Dna Profiling Using Capillary Gel Electrophoresis Biology

Table of Content

Everyone have unique DNA fingerprint except indistinguishable twin and it can be used to separate between persons. Deoxyribonucleic acid profiling uses the non-coding sequence of DNA strands to execute the analysis. It can be used in both wellness and judicial system. The application of DNA profiling in judicial system is discussed merely in this paper.

The most common DNA profiling techniques are restriction fragment length polymorphism ( RFLP ) and polymerase concatenation reaction – short tandem repetitions ( PCR-STR ) . Nowadays, the PCR-STR has replaced the traditional RFLP method to execute the Deoxyribonucleic acid analysis. The capillary gel cataphoresis is used for the separation of DNA molecules and the fluorescence primer is detected by CCD. The rule and methodological analysis of DNA profiling by capillary gel cataphoresis utilizing RFLP and PCR-STR are discussed in item within this paper.

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Although DNA profiling helps a batch in wellness and judicial system, public have great concern in privateness and security of DNA database. Besides, DNA profiling faces a batch of challenge in managing some complex sample, such as bone or hair sample, mixture of human DNA.


Deoxyribonucleic acid profiling is one of the most analytical tools in forensic scientific discipline. It can be applied in wellness system to name the wellness diseases and judicial system to give the back uping grounds to the tribunal to do a right strong belief. In the catastrophe, DNA profiling helps to place the persons. Deoxyribonucleic acid profiling uses the non-coding DNA part which does n’t incorporate any familial information. Two most common methods in DNA profiling are restriction fragment length polymorphism ( RFLP ) and polymerase concatenation reaction – short tandem repetitions ( PCR-STR ) . Capillary gel cataphoresis is used for the separation of DNA strands in harmonizing to its molecular size. The gel in the capillary Acts of the Apostless as the molecular screen to divide the DNA strands in the footing of molecular size.


Deoxyribonucleic acid consists of phosphate groups which bonded with deoxyribonucleotide by the formation of phosphodiester bonds with 3-hydroxyl of the deoxyribonucleotide and 5-hydroxyl of the following sugar. Four major bases available to attach with the sugar are adenine ( A ) , G ( G ) , T ( T ) and C ( C ) . Adenine ( A ) interacts with T ( T ) while G ( G ) interacts with C ( C ) merely due to the steric hinderance. With the exclusion of indistinguishable twin, everyone should hold alone DNA sequence. Everyone inherits half of the Deoxyribonucleic acid from their female parent and male parent severally. Deoxyribonucleic acid can be found in every cell except ruddy blood cells and located at the karyon. The construction of DNA is shown as follows:

Figure 1: Structure of Deoxyribonucleic acid

The atomic DNA contains 23 braces of long molecules called chromosome. The human atomic genome consists of 50,000 – 100,000 cistrons and merely minor portion of DNA molecule contains such coding sequence that holds familial information. Most of the parts of DNA molecules do non keep any familial information and is the spacer DNA between the cistrons. These parts belong to non-coding sequences organizing noncoding DNAs and are used in forensic scientific discipline to separate between persons. About 3 -5 % of Deoxyribonucleic acid are in coding sequence and are used for protein look. In the non-coding part, about 99.9 % of Deoxyribonucleic acid does n’t hold any difference between persons and merely 0.1 % of Deoxyribonucleic acid shows polymorphism. In the forensic DNA profiling, the parts of genome with a specific variable figure of times of perennial sequence of base braces are used for the analysis. On the other word, the part of genome with high length polymorphism is used for DNA profiling. These parts are called variable figure of tandem repetitions ( VNTR ) with 20 – 50 base braces per repetition. Recently, short tandem repetitions ( STR ) which have repeated sequence of 2 – 4 base braces per repetition are used for modern advanced method in forensic DNA profiling. VNTR and STR parts are the venue with a figure of allelomorphs that constitute a familial polymorphism. Most of the mutant takes topographic point in these non-coding sequences.

