Patent Application
20100035303
This application claims the benefit of Korean Patent Application No. 10-2008-0078141, filed on Aug. 8, 2008, in the Korean Intellectual Property Office, the contents of which are herein incorporated by reference in their entirety.
1. Technical Field
Exemplary embodiments of the invention are directed to a method of amplifying a target nucleic acid sequence by multiple displacement amplification, and more particularly, to a method of amplifying a target nucleic acid sequence by multiple displacement amplification including thermal cycling.
2. Description of the Related Art
Various methods of amplifying a nucleic acid are known. Those methods include polymerase chain reaction (PCR), ligase chain reaction (LCR), self-sustained sequence replication (3SR), nucleic acid sequence-based amplification (NASBA), strand displacement amplification (SDA), amplification using Qβ replicase and multiple displacement amplification (MDA).
MDA is based on strand displacement amplification of a target nucleic acid sequence performed by a multiplex primer. In MDA, a replicated strand is generated and during replication, at least one replicated strand is displaced from the target nucleic acid sequence by strand displacement replication of another replicated strand. With regard to MDA, an available primer may include a primer set complementary to one strand of a target sequence and a primer set complementary to the other strand of the target sequence. Also, the primer may be a set of primers having a random sequence. Further, the primer may be a set of primers in which each member primer of the set is hybridized to only one strand of a target sequence.
A related art discloses a method of amplifying a target nucleic acid sequence, where the method includes bringing into contact a set of primers, DNA polymerase, and a target sample, and incubating the target sample under conditions that promote replication of the target sequence. The target sample is not subjected to denaturing conditions, and the replication of the target sequence results in replicated strands, in which during replication at least one of the replicated strands is displaced from the target sequence by strand displacement replication of another replicated strand.
MDA is performed at a substantially isothermal temperature and the incubation is performed at a sufficiently low temperature to promote hybridization of the primer with respect to the target sequence. That is, to promote hybridization of the primer, the incubation is performed at a temperature lower than the optimal temperature of a polymerase for its activity. As a result, amplification occurs only with a primer bound in the initial denaturing and annealing phases and at the corresponding location and thus, an amplification bias may occur, thereby reducing the amplification efficiency.
Exemplary embodiments of the invention include a method of amplifying a target nucleic acid sequence by multiple displacement amplification (MDA) including thermal cycling.
Additional aspects will be set forth in part in the description which follows and, in part, will be apparent from the description, or may be learned by the practice of the presented embodiments.
Exemplary embodiments of the invention may include a method of amplifying a target nucleic acid sequence, wherein the method includes: bringing into contact a set of primers, a DNA polymerase, and a target nucleic acid sequence in a solution; and incubating the solution to replicate the target nucleic acid sequence, wherein the replication of the target nucleic acid sequence results in replicated strands and during replication, at least one of the replicated strands is displaced from the target sequence by strand displacement replication of another replicated strand, wherein the incubating is performed while thermal cycling is carried out at a temperature between an optimal temperature range of the DNA polymerase for its activity and a temperature range in which hybridization between the primer and the target nucleic acid sequence is promoted.
Reference will now be made in detail to exemplary embodiments, examples of which are illustrated in the accompanying drawings, wherein like reference numerals refer to the like elements throughout. In this regard, the present embodiments may have different forms and should not be construed as being limited to the descriptions set forth herein. Accordingly, the embodiments are merely described below, by referring to the figures, to explain aspects of the present description.
A method of amplifying a target nucleic acid sequence according to an embodiment of the invention includes bringing into contact a set of primers, a DNA polymerase, and a target nucleic acid in a solution.
