What is one thing you do not want at the 3' end of the primer?
Multiple C or G's
What is the age limit for aDNA?
What is autolysis?
destruction of cell through the actions of it's own enzymes
What is the complex of changes caused by chemical, biological, and physical processes acting on a specimen while buried underground?
What is hydrolysis?
Decomposition of chemical compounds by water. RNA is very susceptible to this and does not preserve as well as DNA.
What happens to DNA when hydrolysis occurs?
OH and H of water molecule form new chemical bonds with parts of DNA molecule, resulting in breaking down and damaging DNA molecule
What is depurination?
The process that a purine (A or G) is disassociated from sugar due to hydrolysis. Pyrimidines (T or C) do not dissassociate from sugar as readily. Can occur sporatically in living cells, but the problem is fixed by the cell.
What is DNA Deanimation?
The removal of NH2 from a base which results in the base not being recognized and ultimately wrongly base-paired. Cytosine is the most vulnerable to this damage.
What is DNA oxidation?
DNA molecule is modified and broken down by hydroxyl and superoxide radicals. Happens when DNA is exposed to oxygen. Will modify bases and distort the DNA structure.
What happens to DNA after the organism dies?
Chemical damages to DNA are mainly
hydrolysis of bonds between base and sugar residues, breakage of the sugar backbone, and oxygen radical-induced attacks on bases and sugar residues
What conditions may help DNA preservation?
Absence of oxygen,water, neutral pH, and lower temperatures.
Morphological and molecular preservation are correlated in many cases but they are not the same. Why?
Both bone and DNA are under the same
diagenetic process but their responses can be significantly different.
What types of remains tend to favor well?
Cells inside bones OSTEOCYTES OSTEOCLASTES (have protection of bone tissue), teeth are better than bone.
Can the degradation of DNA be approximated by any other tests?
Amino acid racemization. Amino acids convert from L-form to D-form when proteins denature. More D-form amino acids means the DNA is probably looking rough too.
What length of DNA is a good idea to aim for?
300bp is a happy medium, because anything too far below and you have really short fragments, and anything too far above and you have long fragments with very few templates.