Mitochondrial DNA Analysis And Technology Biology

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In cells of human existences Deoxyribonucleic acid ( DNA ) is found in the karyon every bit good as in chondriosome. The mitochondrial cell organ is referred to “ power house of cell ” because molecular merchandises produced by it, provides the energy to the cell and responsible for oxidative phosporylation. Each karyon in the cell has 2 transcripts of DNA i.e. one from each parent. But it ‘s non the instance with chondriosomes. Human cells have several chondriosomes and the Deoxyribonucleic acid in each chondriosome is copied figure of times ( Goodwin.W, 2007 ) . Other variable characteristics between these are: –

a ) Nuclear DNA is different for each person ( except indistinguishable twins ) and provides a higher favoritism power than mt-DNA ( Butler,2005 ) . Mt-DNA is the same for all maternal relations, so any maternal sample can supply the same information.

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B ) Codon for tryptophan in mt-transcription is UGA while in atomic DNA UGA is referred as a halt Codon ( Butler & A ; Coble 2006 ) .

degree Celsius ) High mutant rate occurs in mt-DNA because of the less efficient fix mechanism. Continuous cogent evidence reading mechanism by polymerase enzyme reduces the mutant rate in nuclear-DNA

Mt-genome makes about 16569 base brace and has 37 cistrons which codifications for the different merchandises in the mitochondrial cell.

This above stated fact makes it tremendously utile for work outing many of the violent offense instances where DNA was extremely degraded ( like by the environmental factors ) . Apart from that the mt-DNA analysis is utile in the instances where nuclei DNA is absent like hair shafts, dentitions and castanetss ( Butler, 2005 ) . STR ( short tandem repetitions ) analysis do non work good in debauched sample nevertheless the power of favoritism is really low in mt-DNA analysis. The STR merchandise length is really little ( upto 350 base brace ) which provides more elaborate survey ( Budowle & A ; Daal, 2008 ) . The sensing bound in some of the samples is up to 33-330 femtograms of mt-DNA genome ( Allen et al. 1998 ) .

Mitochondrion DNA and Y chromosomes is specific line of descent marker. Mt-DNA is inherited from the female parent. The ground behind this is when the sperm caput fused or fertilizes an egg, the other part of the sperm like middle and tail are left behind ( normally have 50-70 figure of chondriosome ) .

This left over part is rich in mt-DNA which ne’er reaches inside of egg ( Goodwin, 2007 ) . In effect, all the mt-DNA comes from egg ( 1000 ‘s of chondriosome ) i.e. female parent which finally makes it extremely utile for supplying maternal relationship in many of the of import instances, losing individual and mass catastrophe instances. In one of the survey in England shows that complete absence of parental mt-DNA heritage is impossible. In some of the instances they do inherent the parental mt-DNA ( Schwartz M, 2002 ) . This is strictly based upon alterations, as 1000000s of mt-DNA samples showed maternal heritage.

Survey of mt-DNA mutant proves effectual in medical field and helps scientist to associate with assorted diseases. Comparison between the different species is made by mt-DNA in some of the instances ( Butler, 2005 ) .

2. Mitochondrial DNA Genome:

Mt-DNA is round in construction and has 16569 base brace which make it less prone to exo-nucleases and finally assist in forensic DNA profiling. But the entire sum of base in mt-Genome varies. The chief ground of fluctuation is mutant that either causes omission or interpolation in the existent genome ( Butler & A ; Coble 2006 ) . This can alter the entire figure of mt-Genome. The common illustration for this is that many of the person have 5 times repeat of ( AC ) base braces but it varies from 3 to 7 repeats of this base brace ( Butler, 2005 ) and age independent.

Figure 1. mt-DNA genome demoing 37 RNA and protein coding part. HVI and HVII are the parts for forensic involvement. These hyper variable parts are located in displacement cringle ; Photo Courtesy: ( Holland & A ; Huffine, 2001 )

Control part: Its 1122 bp and responsible for the reproduction of mt-DNA strands. It does non code for the cistron merchandises and besides known as non coding part. Transcribed cistrons codification for 13 different proteins, 22 for t-RNA and 2 for r-RNA ( Butler, 2005 ) . The cryptography cistrons are closely packaged to each other which lead to exclusion of noncoding DNAs and cut down the variableness.

When these mt-DNA molecules separated in the CsCl gradients so this invariable nucleotide leads to heavy ( guanine content is high as compared to visible radiation ) and light ironss ( Holland & A ; Huffine, 2001 ) .

H Strand ( Displacement cringle )

Reproduction of mt-DNA ( in control part )

28 cistrons merchandises

D-loop is variable in nature because it does non code for any merchandises.

L strand

Transcribes 8t-RNA, ND6 enzyme

This in entire makes 37 cistrons merchandise.

