Exam 3 Flashcards
Satalite DNA
DNA with restriction enzymes that cut out and show up as small bands
genome
set of chromosomes in an organism
mini statlite
VNTRs. medium tandum repeats
RFLP
technology that is used to detect mini satalites, uses large amounts of DNA
micro satalites
strs, short tandem repeats
STR loci
vary by length of repeats
have motifs
partial repeats
intervening sequences
motif
repeated elements across multiple organisms (conserved)
partial repeats
repeats that are missing a base pair aaaa to ataa
intervening sequences
interupting sequence within set of repeats
CODIS
database that compares target dna sequences
four categories to classify STRs
simple repeats
nonconsensus alleles
compound
complex compound
use tetreanucleotide repeats
di and tri give stutters
allelic dropout
loss of alleles
STR are moderately variable
VNTR are hypervariable
discriminating power
high heterozygosity
specific STR nuclei used in forensics are
not linked
reproducable
less than 350 bp
2 theories STR arise
crossing over
DNA polymerase error
Nomenclature for consistancy named based on
loci
alleles
databases
alleic ladders
all common alleles
serves as control
forensic codis loci
13 different
us uses in forensics
codis loci
combined DNA index system
codis loci are not informative for
phenotype are intergenic and use introns
multiplex
look at multiple different sites
ameloglgenin
locus on both x and y chromosomes
x has deletion on intron 1
teo companies for STR kits
promega: powerplex 16
applied biosystems: ampf/str
multiplexing is acheived
channels-colors
silverstaining
only one channel and dna looks same
florescent detection
different colors on dyes
one channel is used as
internal size control
non-nucleotide linkers
mobility modifiers
gap between loci
STRbase
NIST
DNA properties in solution
negatively charged polyion (anion)
native double stranded
dingle stranded is denatured
random walk
movement in rnadom direction at only point in time
electrophoresis
DNA seperated by size
electrical force
current pulls DNA to positive ens
voltage
proportional gradient v/cm
resistance
semi solid matrix in solution pores are the holes
teo mechanisms dna movement
ostong seiving
repatition
ostong seiving
small slips through
reptation
lerge fits in different shape, use linear instead of sperical
resistance to DNA increases — with size
exponentially
agarose
dnDNA
plysacharide non-covalent gel
native
stain w ethidium bromide
polyacrylamide
denature using formamide in sample urea in gel
silver staining ises
silver cations to bind dna
capillary electophoresis
runs through a capillaey uses florescent detection
DNA sequencers
developed for human genome project
platform used in forensics
ABI prism 310 a genetic analyzer
capliaary electrophoresis controls
temp in oven
capilary electrophoresis uses
microtiter tray for automatic loading
capillary detection
blue laser driven florescence
data for capilarty recorded as a
elecectrpherogram in RFU
310 platform
3 sample one controll
usus special calibration for dyes
had raw data for strngth of signal
uses blue green yellow black and red
3100 platform
4 sample 1 control
uses orange for deteection (near and far red)
31xx
multiple capillaries
artifact
there from human activity
stutters in artifacts
cause polymerase slippage- slip out of template
penta a-g
loci with no stutter for mixtures
processive polymerase
faster without pausing as much
non-template addition
usually plus or minus a and usually in reverse
micro-variants
allele in individual but not in ladder
insertion or deletion
called off-ladder alleles
interpolate ijn microvariants
insert
extreme off ladder
fall between two ranges use single plex
tri allelic
tripple peaks only locus with three peaks
null allele or allelic dropout
only one peak for heterozygous indiv
primer binding site mutation
prevents primer from binding
avaioid lack of primer binding using
degernerate primers
prevent peak dropout by reducting
stringency
generation mutation affects
paternity ad mass disaster cases
mutation caused by
polymerase slippage
dna interpreted by
dna iq
q pcr
multiples str- pcr, thermocycler
genetic analyzer- 310, 3100, 31xx
data colletion
raw data- deleted signals with different x and time
color seperation
use matrix file for special calibration with gene maooer/id software
detele secondary detect peak
peak identification
set threshhold
peak sizing
internal size standard
sample issues
degreadation
low quantity
three responses
degredation leads to
allelic dropout
ameglobin last
vntrs are too long
covalent modification
three responsed
miniSTR- STR
LCN-STR
mtDNA sequencing- no STR
mini STR
smaller amplicon size
common Tm
ini STR works for
telogenic hair
mini str looks at
concordance studies
lcn- low copy number
0.1 ng concnetration
lcn issues
mainly stochastic with allelic drop in and out
str in non-forensics
purity and id cell lines and chimeric indiv
mixtures
more polymorphic loci are more useful
minor contributor above minimal value
allele imbalance
quantification in rfu
heterozygousy
varioation in peak intensities
mixture steps
id prescence
designate peaks
identify number contributors
estimate relative ratioconsider genotype combinations
compare to referance samples