From the condemnable scene, blood, hair, spit, seeds or even bone samples can be collected. To guarantee the samples collected from the scene is from the human being, the sample should be verified before executing the Deoxyribonucleic acid profiling. For illustration, the ruddy discoloration on the floor is suspected to be the human blood. The phenolphthalein trial should be performed. The blood haemoglobin possesses peroxidase which is the enzyme to speed up the decomposition of H peroxide and produces O. The O will oxidise the phenolphthalein to give the colour alteration from colorless to tap. The chemical reaction is shown as follows:

Figure 2: Phenolphthalein trial

Afterwards, the nucleus DNA should be isolated before executing the Deoxyribonucleic acid analysis. The basic stairss in the Deoxyribonucleic acid extraction are shown as follows:

Cytolysis to interrupt the cell and expose the Deoxyribonucleic acid by adding the lysis buffer. The common lysis buffers are tris-HCl, EDTA in Na chloride solution. Incubate the sample with lysis buffer for 30 proceedingss on ice and extractor for 10 proceedingss at 4oC to acquire the DNA pellet.

Removal of cell membrane by the add-on of detergent, such as Na dodecyl sulphate ( SDS )

Removal of protein by the add-on of peptidase K and incubate it at 37oC in the H2O bath overnight.

Perform the phenol-chloroform extraction by the add-on of same volume of phenol: trichloromethane mixture and aqueous buffer solution and centrifugate the mixture at 4oC. After the stage separation, the aqueous bed is on the top while the organic bed is at the underside. Most of the Deoxyribonucleic acid is in the aqueous bed so that it can be isolated.

Precipitation of DNA in ethyl alcohol or iso-propanol and re-dissolve in Tris EDTA buffer at pH 8.0.

Chelating agent can be used to adhere with metal ions, such as Mg and Ca ions that inhibit the Polymerase concatenation reaction ( PCR ) .

Two common techniques are used for the Deoxyribonucleic acid analysis. They are restriction fragment length polymorphism ( RFLP ) and polymerase concatenation reaction – short tandem repetitions ( PCR-STR ) . RFLP is the traditional DNA profiling technique which uses the variable figure of tandem repetitions ( VNTR ) in the non-coding parts. The limitation enzyme should be used which cut the long Deoxyribonucleic acid strand into a fragment at a precise sequences of 4 – 8 base brace called acknowledgment sites.

The common limitation enzymes are shown as follows:

  1. Enzyme
  2. Beginning
  3. Recognition sites
  4. EcoRI
  5. Escherichia spiral RY 13
  7. BamHI
  8. Bacillus amyloliquefaciens H
  10. HaeIII
  11. Haemophilus aegyptius
  12. GGCC
  13. HindIII
  14. Haemophilus influenzae Rd
  15. AAGCTT
  16. HpaI
  17. Haemophilus parainfluenzae
  18. GTTAAC
  19. HpaII
  20. Haemophilus parainfluenzae
  21. CCGG
  22. Mbol
  23. Moraxella bovis
  24. GATC
  25. NotL
  26. Norcardia otitidis-caviarum
  28. TaqI
  29. Thermus aquaticus
  30. TCGA

Table 1: Restriction enzymes and its acknowledgment sites

The limitation enzyme cuts the Deoxyribonucleic acid at the acknowledgment site in the VNTR parts. The fragments will be separated by gel cataphoresis. The agarose gel which immersed in an alkaline buffer solution acts as a mesh to divide the mixture of fragments in harmonizing to its size of molecule. Under the alkaline medium, the Deoxyribonucleic acid molecule carries negative charge. When a high potency is applied across the agarose gel, the negative charge DNA molecules will travel toward positive electrode with different velocity. Deoxyribonucleic acid fragments with smaller size will travel faster than 1s with larger size. As a consequence, the mixture of Deoxyribonucleic acid fragments can be separated by gel cataphoresis. The Deoxyribonucleic acid fragments so transfer to a nylon membrane by puting it on top of the membrane and covering it with absorptive paper towels. Denature the Deoxyribonucleic acid fragments by adding strong alkalic solution to the gel to interrupt the H bond between the strands and edge to the nylon membrane with individual strands. This method is called southern blotting. To visualise the DNA fragment in different place of the nylon membrane, the radioactive DNA investigation is added which is complementary to portion of the interesting venue in VNTR part. The investigation hybridizes with single-strand complementary fragments. The boundless investigation is washed out and the Deoxyribonucleic acid fragments can be detected by photographic movie. The multiple venue can be identified by adding the mixture of individual venue investigations that identify multiple venue in VNTR part and give the multiple venue DNA fingerprint.

