WO2002086444A9 - Methods and compositions for mutation analysis - Google Patents
Methods and compositions for mutation analysisInfo
- Publication number
- WO2002086444A9 WO2002086444A9 PCT/US2002/012583 US0212583W WO02086444A9 WO 2002086444 A9 WO2002086444 A9 WO 2002086444A9 US 0212583 W US0212583 W US 0212583W WO 02086444 A9 WO02086444 A9 WO 02086444A9
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- WIPO (PCT)
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- pcr
- double stranded
- polymerase
- stranded dna
- composition
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6813—Hybridisation assays
- C12Q1/6827—Hybridisation assays for detection of mutation or polymorphism
Definitions
- the present invention concerns improvements in the detection of mutations in nucleic acids.
- the invention concerns methods, compositions, and kits for mutation analysis using denaturing high performance liquid chromatography (DHPLC).
- DHPLC denaturing high performance liquid chromatography
- the invention concerns DNA polymerase enzymes, and PCR buffers used in preparing samples for mutation analysis by DHPLC.
- the ability to detect mutations in double stranded polynucleotides, and especially in DNA fragments, is of great importance in medicine, as well as in the physical and social sciences.
- the Human Genome Project is providing an enormous amount of genetic information which is setting new criteria for evaluating the links between mutations and human disorders (Guyer et al., Proc. Natl. Acad. Sci. U.S.A 92:10841 (1995)).
- the ultimate source of disease for example, is described by genetic code that differs from wild type (Cotton, TIG 13:43 (1997)). Understanding the genetic basis of disease can be the starting point for a cure.
- determination of differences in genetic code can provide powerful and perhaps definitive insights into the study of evolution and populations (Cooper, et.
- DNA molecules are polymers comprising sub-units called deoxynucleotides.
- the four deoxynucleotides found in DNA comprise a common cyclic sugar, deoxyribose, which is covalently bonded to any of the four bases, adenine (a purine), guanine (a purine), cytosine (a pyrimidine), and thymine (a pyrimidine), hereinbelow referred to as A, G, C, and T respectively.
- a phosphate group links a 3'-hydroxyl of one deoxynucleotide with the 5'- hydroxyl of another deoxynucleotide to form a polymeric chain.
- double stranded DNA two strands are held together in a helical structure by hydrogen bonds between, what are called, complementary bases. The complementarity of bases is determined by their chemical structures.
- double stranded DNA each A pairs with a T and each G pairs with a C, i.e., a purine pairs with a pyrimidine.
- DNA is replicated in exact copies by DNA polymerases during cell division in the human body or in other living organisms. DNA strands can also be replicated in vitro by means of the Polymerase Chain Reaction (PCR).
- PCR Polymerase Chain Reaction
- double stranded DNA is referred to as a duplex.
- a duplex When the base sequence of one strand is entirely complementary to base sequence of the other strand, the duplex is called a homoduplex.
- a duplex contains at least one base pair which is not complementary, the duplex is called a heteroduplex.
- a heteroduplex can be formed during DNA replication when an error is made by a DNA polymerase enzyme and a non- complementary base is added to a polynucleotide chain being replicated.
- a heteroduplex can also be formed during repair of a DNA lesion.
- heteroduplexes which are heterozygous, i.e., these homoduplexes will have an altered sequence compared to the original parent DNA strand.
- parent DNA has the sequence which predominates in a natural population it is generally called the "wild type.”
- DNA mutations include, but are not limited to, "point mutation” or “single base pair mutations” wherein an incorrect base pairing occurs.
- the most common point mutations comprise “transitions” wherein one purine or pyrimidine base is replaced for another and “transversions” wherein a purine is substituted for a pyrimidine (and visa versa).
- Point mutations also comprise mutations wherein a base is added or deleted from a DNA chain.
- Such "insertions” or “deletions” are also known as “frameshift mutations”. Although they occur with less frequency than point mutations, larger mutations affecting multiple base pairs can also occur and may be important.
- a more detailed discussion of mutations can be found in U.S. Pat. No. 5,459,039 to Modrich (1995), and U.S. Pat. No. 5,698,400 to Cotton (1997).
- the sequence of base pairs in DNA codes for the production of proteins.