The primer may have a length of about 5 to about 20 bp. A melting temperature Tm may vary according to a length and nucleotide composition of the primer used and a component in a reaction solution, for example, a concentration of a cation. The term “melting temperature Tm” used herein refers to the temperature at which half of the strands of nucleic acid molecules among multiple copies of nucleic acid molecules are in the double stranded state and half are in the “random-coil” state. For example, when the primer has a length of about 5 to about 20 bp and a nucleotide of the primer is a natural nucleotide, Tm may be about 10° C. to about 80° C. The primer may have a length of about 5 to about 8 bp. The primer may have a length of about 6 bp. The primer may include, in addition to the natural nucleotide, a modified nucleotide. For example, the primer may include at least one modified nucleotide and thus, is resistant to a nuclease, for example to an exonuclease. The modified nucleotide may be a biotinylated nucleotide, a fluorescent nucleotide, 5 methyl dCTP, BrdUTP, or 5-(3-aminoallyl)-2′-deoxyuridine 5′-triphosphate. The primer may include a DNA or an RNA primer. Also, the primer may be labeled with a detectable label. The set of primers may include a plurality of primers. The set of primers may include 2 or more, for example, 3 or more primers, or 4 or more primers, or 5 or more primers, complementary to the same strand of the target nucleic acid. The set of primers may also include at least one primer complementary to the other stand of the target nucleic acid. The set of primers may include a plurality of primers and each primer may include a complementary portion, wherein the complementary portions of the primers are each complementary to a different portion of the target nucleic acid. The set of primers may include primers having a random nucleotide sequence. In an embodiment of the invention, the primer may be a random primer having a length of 5 bp, 6 bp, 7 bp, or 8 bp, or a mixture thereof.
An optimal temperature of the DNA polymerase for its activity may be higher than a hybridization temperature at which the primer is hybridized to the target sequence. In detail, the optimal temperature of the DNA polymerase may be higher than a denaturation temperature at which the primer hybridized to the target sequence is denatured In this case, a ‘denaturation temperature’ may be a temperature at which about 50% or more of the double strand is denatured, a temperature at which about 60% or more of the double strand is denatured, a temperature at which about 70% or more of the double strand is denatured, a temperature at which about 80% or more of the double strand is denatured, or a temperature at which about 90% or more of the double strand is denatured. That is, when a part of the double strand of the primer strand and the target sequence, for example, about 10%, about 20%, about 30%, about 40%, or about 50% or more is not denatured and remains, amplification may be improved through annealing of a new primer.
According to an embodiment of the invention, the term ‘optimal temperature’ may vary according to a condition, such as a reaction solution, but the optimal temperature of a polymerase used may be obvious to one of ordinary skill in the art under given buffer conditions. The term ‘optimal temperature range’ used herein may be the optimal temperature ±10° C., or the optimal temperature ±5° C., or the optimal temperature ±2.5° C., and lower than a denaturation temperature at which a strand replicated by incubation is denatured within the temperature range in which hybridization between the primer and the target sequence is promoted. The term ‘denaturation temperature’ is the same as described above.
According to an embodiment of the invention, the term ‘hybridization temperature’ refers to, unless additional description is provided, the temperature at which half of hybridizable sites are hybridized by hybridization between the primer and the target sequence. The hybridization temperature may be obvious to one of ordinary skill in the art through experiments or calculation. The hybridization temperature may be calculated by using a method disclosed in SantaLucia. & Hicks (2004) Annu. Rev. Biophys. Biomol. Struct. 33:415-40.
According to an embodiment of the invention, ‘the temperature range in which hybridization between the primer and the target sequence is promoted’ may be a temperature range in which hybridization between the primer and the target sequence is promoted. In this regard, such temperature range may be equal to or lower than the optimal temperature of the DNA polymerase—5° C., the optimal temperature of the DNA polymerase—10° C., or the optimal temperature of the DNA polymerase—15° C.
According to an embodiment of the invention, the optimal temperature range of the DNA polymerase may be in the range of about 30° C. to about 75° C., and the temperature range in which hybridization between the primer and the target sequence is promoted may be in the range of about 0° C. to about 30° C. According to an embodiment of the invention, the optimal activation temperature range of the DNA polymerase may be in the range of about 30° C. to about 75° C., and the temperature range in which hybridization between the primer and the target sequence is promoted may be in the range of about 0° C. to about 30° C. The optimal temperature range of the DNA polymerase, for example, the optimal temperature range of a φ29 DNA polymerase may be about 32° C., the optimal temperature range of an exo(−) Bst DNA polymerase may be about 65° C., the optimal temperature range of a VENT™ exo− DNA polymerase may be about 75° C., the optimal temperature range of a 9°Nm DNA polymerase may be about 75° C., the optimal temperature range of a Klenow fragment may be about 37° C., and the optimal temperature range of a MMLV reverse transcriptase may be about 42□.