Polymerase concatenation reaction – short tandem repetitions ( PCR-STR ) is the modern technique in DNA profiling. The Deoxyribonucleic acid molecules magnify its figure by the polymerase concatenation reaction. 1,2 This method is applicable for hint sum of familial stuffs in the sample. To originate the synthesis of DNA, the fluorescence primers, four deoxyribonucleoside triphosphates ( dATP, dGTP, dTTP and dCTP ) , polymerase are needed. The primer is oligonucleotide which flanks the venue of STR part to be amplified in PCR. The reaction mixture is heated to 90 – 95oC to denature the mark DNA and makes it single-stranded. The temperature is lowered to 50 – 60oC so that the fluorescence primers will adhere with complementary sequences of mark DNA. The temperature is raised up to 72oC so that the polymerase starts to synthesise the new DNA strand.3 The PCR is performed for a suited figure of rhythms in order to synthesise adequate DNA strands. Normally, 25 – 30 rhythms should be repeated to magnify adequate DNA strands for the Deoxyribonucleic acid analysis. After the first temperature rhythm, the replicated DNA strands are produced which is shorter than the original templet strands but still longer than the length of STR venue. This intermediate DNA strands will be amplified in each temperature rhythm to bring forth precise-length DNA strands.4 The DNA allelomorph ladder that represents all possible allelomorphs at the venue should be prepared so that to judge the size of the Deoxyribonucleic acid fragments after the PCR. In the United States, the FBI has standardized a set of 13 STR venue on chromosomes for DNA profiling and organizes the CODIS database for the forensic designation in condemnable instances.

Figure 3: Polymerase Chain Reaction – Short Tandem Repeats

Figure 4: 13 sets of STR venue

In the capillary gel cataphoresis, a mixture of Deoxyribonucleic acid can be separated base on the size of the molecule. For the DNA molecule, it is impossible to be separated base on the cataphoretic flow because the charge increases with the mass of the molecule., where = cataphoretic mobility, q = charge, R = radius and= viscousness vep = E, where E = electric field

If the capillary packed with gel, such as polyacrylamide, it is possible to divide the Deoxyribonucleic acid molecules base on the size. Under the low field strength, the DNA strands spiral into the spherical atom. The cataphoretic mobility is relative to the volume fractions of the pores of gel that the Deoxyribonucleic acid can come in. As a consequence, the cataphoretic mobility decreases with increasing the molecular size. Deoxyribonucleic acid with smaller molecular size moves faster because it can travel more freely through the web of the gel.

The polyacrylamide gel will be injected into the capillary and it will be ejected out after the analysis. The gel will be used one time merely so that to cut down the opportunity of taint by the old sample. To synthesise the polyacrylamide gel, the dimethyl acrylamide is distilled to take the stabilizers. It is so added into the 1: 3 mixture of methyl alcohol and deionized H2O. The solution is purged with N for 1 hr to take O. The ammonium persullfate is added to organize the sulfate free group to originate the vinyl add-on reaction. The dissolver is evaporated to roll up the polyarylamide.