- a DNA sequence in the exon portion of a DNA chain codes for a corresponding amino acid sequence in a protein. Therefore, a mutation in a DNA sequence may result in an alteration in the amino acid sequence of a protein. Such an alteration in the amino acid sequence may be completely benign or may inactivate a protein or alter its function to be life threatening or fatal.
- Detection of mutations is, therefore, of great interest and importance in diagnosing diseases, understanding the origins of disease and the development of potential treatments. Detection of mutations and identification of similarities or differences in DNA samples is also of critical importance in increasing the world food supply by developing diseases resistant and/or higher yielding crop strains, in forensic science, in the study of evolution and populations, and in scientific research in general (Guyer et al., Proc. Natl. Acad. Sci. U.S.A 92:10841 (1995); Cotton, TIG 13:43 (1997)). These references and the references contained therein are incorporated in their entireties herein.
- any alterations in the DNA sequence, whether they have negative consequences or not, are called “mutations”. It is to be understood that the method of this invention has the capability to detect mutations regardless of biological effect or lack thereof.
- the term “mutation” will be used throughout to mean an alteration in the base sequence of a DNA strand compared to a reference strand. It is to be understood that in the context of this invention, the term “mutation” includes the term “polymorphism” or any other similar or equivalent term of art.
- IP-RP-HPLC ion-pair reverse-phase high pressure liquid chromatography
- Ml PC Matched Ion Polynucleotide Chromatography
- IP-RP-HPLC IP-RP-HPLC analyses were carried out at a partially denaturing temperature, i.e., a temperature sufficient to denature a heteroduplex at the site of base pair mismatch, homoduplexes could be separated from heteroduplexes having the same base pair length (Hayward- Lester, et al., Genome Research 5:494 (1995); Underhill, et al., Proc. Natl. Acad. Sci. U.S.A 93:193 (1996); Doris, et al., DHPLC Workshop, Stanford University, (1997)). These references and the references contained therein are incorporated herein in their entireties.
- DPLC denaturing high performance liquid chromatography
- test nucleic acid fragment is hybridized with a wild type fragment and analyzed by
- the hybridization product ideally includes both homoduplex and heteroduplex molecules. If no mutation is present, then the hybridization only produces homoduplex wild type molecules.
- the elution profile of the hybridized test fragment can be compared to a control in which a wild type fragment is hybridized to another wild type fragment. Any change in the elution profile (such as the appearance of new peaks or shoulders) between the hybridized test fragment and the control is assumed to be due to a mutation in the test fragment.
- SNPs Single nucleotide polymorphisms
- SNPs Single nucleotide polymorphisms
- the human genome may contain over 3 million SNPs. Due to their propensity they lend themselves to very high resolution genotyping.
- the SNP consortium a joint effort of 10 major pharmaceutical companies, has announced the development of 300,000 SNP markers and their placement in the public domain by mid 2001.
- DHPLC denaturing gradient gel electrophoresis
- the ability of DHPLC to detect mutations may be less than 100% in some cases.
- the invention provides a method for mutation detection of a double stranded DNA fragment by DHPLC (denaturing high performance liquid chromatography), the double stranded DNA fragment corresponding to a wild type double stranded DNA fragment having a known nucleotide sequence.
- the method includes (a) amplifying a section of the double stranded DNA fragment by PCR using a set of primers which flank the ends of the section, wherein the PCR is conducted with Pho DNA polymerase; (b) hybridizing the amplification product of step (a) with wild type double stranded DNA corresponding to the section, whereby a mixture comprising one or more heteroduplexes is formed if the section includes a mutation; and (c) analyzing the product of step (b) by denaturing high performance liquid chromatography.
- the section being amplified can be indicative of a disease state.
- the invention concerns a method for mutation detection of a double stranded DNA fragment by denaturing high performance liquid chromatography, the double stranded DNA fragment corresponding to a wild type double stranded DNA fragment having a known nucleotide sequence, in which the method includes the steps of: (a) in a PCR mixture, amplifying a section of the double stranded DNA fragment by PCR using a set of primers which flank the ends of the section, wherein the PCR is conducted with a proofreading DNA polymerase; (b) hybridizing the amplification product of step
- step (a) with wild type double stranded DNA corresponding to the section, whereby a mixture comprising one or more heteroduplexes is formed if the section includes a mutation; and (c) analyzing the product of step (b) by denaturing high performance liquid chromatography, wherein the PCR is conducted in a
- PCR buffer wherein the PCR buffer is characterized by having a DHPLC
- the PCR buffer can include one or more non-ionic detergents having a total concentration no greater than 0.01% volume/total volume of the PCR buffer.
