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Flashcards in genetics Deck (32):

what is Molecular genetic methods in medicine
used for?

Manufacture of medicinal products
Detection of pathogens
Identity and related issues (court medicine)

Diagnostic questions:
Diagnosis of monogenic and hereditary diseases
The investigation of genetic risk for diseases
Preconceptive / Preimplantation / Prenatal Diagnostics


Gene therapy


how to diagnose Genetic diagnosis of Fragile-X syndrome

Cytogenetic examination: cell culture on folate-poor substrate  „break point”
(not used since ~1990) due to:
lot of work;
takes long;
high rate of false positive and false negative results

PCR-based examination
(for screening only)
Southern-blot-based examination
(most appropriate)


The basic principles - the most important molecular genetic methods can be classified into four types

"Cut-and-paste”--> Restriction endonucleases + ligases
Visualize Electrophoresis
Hybridization--> E.g. FISH
Amplify---> PCR


1) Cut and paste: The restriction endonucleases

restriction endonucleases- enzymes that cut DNA at specific (palindromic) recognition nucleotide sequences

blunt and sticky ends.

application- recombinant dna techniques;
1) restriction endonulcease,
2) sticky ends are sealed together with dna ligase-> recomb dna.
used for gene cloning and inserted into vector (bacteriophage


other application of dna recombination

proteins hormones, vaccine- antigens, antibody, cytokines growth factors coag factors etc.


features of expression vectors

Gene for expression does not
contain intron

ORF codon is optimized

May contain Tags helping in
protein purification

Optimal enhancers, promoters
and teminators

Replication origin

Contain selection


2) Separation and visualization ofDNA / RNA fragments: gel electrophoresis

Agarose concentration in the gel ~ size of the pores (the more concentrated, the smaller)
The negatively charged nucleic acid molecules are drawn through the gel matrix by means of an electric field.
  The smaller molecules can move faster through the gel Separation of the fragments according to their size
Stained by eg. Ethidium bromide + UV light - not specific


Stained by eg. Ethidium bromide + UV light - not specific

Many samples at the same time

Main advantage is that different gel matrix can be used – different separation (RNA, DNA, protein)

Special advantage in the separation of DNA sequences (eg. PCR products) of very small size (1bp) difference


3) Hybridization

The basis of genetic methods: DNA-RNA structure A variety of modern methods are based on the ability of double helix formation of nucleotide chains.

hybridization of the complementary strands



steps of southern blot

dna 32p labled size markers,
2) electrophoresis and migration
3) solution passes through gel and filter to papertowel.
4) dna transferred to filter.
5) hybridize /w 32p labeled nucleic acid probe.
6) wash away unwanted probe.
7) x ray filter the hybridized complementary sequence.


Applications of Southern blot

Detection of Fragile X syndrome
Identification of methylation sites
in both cases methylation sensitive
restriction enzymes are used

Formerly– to detect point mutations, SNP-s
DNA fingerprint


Comparison of Blot-Hybridization techniques

southern- dna, uses labled dna /w restriction digestion and the result is restriction map.

northern identifies rna, with the use of a dna probe, NO restriction digestion and detects amount and size of RNA.

western blot detects protiens, uses a antibody probe! no restriction digestion and.


4) Amplify: PCR and its variants

Heat stable DNA polymerase and reverse transcriptase enzymes allow PCR and RT-PCR


Polymerase chain reaction-PCR

generation of thousands to millions of copies (amplification) of a or a few copies of DNA sequences in a short time (about 2 hours) (in vitro DNA synthesis)

The thermostable DNA polymerase (Taq polymerase) enzyme of Thermus aquaticus (lives in extremely high temperature) is needed

Necessary: three temperature dependent steps- melt anneal and extend- repeat cycle.


Applications of recombinant DNA technology

polymorphisms in human genome (~ 5%) - may be used for markers
~ 65 millions SNP, 30 thousands microsatellite (STR,
VNTR) are known
- recognition site of restriction enzymes or the distance between them may change due to polymorphisms and mutations (SNP, STR or VNTR InDel)
Size of fragments may be checked by electrophoresis, different cleavage results different fragment pattern = RFLP (restriction fragment length polymorphism)


Southern - RFLP

Genetic diagnosis with RFLP analysis and detection with Southern blot
(RFLP: restriction fragment length polymorphism)

The probe used in the Southern blot hybridizes to a portion of the phenylalanine hydroxylase (PAH) gene that is responsible for phenylketonuria, and detects a restriction fragment length polymorphism with two alleles



1) The DNA region is amplified with specific primers in PCR
2) Digestion of DNA with restriction enzymes (for PCR-RFLP).
3)Gelelectrophoresis to identify of cleavage pattern (genotype)
4) Staining with DNA-binding dyes, eg. Ethidium bromide
5) Evaluation in UV light



VNTR - (variable-number tandem repeats) may be in coding, or non-coding regions

Between two individuals restriction sites show variations in length

VNTR show unique patterns: DNA fingerprint

VNTR can be
minisatellite- 10-60bp,
microsatellite- 1-4bp
(STR-short tandem repeat)

VNTR is inherited codominantly



1) The DNA region is amplified with specific primers in PCR
2) Digestion of DNA with restriction enzymes (for PCR-RFLP)
3) Gel electrophoresis
4) Staining with DNA-binding dyes, eg. Ethidium bromide
5) Evaluation in UV light


clinical significance of vntr

1) Triplet repeat diseases (TRD) – expansion of triplet (eg. CAG) in mutant allele

Wild type allele - few triplet repeat (below a limit), but in mutant the number of repeats are multiplied (above a limit)

blood groups


Multiplex PCR

Allows simultaneous amplification of multiple target regions within single reaction using different primer pairs.