Figure 5: Formation of polyacrylamide

The electro-osmotic flow is created by the negative charge of the silanol group on the capillary wall and the majority solution will travel toward the negative electrode. The electro-osmotic flow creates the job of consistent Deoxyribonucleic acid separation because the velocity of DNA molecules will alter from tally to run. The polymer gel which adsorbed on the capillary wall will dissemble the charged sites and minimise this consequence. The buffer solution should be used to stabilise and solubilize the Deoxyribonucleic acid and supply the charge bearers for the cataphoretic current. The common buffer used in capillary gel cataphoresis is N-tris- ( hydroxymethyl ) methyl-3-aminopropane-sulfonic acid and EDTA at pH 8. The linear such as formamide, urea and 2-pyrrolidinone are added to maintain the Deoxyribonucleic acid remains denatured.5 The Deoxyribonucleic acid fragments should be heated to denature at 95oC for 2 proceedingss and cool to 4 oC in thermocycler. Sample will stay denaturized for at least 3 yearss. It will be injected into the filled gel capillary by electrokinetic or hydrodynamic injection method. Most of the capillary gel cataphoresis usage electrokinetic injection, where a high positive electromotive force is applied in a defined clip so that to travel the negative charge Deoxyribonucleic acid fragments into the capillary. When a high electromotive force is applied, the Deoxyribonucleic acid fragments which carry negative charge will travel toward the positive electrode and the mixture will be separated base on the size of molecule. The Ar optical maser emits the electromagnetic moving ridge at specific wavelength ( 488 nanometer and 514.5 nanometer ) to excite the fluorescence primers. The emanation of visible radiation from the primer will be dispersed by the prism and eventually detected by CCD. Four reactive dyes used in labeling Deoxyribonucleic acid are shown as follows:

FAM ( blue ) TAMRA ( yellow )

JOE ( green ) ROX ( ruddy )

Figure 6: Structure of Four reactive dyes for Deoxyribonucleic acid labeling

Figure 6: Conventional diagram of capillary gel cataphoresis


Deoxyribonucleic acid profiling can be used in diagnosing of familial disease and chromosome aberrances. Besides, it is used in judicial system to place the suspects in the condemnable instances, such as slaying, colza, violent assaults. Every contact leaves a hint. In the condemnable scene, we can acquire some familial stuffs, such as hair, bone, spit, blood, epithelial tissue cell under the victim fingernail and seeds. In the colza instance, we can roll up the seeds, spit and hair samples from the scene. In the assault instance, blood sample can be collected. Deoxyribonucleic acid profiling helps to include or except the suspect in the condemnable instance and supply back uping grounds to the tribunal. In the paternity and in-migration instances, DNA profiling helps us established or disproved the petition of citizenship on the footing of household relationship. For illustration, a kid requests to acquire the Hong Kong citizenship because of his male parent is Hong Kong people. Then we need to work out the Deoxyribonucleic acid profiles of his female parent, kid and male parent to make up one’s mind if the adult male is the kid male parent or non. DNA profiling can besides be used for the designation of organic structures by the comparing with possible relations. For illustration in the air accidents when the victims or dead organic structures can non be recognized, so the DNA profile of the victims or dead organic structures can be compared with the DNA profiles of possible relatives.6 For the designation of long dead organic structure, all karyons DNA have been degraded. As a consequence, the chondriosome DNA ( mtDNA ) in the bone or dentitions can be used for the designation by comparing with the possible relations. Deoxyribonucleic acid profiling can be used in the survey of virus, bacteriums, workss and animate beings. It can be used to name the infective diseases and illegal transit of animate being.


For the traditional RFLP technique, it uses high polymorphism VNTR parts for the analysis. There are a big figure of allelomorphs for each venue so that it is really rare to hold indistinguishable DNA profiles from two unrelated person. The polymorphism of RFLP is higher than STR. However, the limitation fragments are big and demo a uninterrupted distribution. As a consequence, it is really hard to separate between fragments with similar mass. Besides, it is really hard to automatize the sample readying and need a batch of manpower to execute the analysis. The duplicability is non every bit good as short tandem repetitions.

For the modern STR technique, polymerase concatenation reaction helps to magnify the venue of DNA strands so that to increase the sensitiveness of sensing. Besides, the familial stuffs collected from the scene usually are in hint sum. This technique is suited for the hint sum analysis. The sample readying can be automated and the taint and labeling error can be reduced. However, taint with Deoxyribonucleic acid from other persons may do false consequence or incorrect decision because of its high sensitiveness. The polymorphism of STR is lower because the figure of allelomorphs in each venue of STR part is smaller.