- the PCR buffer can include a non-ionic detergent having a concentration no greater than 0.01 % volume/total volume of the total reaction mixture.
- the PCR buffer preferably is substantially free from substances that can interfere with DHPLC analysis.
- the substances include BSA, metal ions, quanidinium, and formamide.
- the preferred PCR mixture is characterized by having a DHPLC Incompatibility Index no greater than 0.05, and more preferably no greater than 0.01.
- the detergent is present in the PCR mixture at a concentration no greater than 0.09%, preferably no greater than 0.05%, and more preferably no greater than 0.01% volume/total volume of the PCR mixture.
- a suitable detergent is TRITON X-100 (t-octylphenoxypolyethoxyethanol).
- the polymerase is preferably Pho polymerase.
- the proofreading DNA polymerase can be Taq, Tbr, Tfl, Tru, Tth, Tli, Tac, Tne, Tma, Tih, Tfi, Pfu, Pwo, Kod, Bst, Sac, Sso, Poc, Pab, Mth, Pho, ES4, VENT, DEEPVENT, PFUTurbo, AmpliTaq, or a combination thereof.
- the polymerase can be an active mutant, variant or derivative of a proofreading DNA polymerase.
- a method for preparing a sample of double stranded DNA fragment for mutation detection by denaturing high performance liquid chromatography the double stranded DNA fragment corresponding to a wild type double stranded DNA fragment having a known nucleotide sequence
- the method including: in a PCR mixture, amplifying a section of the double stranded DNA fragment by PCR using a set of primers which flank the ends of the section, wherein the PCR is conducted with Pho DNA polymerase, wherein the PCR is conducted in a PCR buffer, wherein the PCR buffer is characterized by having a DHPLC Incompatibility Index no greater than 0.01.
- the invention provides a composition for use in preparing samples for analysis by DHPLC, in which the composition consists of a PCR buffer which is characterized by having a DHPLC Incompatibility Index of no greater than 0.1 , preferably no greater than 0.05 and most preferably no greater than 0.01.
- the composition can also include a proofreading polymerase, preferably Pho DNA polymerase, and one or more non-ionic detergents present in a concentration no greater than 0.01% volume/total volume of said composition.
- the composition is preferably devoid of bovine serum albumin or other substances that can interfere with DHPLC analysis.
- An example of such a composition is a PCR mixture.
- a composition for use in preparing samples for analysis by DHPLC including: a proofreading polymerase, preferably Pho DNA polymerase, wherein the polymerase is stored in a storage solution, wherein a portion of the storage solution is included in a PCR mixture which also includes a PCR buffer, wherein the PCR mixture is characterized by a DHPLC Incompatibility Index of no greater than 0.05, and preferably no greater than 0.01.
- the storage solution can include a non-ionic detergent, such as t-octylphenoxypolyethoxyethanol at a concentration no greater than 0.5% volume/total volume of the storage solution, and preferably no greater than 0.1%.
- the storage solution is preferably devoid of substances, such as BSA, that can interfere with DHPLC analysis.
- the invention includes a composition for use in preparing samples for analysis by denaturing high performance liquid chromatography, the composition including: a proofreading polymerase, wherein the polymerase is stored in a storage solution, wherein when the storage solution is characterized by having a DHPLC Incompatibility Index no greater than 0.05 and preferably no greater than 0.01.
