Lecture 9: DNA degradation Flashcards Preview

2nd year sem 1: Forensic Genetics > Lecture 9: DNA degradation > Flashcards

Flashcards in Lecture 9: DNA degradation Deck (47)
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1

what stem DNA structure?

– A deoxyribose sugar.
– A phosphate group.
– A nitrogenous base

2

what happens when tissue is showing advance stages of decomposition?

cellular structures have begun to break down, in doing so the cells release nucleases which degrade DNA.

3

DNA is subject to nucleases from where?

– Endogenous nucleases released by host cells.
– Exogenous nucleases from microorganisms (bacteria and fungi) and environmental invertebrates.

4

what 2 main processes breakdown DNA?

hydrolysis
oxidation

5

what does hydrolysis first do?

removal of bases particularly purines , A and G
also bases with second amines, A, C and G, deamination leads to change of nucleotide

6

what does oxidative damage lead too?

- lesions in the sugar-phosphate backbone
- chemical alterations of the bases
- Pyrimidines such as Thymine are more sensitive to oxidative damage than purines.

7

Name 4 types of ancient DNA damage?

strand breaks
miscoding lesions vis hydrolysis +oxidation
cross links

8

what's the effect and solution if the strand of ancient DNA breaks?

low quantity survives, amplify is short 100-300bp

9

whats the most important factor in preserving DNA?

Low temperatures

10

what else plays a role in degradation rate ?

humidity
soil ph
chemicals

11

how does humidity play a role in degradation?

water encourages growth of bacteria

12

how does soil ph play a role in degradation?

Neutral and alkaline soils favour DNA preservation.

13

how do chemicals ph play a role in degradation?

Specific chemicals prevent the action of degrading enzymes e.g. limestone in soil.

14

what needs to be assessed when considering recovery of DNA from human remains?

state of degradation

15

what happens if theres been severe degradation + long post mortem period ?

samples such as muscle, tissue and hair may be of limited use.

16

what should be sued to find DNA if theres been severe degradation?

hard tissue such as bone, teeth (and nails) may be more successful at yielding a DNA profile

17

what 2 things can been tissue be categorised as?

compact or spongy

18

Most DNA in compact bone is located where?

osteocytes, these cells are the most common source of nucleated cells.

19

Bone is useful as the ____ _____ helps to preserve DNA as well as the presence of ________ which stabilises DNA molecules.

physical barrier
hydroxyapatite

20

Can DNA degradation occur in bone?

yes extraction can be complex

21

why are teeth a good source of DNA?

well protected by enamel.

22

what cells form teeth can be used?

Fibroblasts - pulp cavity, more sensitive to purefaction, humidity an bacteria.
Cementoblasts - cementum
Odontoblasts - in dentin mtdna

23

how to assess degradation of hard tissue?

1. Morphological
 deformationandfragmentation 2. Structural
 loss of water and collagen 3. Chemical
 organicandinorganiccomponent 4. Biological
 AA racemisation

24

How can degradation index be calculated?

using the ratio of the small and large autosomal target.

25

whats the degradation index equation?

DI = conc of small DNA/conc of large DNA

26

what's an advantage of hard tissue?

it can be cleaned (sanded) to remove:
– any commingled remains
– Adhering inhibitors
– Bacterial contamination

27

what's the first stage of extracting from hard tissue?

Cleaning
- abrasion to remove outer surface
- washing with bleach and detergent
-expose to UV prevent amplification of exogenous DNA

28

what's the second and third stage of extracting from hard tissue?

2. Material is broken down into a powder by drilling or grinding under liquid nitrogen.
3. Powder is then decalcified using EDTA followed by cell lysis using proteinase allowing access to the enclosed DNA

29

what's the fourth stage of extracting from hard tissue?

Extraction using organic phenol-chloroform method or silica binding methods.

30

whats Jörg Jenatsch case study ?

died 1639, body exhumed for second time in 2012, material from femur nd tooth, amplified using AmpF/STR Yfiller, Y23 for Y-STR analysis.
20 out of 23 Y matched male relatives. Y-SNP haplogroup’s of the skeleton and the male relatives haplogroups were the same.