PCR products have to be of different length

Simultaneous detection of several pathogenic E.coli strains found in dairy products



Determination of the nucleotide sequence of DNA fragments

Maxam-Gilber and Sanger methods

Sanger method (chain termination) is widespread

Automation with labelled di-deoxynucleotides and capillary electrophoresis


Detection of point mutations: sequencingSanger method

Chain termination synthesis

1) PCR reaction with dNTP and ddNTP (dideoxyribonucleotides)
2) Because of the absence of 3'OH, the synthesis ends when ddNTP is incorporated
3) Shorter and longer fragments arise
4) electrophoresis: all four ddNTPs fluorescently labeled (four colors)
5( Laser reading: colored ladder peaks  base sequence

The sequence of nucleotides and the corresponding signal strength is analyzed.

Color-coded chromatograms facilitate evaluation.

on the chromatogram only one nucleotide specific signal is shown in homozygotes (for a nucleotide).

on the chromatogram two nucleotides specific signals (which are a little decreased) can be seen in heterozygotes


Genotyping by sequencing

Aim: not looking for a specific known mutation or polymorphism, but for sequence differences in a not too large, known gene

700 -1000 bp can be sequenced

Detectable: point mutations, smaller insertions, deletions, duplications, heterozygosity, mitochondrial heteroplasmy

Applications of sequencing:

clinical suspicion of cystic fibrosis, detection of hundreds of mutations,
Mutation detection in dystrophin gene, galactosemia (GALT), galactokinase deficiency (GALK1), neurofibromatosis (NF-1)
mitochondrial DNA analysis
In case of infection outbreak sequence analysis of viruses and detection of propagation


NGS-next generation sequencing

Limit of traditional sequencing: approx. 800 nucleotides
Different NGS methods exist, parallel sequencing of millions of DNA
1 run - hundreds Mb or few Gb sequence
Nowdays used more or less for research, for whole genome sequencing, in the future will be used for diagnostics as well (SureSelect Human Kinome Kit)
Future: to decrease the cost and increase the speed of sequencing.


ngs steps

1) sequence primer hybdridize to the template.
2) incorporation of each dntp is accompanied by the release of pyrophosphate group.
3) ppi generated visible light can be detected and presented in the pyrogram.
4) an enzyme degrades unicorporated dntps. then the next dntp is added.
5) addition of dntps iis performed one at a time, and the pyrogram generated from the visible light show the sequence..



1) The DNA region is amplified with specific primers in PCR
2 Digestion of DNA with restriction enzymes (for PCR-RFLP)
3 Gel electrophoresis
4 Staining with DNA-b inding dyes, eg. Ethidium bromide
5 Evaluation in UV light


RT-PCR Reverse transcriptase polymerase chain reaction

For the analysis of mRNA expression- BUT: mRNA is not particularly stable we need cDNA from the mRNA
- cDNA can be analyzed using a traditional PCR reaction

Preparation of cDNA

Primers for synthesis:
An oligo dT nucleotide (15-25 deoxythymidine),  complementary to the poly A tail of the mRNA, or
Random hexamer oligonucleotides (consisting of six randomly assembled nucleotides) 


Reverse transcription (RT) PCR

The template is mRNA
is reverse transcribed to cDNA
is amplified by PCR (qualification)
Application of real time PCR allows quantification, to study gene expression, too


The real-time / quantitative PCR(qPCR)

Is a further development of the "traditional" PCR reaction

Is based on the principle of conventional polymerase chain reaction (PCR)

The reaction is followed in real-time

This allows accurate quantification of the amplified DNA by means of fluorescence measurements

Enables both quantitative analysis of DNA (qPCR, e.g., bacterial DNA, human gene amplification, etc.)

As well as the determination of the amount of RNA (qRT-PCR, e.g., measurement of gene expression, viral RNA, etc.)

It allows to detect the PCR product as it is produced (as the fluorescent signal is generated)

Genotyping (detection of SNP-s)
Qualitative real time PCR (yes/no)
Quantitative real time PCR (Q-PCR) (g or cDNA)


Real time – PCR

Quantitative PCR - it allows the scientist to actually view the increase in the amount of DNA as it is amplified.
TaqMan® probe detection

probe with a fluorescent reporter at
one end and a quencher of
fluorescence at the opposite end
of the probe. The close proximity
of them prevents detection of

The probe hybridize to the middle
of DNA region to be amplified. In each
cycle these probes are degreded by
DNA polymerase physically separating
the fluorescent reporter from the
quencher, resulting in an increase
in fluorescence.

Fluorescence is detected and
measured in a real-time PCR machine,
and its geometric increase corresponding
to exponential increase of the product is
used to determine the quantification cycle
(Cq) in each reaction.

In positive samples (containing the studied DNA sequence) after some PCR
cycles fluorescence above threshold is measured

In negative samples the fluorescence remains below threshold



Reverse transcription polymerase chain reaction (RT-PCR), a variant of polymerase chain reaction (PCR), is a technique commonly used in molecular biology to detect RNA expression.[1] RT-PCR is often confused with real-time polymerase chain reaction (qPCR) by students and scientists alike, but they are separate and distinct techniques.[2] While RT-PCR is used to qualitatively detect gene expression through creation of complementary DNA (cDNA) transcripts from RNA, qPCR is used to quantitatively measure the amplification of DNA using fluorescent dyes. qPCR is also referred to as quantitative PCR,[2] quantitative real-time PCR,[3] and real-time quantitative PCR.