- kits for preparing a double stranded DNA for mutation detection by denaturing high performance liquid chromatography can include one or more of: a container which contains a composition including a proofreading polymerase, preferably Pho polymerase, and which contains one or more non-ionic detergents present at a concentration no greater than 0.1%, wherein the composition is devoid of bovine serum albumin; a container which contains a mutation standard; a container which contains one or more PCR primers; a container which contains a PCR buffer, wherein the buffer is characterized by having a DHPLC Incompatibility Index no greater than 0.05 and preferably no greater than 0.01; a separation column for use in denaturing high performance liquid chromatography; a DHPLC system; a container which contains a composition comprising Pho DNA polymerase containing non-ionic detergent present in a concentration no greater than 0.1% (volume/total volume of the composition) with a container which contains a reaction buffer, wherein the reaction buffer
- a method for preparing a sample of double stranded DNA fragment for mutation detection by denaturing high performance liquid chromatography the double stranded DNA fragment corresponding to a wild type double stranded DNA fragment having a known nucleotide sequence
- the method including: in a PCR mixture, amplifying a section of the double stranded DNA fragment by PCR using a set of primers which flank the ends of the section, wherein the PCR is conducted with Pho DNA polymerase, wherein the PCR is conducted in a PCR buffer, wherein the PCR buffer is characterized by having a DHPLC Incompatibility Index no greater than 0.01.
- FIG. 1 shows a schematic representation of a hybridization to form homoduplex and heteroduplex DNA molecules and the mutation separation profile of the molecules.
- FIG. 2 illustrates PCR product profiles obtained using various DNA polymerases.
- FIG. 3 illustrates PCR product profiles obtained using two different DNA polymerases.
- FIG. 4 shows the percentage of heteroduplex DNA produces after PCR by various DNA polymerases.
- FIG. 5 illustrates a procedure for calculating the area due to heteroduplex DNA and homoduplex DNA.
- FIG. 6 shows overlaid PCR product profiles obtained from multiple separate injections of the PCR product obtained from Pho polymerase.
- FIG. 7 shows overlaid PCR product profiles obtained from multiple separate injections of the PCR product obtained from a non-proofreading polymerase.
- FIG. 8 shows overlaid PCR product profiles obtained from multiple separate injections of the PCR product obtained from Pfu polymerase.
- FIG. 9 illustrates the effect of multiple injections of a first reaction buffer on the performance of a separation column as measured by the retention time of heteroduplex DNA in a standard mixture of homoduplex and heteroduplex molecules.
- FIG. 10 illustrates the effect of multiple injections of a second reaction buffer on the retention time of heteroduplex DNA in a standard mixture of homoduplex and heteroduplex molecules.
- FIG. 11 is a schematic illustration showing the calculation of a DHPLC
- FIG. 12 illustrates the effect of multiple injections of a third reaction buffer on the retention time of heteroduplex DNA in a standard mixture of homoduplex and heteroduplex molecules.
- FIG. 13 shows an elution profile of a mutation standard.
- a reliable way to detect mutations is by hybridization of the putative mutant strand in a sample with the wild type strand (Lerman, et al., Meth. Enzymol., 155:482 (1987)). If a mutant strand is present, then, typically, two homoduplexes and two heteroduplexes will be formed as a result of the hybridization process. Hence separation of heteroduplexes from homoduplexes provides a direct method of confirming the presence or absence of mutant DNA segments in a sample.
- the DNA sample for mutation detection is routinely the product of a polymerase chain reaction (PCR).
- the instant invention concerns methods and compositions for use during PCR amplification of DNA in preparing samples for analysis by DHPLC.
- the present invention concerns methods, compositions, and kits and devices for preparing a sample for analysis by DHPLC.
- One aspect of the instant invention is based in part on the surprising discovery by Applicants that Pho DNA polymerase exhibited surprisingly improved performance as compared to a variety of other DNA polymerases.
- Other aspects of the invention are based on the discovery by Applicants that certain components commonly included in PCR buffers and storage solutions, such as found in commercially available PCR kits, interfere with analysis of PCR products by DHPLC.
- Mutation analysis involves a DNA separation process and can be performed by a variety of liquid chromatographic separation methods.
- liquid chromatographic methods include IP-RP-HPLC and ion exchange chromatography where these are performed under partially denaturing conditions.
- ion exchange chromatography is disclosed in
- nucleic acids refers to either DNA or RNA. It includes plasmids, infectious polymers of DNA and/or RNA, nonfunctional DNA or RNA, chromosomal DNA or RNA and DNA or RNA synthesized in vitro (such as by the polymerase chain reaction).
- Nucleic acid sequence or “polynucleotide sequence” refers to a single- or double-stranded polymer of deoxyribonucleotide or ribonucleotide bases read from the 5' to the 3' end.
- DNA molecule refers to DNA molecules in any form, including naturally occurring, recombinant, or synthetic DNA molecules.