Deoxyribonucleic acid profiling helps us to name some wellness diseases and viruses, place the suspects in the offense and diagnosing of household relationship. If DNA profiling technique is used in proper manner, it can assist to cut down the figure of unlawful strong beliefs and protect the inexperienced person. However, some people think that the petition of DNA sample violates the person ‘s right to privateness and their civil autonomies. Besides, the security of DNA and the entree right are extremely concerned. For illustration, if a individual who have a certain familial hazard for certain diseases, the wellness insurance company will deny his claims. Besides, inappropriate usage of DNA profiling and the sway of it over other grounds on juries and Judgess can make a system of unlawful strong beliefs. From my point of position, if the Deoxyribonucleic acid profiling merely uses the non-coding sequence of DNA, it should non affect any privateness or security because that are non related to protein look.


One of the advantages of capillary gel cataphoresis over the traditional gel cataphoresis is the samples loaded into the separation medium in an automated in mode. Traditional gel cataphoresis techniques need to lade the sample manually before originating the separation procedure. Besides, merely little measure of DNA sample is needed in each injection. As a consequence, it may be injected for several times for the retesting intent. Most of the capillary cataphoresis uses electrokinetic injection method, where a high electromotive force is applied to pull the negatively charge DNA fragment into the capillary. The measure of DNA injected into the capillary is related to the electric field ( E ) , injection clip ( T ) , concentration of DNA in sample ( [ DNA ] ) , the country of the capillary gap  and the ionic strength of the sample over the buffer.

It can be describe by the undermentioned equation:

[ DNA inj ] = Et ( ?r2 ) ( ?ep +?EOF ) [ DNA ] ( ?buffer /?sample )

Where  is the measure of DNA injected into the capillary, E is the electric field, t is the clip, R is the radius of the capillary, ep is the cataphoretic mobility, ?EOF is the electro-osmostic mobility which is about nothing in coated capillary, [ DNA ] is the concentration of DNA in sample and?buffer /sample is the ionic strength ratio between buffer and sample solution. However, the negative charge ions such as chloride ions in the sample solution that will vie with the negatively charge DNA fragment so that to cut down the entire sum of Deoxyribonucleic acid injected because of the addition of the ionic strength in sample solution . Besides, smaller Deoxyribonucleic acid molecules will go quicker into the capillary gap than the larger 1s because of higher cataphoretic mobility. To cut down the job of the interfering ions, the sample can be diluted with deionized H2O to cut down the sample ionic strength.7,8

Formamide is a strong denaturant and it is normally used in the readying of individual strand DNA samples. Formamide will be decomposed to bring forth the ionic merchandises such as formic acid which is negatively charged and injected into the capillary. Its decomposed ionic merchandises can do the jobs in sensitiveness and declaration. As a consequence, the ultrapure formamide should be used as the denaturant and the sample solution should be frozen instantly before waiting for the analysis.

Sample stacking technique can be used to minimise the set broadening consequence in the injection procedure. As the electromotive force is applied, the sample with low ionic strength will bring forth a high electric field that ends at the interface between the sample zone and buffer inside the capillary. The negatively charged Deoxyribonucleic acid fragments will travel rapidly into the sample zone and halt traveling in low electric field at the zone interface. The Deoxyribonucleic acid fragments will be pre-concentrated at the interface and minimise the set broadening consequence of the peak separation. To bring forth a good stacking interaction, the front terminal of the capillary should hold a low conduction. This can be done by dunking the capillary in H2O prior to try injection.

In the past, cross-linked polyacrylamide gel is used as size separation in capillary cataphoresis. However, the air-bubble formation during the filling of the capillary and hydrolysis debasement of the acrylamide at alkalic medium causes the job in separation of biological sample. Nowadays, the uncross-linked polyacrylamide is used as capillary gel. It can be replaced after each tally to cut down the opportunity of taint. The polymer length and concentration affect the separation features. Increasing the gel concentration and the polymer length better the declaration but decrease the molecular weight scope.