The DNA polymerase is a polymerase that enables strand replacement replication, and may be a φ29 DNA polymerase, a Tts DNA polymerase, an M2 DNA polymerase, a VENT™ DNA polymerase, a T5 DNA polymerase, a PRD1 DNA polymerase, or a Bst DNA polymerase, but is not limited thereto.
aKunkel et al. (1987) Proc. Natl. Acad. Sci. USA, 84, 4865-4869
bMattila, P., Korpela, J., Tenkanen, T. and Pitkanen, K. (1991) Nucleic Acids Res., 19, 4967-4973
dKm DNA is represented by a mole of a primer-template composite.
gKong, H. M., Kucera, R. B. and Jack, W. E., (1993) J. Biol. Chem., 268, 1965-1975.
kPolesky, A. H., Steitz, T. A., Grindley, N. D. F. and Joyce, C. M. (1990) J. Biol. Chem., 265, 14579-14591.
pRicchetti, M. and Buc, H. (1990) EMBO J., 9, 1583-1593
xSouthworth, M. W. et al. (1996) Proc. Natl. Acad. Sci. USA, 93, 5281-5285.
wBebenek, K., Joyce, C. M., Fitzgerald, M. P. and Kunkel, T. A. (1990) J. Biol. Chem., 265, 13878-13887.
yAmount of dNTP introduction into a RNA or DNA primer is compared to when a single-strand M13 DNA is used as a template.
According to an embodiment of the invention, the DNA polymerase may be the φ29 DNA polymerase, and the optimal temperature range may be about 30° C. to about 34° C., for example about 32° C. and the temperature at which hybridization is promoted may be about 4° C. to about 22° C., for example about 20° C. In this case, the primer may be a random primer having a length of about 6 bp or a primer having a particular sequence.
According to an embodiment of the invention, the DNA polymerase may be the exo(−) Bst DNA polymerase, the optimal temperature range may be about 46° C. to about 75° C., for example about 65° C., and the temperature at which hybridization is promoted may be about 4° C. to about 35° C., for example about 30° C. In this case, the primer may be a random primer having a length of about 6 bp or a primer having a particular sequence.
The target nucleic acid may be in the form of a material selected from the group consisting of blood, urine, semen, a lymphatic fluid, a cerebrospinal fluid, an amniotic fluid, a biopsy sample, a needle-aspiration biopsy, a maycer sample, a tumor sample, a tissue sample, a cell, cell debris, auxiliary debris, and combinations of at least two of the foregoing materials. The target nucleic acid may be a sample including the whole genome, or the whole genome itself.
The primer, the DNA polymerase, and the target nucleic acid may be brought into contact in an appropriate solution. The appropriate solution may vary according to the type of a polymerase used in amplification of a nucleic acid sequence, selected by one of ordinary skill in the art. For example, when the DNA polymerase is the φ29 DNA polymerase, the appropriate solution may be a solution including about 37 mM Tris-HCl, pH 8.0, about 50 mM KCl, about 10 mM MgCl2, and about 5 mM (NH4)2SO4.
In a method according to an embodiment of the invention, bringing into contact may or may not include an initial operation that includes denaturing, for example, high-temperature denaturing the primer and the target sequence and annealing. However, except for the initial operation, the target sequence may not be exposed to conditions for denaturing the target sequence. If the polymerase is thermally stable, the denaturing and annealing may be performed in the presence of the polymerase.
A method according to an embodiment of the invention may include incubating the solution to replicate the target nucleic acid sequence. The incubating may be performed while thermal cycling is carried out between an optimal temperature range of the DNA polymerase for its activity and a temperature range in which hybridization between the primer and the target sequence is promoted. The optimal temperature range of the DNA polymerase and the temperature range in which hybridization between the primer and the target sequence is promoted may be the same as described above. The thermal cycling may include incubating the solution in the ‘optimal temperature range of the DNA polymerase’ for a predetermined time period, for example, from about 30 seconds to about 6 hours, and incubating the solution in the ‘temperature range in which hybridization between the primer and the target sequence is promoted’ for a predetermined time period, for example, from about 30 seconds to about 3 minutes. In detail, the solution is first incubated in the ‘temperature range in which hybridization between the primer and the target sequence is promoted’ to induce annealing and elongation of the primer with respect to the target sequence, and then incubated in the ‘optimal temperature range of the DNA polymerase.’ However, the opposite case is also possible.
The incubating may be performed in a condition including a reaction component used for polymerization of a polymerase, such as dNTPs, ATP or salt.
In a method according to an embodiment of the invention, the incubating may be performed in a condition under which the target nucleic acid is not denatured.