Table1: Information of some of import mt-DNA genome and cistrons. Table courtesy ( Butler, 2005 )

Nucleotide place



Control part ( D-loop )





16104-16569, 1-191

Replication beginning ( H-strand )



D-loop expiration signal



H-stand written text booster



L-stand beginning



Harmonizing to Dr.Amarjit chahal ( 2010 ) another characteristic of mt-DNA is heteroplasmy. It ‘s the presence of more than one mt-DNA in an person. Assorted factors give rise to heteroplasmy and it can be more than one mt-DNA type in a individual tissue or the two tissue samples of the suspect have different heteroplasmy or sample may incorporate homoplasmy.

It ‘s normally of two types and increases the power of favoritism.

1. Point heteroplasmy: It is observed when the 2 base is present at individual site which in the analysis consequence shows 2 overlapping extremums.

2. Length heteroplasmy: It occur in the c-stretches or polycytosine stretches ( homopolymeric ) of hyper variable part 1 ( 16184-16193 ) and 2 ( 303-310 ) ( Lee.H et al. 2004 ) . In Anderson mention sequence tyrosine is found in both HVI ( at 16189 ) and HV II ( at 310 ) . In some samples this tyrosine is replaced by the C which consequences in hundred stretches.

Due to sequencing method restrictions it ‘s difficult to construe ate length heteroplasmy. These assorted length discrepancies cause assorted common diseases like diabetes mellitus ( Lee.H et al. 2004 ) .

Triplasmy was recorded in some of the instances but in really less frequences as comparison to individual site heteroplasmy ( Tully et al.2000 ) . The chief places of the heteroplasmy in hyper variable part I are eight and five in hyper variable part II. The part why heteroplasmy is of import for the single designation is that it remain stable over coevals and can be inherited ( Butler,2005 ) .

Another fluctuation in mt-DNA analysis is caused by ‘nuclear Pseudo cistrons ‘ . Sometimes what happened is that parts of mt-Genome are migrated to atomic genome. Most normally this mt-DNA control part appears in 11th chromosome figure and history for 7.5 per centum sequence fluctuation ( Butler & A ; Coble, 2004 ) . It creates fluctuation in forensic surveies when genomic mt-DNA transcript amplifies up alternatively of mark mt-DNA but careful design of the primers with less PCR rhythms can cut down this job ( Butler, 2005 ) .

3. Mitochondrial-DNA analysis

The basic rule in mt-DNA analysis is to aim the fluctuation that occurs between the single Displacement cringle which is found in the control part of round mt-DNA ( Butler.JM, 2004 ) . PCR amplify the hyper variable part I ( 342bp evaluated ) & A ; II ( 268 bp evaluated ) and the consequences are compared with the mention sequence. When HV I and HV II failed to bring forth the consequence so the HV III part ( nucleotide place 438-574 ) sometimes provides the valuable base for analyzing ( Butler,2005 ) .

3.1 Method: -The foremost basic cardinal issue in the analysis is taint. The trial sample which is to be analysed by this techniques is normally degraded so excess attempt is needed to avoid taint by proper erosion of protective apparels and maintain the lab clean by continuously rinsing the working slab.

Extraction of the mt-DNA requires particular attention because the beginning of it like dentitions, hair and castanetss provides really little sum of DNA and many of the samples like castanetss and dentitions is needed for farther probe and its utilizations in anthropological surveies ( Butler, 2005 ) .

Mt-DNA extraction from hair fibers is small spot hard and dearly-won hence if Scene of Crime Officers found such sort of grounds ( hair fibres ) so they go for microscopic scrutiny instead than mt-DNA extraction.

However mt-DNA in hair shaft is available by crunching tissue and pull outing mt-DNA from ceratin of hair. In one of the surveies it shows that adding of Bovine serum albumen helps to transport out the successful PCR procedure by suppressing the effects of melanin ( Butler, 2005 ) .

Quantification of extracted sample is necessary to see the handiness of mt-DNA to transport out the remainder of the procedure. Alternatively of comparing of measure and repairing the ratio with atomic DNA existent clip PCR provides the direct quantification of mt-DNA molecules ( Butler.JM, 2004 ) .

Amplification of the mt-DNA by PCR normally requires 35 rhythms on an norm which in bend increases the sensitiveness and more opportunities of taint. It amplifies the whole control part or specific part. The sequencing is done by Sanger method where fluorescent ddNTPs was processed with DNA. A primer binds to the specific site anneals and extension occurred by polymerase enzyme.

The construct behind including ddNTPs is that while extension procedure is carried out by dNTPs, ddNTPs stops some of the merchandises to widen and tag that merchandise because ddNTPs is labelled with different coloring materials brighter dye. Ultimately it provides the best declaration with clear indicant of the bases. Assorted filtration procedures like remotion of primers and dNTPs is done by spin filtration and enzymatic action. Fluorescent dye is removed by spin column filtration.