The concentration and conduction of the buffer solution in the cataphoresis will impact the declaration. Too high concentration and the conduction will bring forth a big J warming and cause overheating of the column and loss of the declaration. The buffer solution dissolves and stabilizes the DNA fragment, provides charge bearer for the cataphoretic current and can heighten injection. To avoid the secondary construction of the DNA molecules, the buffer habit-forming such as formamide or carbamide is added into the buffer solution. Besides, the capillary temperature should be kept at 60oC. Since the cataphoretic mobility of the Deoxyribonucleic acid molecules are affected by its conformation. As a consequence, it is really of import to maintain a stable temperature. The internal size criterion such as ABI GS500 which is sensitive to temperature fluctuation should be used to guarantee the stableness of the capillary electrophoresis.9

For the gel-filled capillary, the syrupy polymer solution will dissemble the charged sites on the capillary along the wall. As a consequence, the electro-osmostic flow is about nothing. However, the contaminations trapped inside the capillary after a series of injection will bring forth the active site along the capillary wall and bring on the electro-osmostic flow. This causes the peak widening and switch the elution clip. Besides, the contaminations may interact with the Deoxyribonucleic acid fragments and do the loss of declaration. The best manner to avoid the jobs is to replace the capillary before the declaration failure. Normally, the capillary should be replaced at around 100 injections. By take downing the field strength, increasing polymer concentration and polymer length and utilizing longer capillary can increase the declaration. However, longer analytical clip is needed to accomplish higher declaration.

In the PCR-STR analysis, at least 13 venue of different chromosomes should be analyzed to guarantee the DNA profile of the suspect is really rare to happen in the population. The chance of happening can be calculated by the merchandise regulation. The frequences of all single allelomorphs are multiplied for the homozygous venue ( p2 ) . For the heterozygous venue, an add-on of factor 2 should be multiplied ( 2pq ) . The chance of happening of indistinguishable DNA profile at 13 STR venue is really rare in the population except indistinguishable twin.


Polymerase concatenation reaction-short tandem repetitions ( PCR-STR ) is the modern technique in DNA profiling and can be used to name the wellness diseases and judicial system. The Deoxyribonucleic acid fragments can be separated in conformity with molecular size utilizing the capillary gel cataphoresis. Although PCR-STR is a good forensic tool in DNA profiling, privateness and security are extremely concerned and worried in the populace.


The familial stuffs collected from the scene are limited. As a consequence, it is really of import to hold high efficiency of DNA extraction. For some of the difficult tissue, such as bone and dentition, the DNA extraction is hard. In the yesteryear, the bone or dentition should be pulverized to accomplish higher extraction efficiency. Pressure cycling engineering ( PCT ) helps to pull out the Deoxyribonucleic acid from difficult tissue without powder. PCT uses jumping rhythms of high and low force per unit areas to bring on the cell lysis. The sample and lysis buffer in the pulsation tubing is subjected to jumping rhythm of high ( up to 35,000 PSI ) and ambient force per unit area for 5 – 1 0 rhythms to bring on the cell cytolysis. The usage of PCT for DNA extraction helps to increase the extraction efficiency and shorter the extraction clip.

Mitochondria DNA ( mtDNA ) is used for DNA profiling when all karyons DNA are degraded or the sum is really limited. A cell has 100s to 1000s of chondriosomes. Each chondriosome contains 5 – 10 mtDNA. Such big sum of mtDNA is really utile if nucleus DNA is non available. The mtDNA is located outside the cell nucleus, it is inherited through the female. This means that the household members linked through an unbroken female line. As a consequence, the polymorphism of mtDNA is lesser than nucleus DNA.

The Deoxyribonucleic acid can be degraded by enzymatic reaction of microbic or under high temperature. Analyze the debauched sample utilizing STR technique consequence in dropout of larger STR venue, merely a partial DNA profile can be obtained. Partial DNA profile does non supply adequate power of discrimination.10 Mini-STR technique uses the primers which target for the larger STR venue. Standard STR primers target longer sequences than STR venue. Mini-STR primers rapid climb in on the STR venue so that the ensuing DNA strands are smaller with base brace less than 100. This increases the opportunity for the successful elaboration of larger venue.

In the hereafter, the capillary gel cataphoresis will be farther optimized to increase productiveness and cut down the work force. Besides, the size-range that maintains single-base declaration should be extended from 50 base brace to 250 or even 500 base brace. The temperature control should be enhanced to enable a high grade of preciseness from run to run.

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