. no longer in its native state. When denatured, the hydrophobic faces of the bases are more exposed to the aqueous environment and the solubility of the DNA strand is greatly decreased. If the concentration of DNA is sufficiently high, you will see the solution become cloudy or flocculant and the DNA can be precipitated by centrifugation. Denaturation can be caused by interfering with hydrogen bonding of the base-pairs by increasing or decreasing the pH or by adding a molecule (e.g. formamide) that will compete for hydrogen bonding with the bases. This denaturation is the basis for many DNA isolation methods. The pH of the solution is increased to about 10.5 to denature the DNA and then lowered to a pH near neutrality. The DNA is too complex to resume correct base pairing and will precipitate from solution. This precipitation is different from that caused by adding alcohols to the solution in that alcohols lower the solubility, but don't greatly disrupt the duplex structure.
DNA can also be denatured by increasing the solution temperature. This increases the kinetic energy of the molecule. At some temperature the kinetic energy is sufficient to overcome the energy of hydrogen bonding and the DNA is 'melted'. When this happens, the environment surrounding the bases changes, causing an increase [local] in the absorbance of ultraviolet light (technically, the increase in oscillator strength of the dipole increases the absorptivity). The result is an increase in absorbance at 260 nm of about 1.4 fold upon denaturation. If the warming is done in a spectrophotometer, the degree of denaturation (change in A260) can be monitored as a function of the temperature. This produces a curve [local]. The temperature at which the DNA is half-melted is the Tm. Since G*C base pairs have three hydrogen bonds and A=T base pairs have only two, it takes more energy to melt DNA with higher percentages of G+C. The Tm tends to be an indicator of the G+C% of DNA.
Once denatured, the DNA solution can be cooled and it will 'renature' or 'anneal'. Renaturation can be similarly followed by monitoring the decrease in A260. Because renaturation is actually a physical process
Strand 1 + Strand 2 = Duplex DNA
It will go faster if the concentrations of Strand 1 and Strand 2 are increased in the solution. This results in the kinetics of renaturation being proportional to a product of the concentration and time (c0t value). This is a useful feature. Read the section labeled renaturation kinetics [local] in the middle of this page.
One can measure relative genome size. For equal concentrations (µg/mL) of DNA from two different species, the one with the smallest genome will show the most rapid kinetics for renaturation because it has more copies (moles) of each gene present in the incubation.
One can measure the amount of repetitive DNA in a sample. A sample containing repetitive DNA will have a fast-renaturing kinetics for part of its DNA and slow kinetics for the remainder.
One can measure the relatedness of two DNA samples. Using methods other than ultraviolet spectroscopy, the renaturation of human DNA can be shown to be much more rapid to gorilla DNA compared to yeast DNA.
The ability of complementary single-stranded DNA strands to anneal to each other and form a duplex is essential to the use of DNA and RNA probes in the detection of DNA sequences and in the amplification of DNA by the technique of PCR.
DNA Tertiary Structure
The DNA helix tends to form a tertiary structure that is also helical. These supercoils [local] look like the cord on the phone that gets progressively more and more knotted with use. This makes the DNA more compact, but for some biological functions (replication, transcription, etc.) the supercoils need to be removed so that enzymes can approach the DNA. DNA Gyrase is an enzyme that unwinds DNA by moving along the strands and hydrolyzing ATP for energy. This enzyme makes it less supercoiled behind and more supercoiled in front as it moves along the strands. Topoisomerases (e.g., DNA gyrase) are enzymes that are able to break one of the strands in a supercoiled helix, release the strain energy and then reform two covalently closed strands.
Chromosomes [local] represent the association of DNA with proteins that form a successive progression of higher-order tertiary structures called nucleosomes, resulting in the ability to pack an enormous length of DNA is a very small space.
See jmol: Necleosome Complex