The cardinal difference between STR analysis and mt-DNA analysis is that in mt-DNA sequencing, separation medium is required in multiple color sensing instruments to decide individual base and merchandises are analysed by capillary cataphoresis.

Consequences are so compared with the mention sequence and comparing was made with databases to place and gauge haplotype frequence. In NCBI database with genbank accession: M63933 the mt-DNA sequence was noted which is used to compare the new sequence. This sequence is referred as ‘Cambridge Reference Sequence.

Earlier in 1981 these sequence was reported by the Anderson from the individual person and uses Bovine sequence to make full the spreads in between these mention sequence but subsequently in 1999 placenta stuff was used to re-sequence.

Assorted consequences are compared by the L-strand mention sequence for illustration if Thymine is present at 16126 place in the CRS and the consequence displayed Cytosine so it would be considered as 16126Cytosine. This is the common discrepancy which consequences into c-stretches in both hyper variable parts.

In many of the forensic instances the hyper variable part ‘1 ‘ and ‘2 ‘ of control part is considered and the consequence is matched with these mention sequences.

4. Technologies associated to mitochondrial-DNA analysis

4.1: Continuous betterment in mensurating mt-DNA fluctuation makes the technique more dependable. Earlier low declaration usage of 5-6 limitation enzymes in RFLP ( limitation fragment lengths polymorphism ) analysis improved to high declaration analysis by PCR elaboration ( Butler, 2005 ) . PCR amplifies the 9 overlapping fragment and so 12-14 limitation enzymes act on it to bring forth good profile of mark sequence and finally usage of fluorescent dye to sequence the mt-DNA ( Holland & A ; Huffine, 2001 ) .

4.2: Assorted attacks are made in quantification of mt-DNA in the mixture of human and non-human DNA beginning. In forensic probe it ‘s hard to place the beginning of DNA so one of the attacks was taken to quantify sample mixture down to 1.7fg mt-DNA ( Tobe et al. 2008 ) . It uses cytochrome B and 12S ribosomal cistron on the mt-Genome.

The specific fragments are quantifed utilizing SYBR Green and amplifed. They take 24 human and 27 non human sample into history for quantification analysis.

4.3: Whole mt-Genome Research- Sequencing the whole mt-Genome helps in Reconstruction of phylogentics of human and helps in understanding genome development and is utile in forensic designation ( Naraa.A et al. 2009 ) The specific agreement of cistrons in mt-Genome makes it more utile than shorter sequence of single cistrons ( Jeffrey L. Boore et Al. 2005 ) .

In this 48 primers are used in PCR elaboration procedure and aim the sizes of 765bp to 1162bp which consequences in 200 bp of convergence ( Butler, 2005 ) between different merchandise of PCR.

Consequences of the polymorphous nucleotide sequence in the genome can be seen and compared in Mito Analyser database. It is bioinformatics platform for mt-Genome analysis and information ( Lee & A ; Levin 2010 ) .

4.4: Rapid Screening of mt-DNA types: Expensive and arduous attempt in informations analyzing and opportunities of mistake in sequencing, testing check helps to get the better of from these full job. Screening methods provides speedy consequence by excepting non-matching sample and helps the scientist to acquire involved in mt-DNA analysis.

Dr. John Butler and his squad give two effectual methods of testing. First method is ‘pattern fiting ‘ in which 3 different mt-DNA sequences can be distinguished from each other. Second one is ‘sequencing at specific place ‘ ( Butler et al. 1998 ) .

This can assist in survey of lineage form with mt-DNA The alone mt-DNA heritage from female parent makes it more powerful tool to analyze the human migration form. The haploid form that is autosomal DNA does non supply so much lineage form because of scuffling effects of recombination ( Butler, 2005 ) .

Mitochondrial DNA analysis and sensing of Deoxyribonucleic acid from the debauched stuff makes it utile to analyze the ancient castanetss and helps in happening its beginning. This can be done by analyzing HV I and HV II part with the usage of same type of Deoxyribonucleic acid markers ( Butler.JM, 2004 ) .

Other of import techniques are Snapshot in which primer particular to aim allelomorphs extended with 11 coding part.

Single nucleotide polymorphism in add-on with individual manifold elaboration and sensing assay makes this technique more utile and fast. In luminex 100 liquid beads assay 30 individual nucleotide polymorphism was studied and used in HV I and HV II.

The allelomorph specific hybridisation technique sequence specific oligonucleotide investigation ( SSO ) was used and labelled with different coloured beads and subsequently on with the aid of flow cytometry beads are separated ( Origene Technologies,2011 ) .

