DNA Structure and Replication

DNA Double Helix http://upload.wikimedia.org/wikipedia/commons/4/4c/DNA_Structure%2BKey%2BLabelled.pn_NoBB.png DNA is a large molecule made up of 4 different building blocks. When the building blocks are assembled into the larger DNA molecule, their assume the shape of a spiral staircase called a double helix. From the model one sees the outer “backbones” of the molecule and the “rungs” that appear to connect the backbones to each other. One also notices the twisting of the backbones around each other.

DNA Building Blocks 4 deoxyribonucleotides adenine thymine guanine cytosine The backbones run in opposite directions which we note as the 5’-3’ strand and the 3’-5’ strand. The numbers derive from specific carbons in the building blocks. Each building block is made up of 3 parts: a phosphate group. a sugar group and a base. Among the building blocks, the phosphate and the sugars are constant, the base are different. The building blocks are called nucleotides and there are four different ones: adenine, thymine, cytosine and guanine.

Building Block Bases The four bases are shown above. Notice that 2 of them are single ring structures and two are double ring structures. Look closely and decide if and where hydrogen bonding might occur.

Building blocks form DNA strands 3’ 5’ 3’ 5’ 3’ 5’ Notice how the building blocks connect to form a DNA strand. The backbone of the strand consists of alternating phosphate-sugar links. Note that the bases (ATCG) are all facing away from the backbone. 3’ 5’

Base Pairing – H Bonding The bases face inward toward the opposing strand and this provides the opportunity for the bases to form hydrogen bonds with their opposing bases in the opposite strand. “A” hydrogen bonds with “T” and “G” hydrogen bonds with “C”. Note that a double ring hydrogen bonds with a single ring. Also “A” forms two hydrogen bonds with “T” and “G” forms three hydrogen bonds with “C”. This assures that “A” always pairs with “T” and “G” always pairs with “C”.

DNA Replication

Three Possible Ways to Replicate DNA Given the structure of DNA, theere are three possible ways it can be replicated in the cell. Remember that DNA replication takes place in the “S” phase of the cell cycle.

DNA Replication in Bacteria Bacteria (Prokaryotes) have a single circular DNA molecule. Replication begins at an origin and moves in opposite directions until the molecule is completely copied, resulting in two identical strands. This is a fairly rapid process, allowing bacteria themselves to replicate rapidly – 20 min per generation.

DNA Replication in Eukaryotes http://faculty.ccbcmd.edu/~gkaiser/biotutorials/dna/fg21.html Eukaryotes contain multiple linear DNA molecules. Replication is slower and more complicated. We won’t go into the molecular process in much detail, but here is the “30,000 foot” view. Replication starts in many places along the molecule.

DNA Replication in Eukaryotes http://bioserv.fiu.edu/~walterm/GenBio2004/new_chap14_DNA/sp07_dna_misc_redo.htm Here is a more detailed diagram of what is happening at one replication site. Replication of the leading strand is straightforward. An enzyme called helicase unwinds the staircase and DNA polymerase III moves along the leading strand forming a new daughter strand. However the same cannot happen on the lagging strand because it runs in the opposite direction. No problem. A complex of RNA enzymes and building blocks initiate replication along several points on the lagging strand of the DNA molecule. DNA polymerase III then moves along these short segments making copies called Okazaki fragments. Then a complex of DNA related enzymes splice the fragments together to form the a daughter lagging strand. DNA Replication

DNA Origami http://en.wikipedia.org/wiki/DNA_origami#mediaviewer/File:DNA_Origami.png DNA origami is a new technology wherein biologists can create any 3 dimensional shape using DNA. Since DNA folds back on itself it is possible to create “origami” using a series of building block shapes. “To produce a desired shape, images are drawn with a raster fill of a single long DNA molecule. This design is then fed into a computer program that calculates the placement of individual staple strands. Each staple binds to a specific region of the DNA template, and thus due to Watson-Crick base pairing, the necessary sequences of all staple strands are known and displayed. The DNA is mixed, then heated and cooled. As the DNA cools, the various staples pull the long strand into the desired shape. Designs are directly observable via several methods, including Electron Microscopy, atomic force microscopy, or fluorescence microscopy when DNA is coupled to fluorescent materials.[5]” http://en.wikipedia.org/wiki/DNA_origami

More DNA Origami http://www.nature.com/scitable/blog/bio2.0/dna_origami