In a method according to an embodiment of the invention, the replication of the target nucleic acid results in a replicated strand and during replication, at least one of the replicated strands is displaced from the target sequence by strand displacement replication of another replicated strand. As described above, a DNA polymerase used in an embodiment of the invention needs to be combined with a single or appropriate strand replacement factor and displace a hybridized strand during replication. Hereinafter, the DNA polymerase will be referred to as a strand replacement DNA polymerase. The strand replacement DNA polymerase may not have 5′→3′ exonuclease activity. The strand replacement is needed to synthesize a multiple copy of the target sequence. If the 5′→3′ exonuclease activity exists, the synthesized strand may be destroyed. The strand replacement may be promoted by a strand replacement factor, such as helicase. The strand replacement DNA polymerase may be highly processive. Due to the strand replacement, replication is made from the multiple displacement copy, and such an amplification method is referred to as a multiple displacement amplification (MDA). Multiple displacement amplification is known in the art (see U.S. Pat. No. 6,124,120, the contents of which are herein incorporated by reference in their entirety).
According to an embodiment of the present invention, the target nucleic acid sequence includes DNA, RNA, and PNA. Also, the target nucleic acid sequence includes, in addition to natural nucleotides, a modified nucleotide. The target nucleic acid may be a double stranded or a single stranded nucleic acid.
The above embodiments will be described in further detail with reference to the following examples. These examples are for illustrative purposes only and are not intended to limit the scope of embodiments of the present invention.
In the current example, an exo(−) Bst DNA polymerase (New England Biolab) was used as a Bst DNA polymerase. The exo(−) Bst DNA polymerase, a hexamer random primer (Bioneer Co., Korea), and a human genome sample obtained by purifying blood using a blood DNA purification kit (Qiagen Co.) were brought into contact in a Bst DNA polymerase buffer (about 20 mM Tris-HCl, about 10 mM (NH4)2SO4, about 10 mM KCl, about 2 mM MgSO4, about 0.1% Triton X-100, pH about 8.8 at about 25° C.) (New England Biolab), and then incubated at about 30° C. or about 60° C., or while thermal cycling was carried out between about 30° C. and about 60° C. When the thermal cycling was performed between about 30° C. and about 60° C., the thermal cycling was performed at 30° C. for about 20 seconds and at about 60° C. for about 40 seconds in a polymerase chain reaction (PCR) device.
The exo(−) Bst DNA polymerase is known to have the optimal activity at a temperature of about 65° C. (Mead, D. A. et al (1991) Biotechniques, 11, 76-87). After the reaction was finished, the obtained amplification product was electrophoresed in an about 1% gel by using an electrophoresis device, and then specifically labeled with SYBR Green I with respect to a double-strand DNA. Then, the resultant product was irradiated with an excitation light having a wavelength of about 480 nm and light emission was detected at 580 nm.
Referring to
As described above, improvement of target sequence amplification efficiency while thermal cycling is carried out may be achieved based on the following mechanism. However, embodiments of the invention are not limited to the mechanism.
First, a random hexamer primer, an exo(−) Bst DNA polymerase, and a human genome were incubated at about 60° C. to denature the sequence of a part of the human genome. However, since 60° C. is a temperature higher than Tm of the random hexamer primer, the random hexamer primer was not hybridized to the target sequence. When the incubation temperature was decreased to about 30° C., the random hexamer primer was hybridized to the target sequence and elongated. Then, the incubation temperature was increased to about 60° C., the elongated random hexamer primer will be partially denatured and may not separate from the target sequence. When the incubation temperature was decreased from about 60° C. to about 30° C., a new random hexamer primer was hybridized to the denatured target sequence part that had been denatured at about 60° C. and elongated. As described above, due to thermal cycling, annealing of the primer is increased and thus, the primer elongation is increased. As a result, the amplification efficiency of the target sequence is increased.
According to a method of amplifying a target nucleic acid sequence according to embodiments of the invention, the target nucleic acid sequence may be efficiently amplified.
It should be understood that the exemplary embodiments described herein should be considered in a descriptive sense only and not for purposes of limitation. Descriptions of features or aspects within each embodiment should typically be considered as available for other similar features or aspects in other embodiments.
| Number | Date | Country | Kind |
|---|---|---|---|
| 10-2008-0078141 | Aug 2008 | KR | national |