5. Mitochondrial-DNA analysis in Forensic Cases

5.1: Case Study 1: In one of the probe of 4 losing individual mt-DNA analysis proves to be effective and linked 3 unidentified skeletal remain to the losing individual. In one of the instance they fail to associate it decently but farther analysis confirm successfully that the bone was non matched to the losing individual ( Bender et al. 2000 ) . Harmonizing to Klaus Bender ( 2000 ) and his squad the consequences can be obtained from the degraded castanetss up to 75 old ages.

Mt-DNA can be obtained from a assortment of beginnings like epithelial cells ( 5000 mt-DNA ) for farther analysis. In this research work DNA was extracted and amplified by the undermentioned procedure:

Boness was cleaned and removed by high velocity cutter

Clean portion of the castanetss was cut in specific size and grinded to ticket pulverization by frozing the bone in liqid N.

Decalcified in EDTA solution and extracted by Phenol trichloromethane protocol ( Sullivan et al. 1994 ) .

Amplification was done on HV I & A ; HV II with the usage of Pt Taq polymerase, and 4 sequence specific primers in forward and change by reversal reaction with 35-40 PCR cylces

For sepration and purification usage of 1.5 agrose gel and QIA speedy purification provides the good consequence ( Bender et al. 2000 ) .

In 2 of the instances constabulary obtained the oral cavity swab from their relations, scientist amplified it and matched with the mark sample. They find the indistinguishable differences with the Anderson and D loop databases for mention. Interpretation of the consequences in 1st instance showed the interpolation of C in both part but interpolation in HV I was uncommon and set as alone designation ( Butler, 2005 ) .

In 2nd instance of losing individual heteroplasmy in HV II part was seen which was besides present in his brother ( Bender et al. 2000 ) . In 3rd instance of losing kid ( harmonizing to anthropologist informations ) consequence was different from the sample obtained from his/her female parent by comparing 7 sequence place. 2 interpolations, few exchanges and heteroplasmy in HV II part exclude the consequences.

In 4th instance both mt-DNA analysis and STR typewriting was done because of the complexness. Clear mismatch of the HV I and HV II part bases were seen with the sample of female parent and male parent DNA ( Blender et al. 2000 ) . These all consequences indicate that mt-DNA provides the hint and verification to the constabulary of losing individuals and can successfully uncover the individuality of the individual.

5.2 Case study 2: In many of the offense scene searches the Scene of Crime officer came across the hair fibers and blood of Canis familiariss which shows their engagement but it ‘s difficult to place them and divide them with other fibers ( Saferstein.R, 2011 ) . In one of the thesis carried out by Sanne Tambeur and his squad sucessfully showed the mt-DNA anaylsis helps to place and characterize domestic Canis familiariss hairs and blood ( Tambeur et al. 2010 ) .

SNPs and polymorphisims in mt-DNA provide the information which helps in forensic instance work. They divide the strains in four haplogroups and finally make the mt-DNA database for the strains of Canis familiariss in Belgium. In many of the samples heteroplasmy and 74 polymorphous places was observed which can increase the sequence designation. The singularity of these polymorphous places was that 46 places in entire showed nucleotide place opportunities.

It will be easy for the forensic analyst to detect the peculiar haplotype groups and helps them to place the beginning from the information set and informations point ( Tambeur et al. 2010 ) .

5.3 Case Study 3: The job with mt-DNA analysis is that it provides the low favoritism power because of the inefficiency of recombination and did non supply the much greater aid in forensic probe. One research paper study assay technique for the mt-DNA analysis which can give power of favoritism ( Nilsson et al. 2007 ) . By reexamining the information from Caucasic mt-DNA sequences they found coding part checks gives 46 % more favoritism power.

Pairwise aligment gives penetration of Caucasic mt-DNA sequences. Measuring HV I & A ; II part and non HV parts provides some of the alone sequences ( Nilsson et al. 2007 ) . But its difficult to separate the population from the same cultural beginning. HV III part can be used to know apart.


Apart from its expensive and arduous undertaking assorted forensic research labs are now utilizing mt-DNA analysis and its showing method for work outing offenses in UK and other portion of states. The techniques is widely accpeted by the tribunals but Youth Justice and Criminal Evidence Act 1999 and Criminal grounds and Justice Act 2003 have many exclusionary powers and legislative acts that can except the mt-DNA grounds. So adept should be really careful while fixing witness statement. They should include chance and statistics of peculiar findings.

FBI had created one of the database called ‘National Missing Person DNA Database ‘ ( National Institute of Justice,2010 ) to supply the inside informations of lost individual and widely uses mt-DNA analysis to decide the things. Array has some job in relation with omission, interpolation and polymorphous sequence which are closed to each other

A SNPs sites can be assayed now and supply the reply to the above stated job and give more favoritism power and avoid farther sequencing ( Coble, 2006 ) . Harmonizing to Micheal Coble ( 2006 ) assorted approches are undertaken by NIST which can supply with the cheaper option for mt-DNA analysis.


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