- the term includes plasmids, bacterial and viral DNA as well as chromosomal DNA.
- the term encompasses DNA fragments produced by cell lysis or subsequent manipulation of DNA molecules. Unless specified otherwise, the left hand end of single-stranded DNA sequences is the 5' end.
- complementary includes reference to a relationship between two nucleic acid sequences.
- One nucleic acid sequence is complementary to a second nucleic acid sequence if it is capable of forming a duplex with the second nucleic acid, wherein each residue of the duplex forms a guanosine-cytidine (G-C) or adenosine-thymidine (A-T) basepair or an equivalent basepair.
- G-C guanosine-cytidine
- A-T adenosine-thymidine
- Equivalent basepairs can include nucleoside or nucleotide analogues other than guanosine, cytidine, adenosine, or thymidine, which are capable of being incorporated into a nucleic acid by a DNA or RNA polymerase on a DNA template.
- a complementary DNA sequence can be predicted from a known sequence by the normal basepairing rules of the DNA double helix (see Watson J. D., et al. (1987) Molecular Biology of the Gene, Fourth Edition, Benjamin Cummings Publishing Company, Menlo Park, Calif., pp. 65-93).
- Complementary nucleic acids may be of different sizes. For example, a smaller nucleic acid may be complementary to a portion of a larger nucleic acid.
- purified DNA or “purified DNA molecule,” as used herein, include reference to DNA that is not contaminated by other biological macromolecules, such as RNA or proteins, or by cellular metabolites. Purified
- DNA contains less than 5% contamination (by weight) from protein, other cellular nucleic acids and cellular metabolites.
- contamination by weight
- unpurified DNA molecules refer to preparations of DNA that have greater than 5% contamination from other cellular nucleic acids, cellular proteins and cellular metabolites. Unpurified DNA may be obtained by using a single purification step, such as precipitation with ethanol combined with either LiCI or polyethylene glycol.
- the term "crude cell lysate preparation” or “crude cell lysate” or “crude lysate” refers to an unpurified DNA preparation where cells or viral particles have been lysed but where there has been no further purification of the DNA.
- IP-RP-HPLC ion-pair reverse-phase high performance liquid chromatography
- MIPC Magnetic Ion Polynucleotide Chromatography
- chromatographic elution profile as used herein is defined to include the data generated by the IP-RP-HPLC method when this method is used to separate double stranded DNA fragments.
- the chromatographic profile can be in the form of a visual display, a printed representation of the data or the original data stream.
- IP-RP-HPLC as used herein includes a chromatographic process for separating single and double stranded polynucleotides using non-polar separation media, wherein the process uses a counter ion agent, and an organic solvent to release the polynucleotides from the separation media.
- IP- RP-HPLC separations can be completed in less than 10 minutes, and frequently in less than 5 minutes.
- IP-RP-HPLC systems e.g., the WAVE® DNA Fragment Analysis System, Transgenomic, Inc. San Jose, CA
- IP-RP-HPLC systems are preferably equipped with computer controlled ovens which enclose the columns. Mutation detection at the temperature required for partial denaturation (melting) of the DNA at the site of mutation can therefore be easily performed.
- the system used for IP-RP-HPLC separations is rugged and provides reproducible results. It is preferably computer controlled and the entire analysis of multiple samples can be automated.
- the system preferably offers automated sample injection, data collection, choice of predetermined eluting solvent composition based on the size of the fragments to be separated, and column temperature selection based on the base pair sequence of the fragments being analyzed.
- the separated mixture components can be displayed either in a gel format as a linear array of bands or as an array of peaks.
- the display can be stored in a computer storage device. The display can be expanded and the detection threshold can be adjusted to optimize the product profile display.
- the reaction profile can be displayed in real time or retrieved from the storage device for display at a later time.
- a mutation separation profile, a genotyping profile, or any other chromatographic separation profile display can be viewed on a video display screen or as hard copy printed by a printer.
- a “homoduplex” is defined herein to include a double stranded DNA fragment wherein the bases in each strand are complementary relative to their counterpart bases in the other strand.
- a heteroduplex is defined herein to include a double stranded DNA fragment wherein at least one base in each strand is not complementary to at least one counterpart base in the other strand. Since at least one base pair in a heteroduplex is not complementary, it takes less energy to separate the bases at that site compared to its fully complementary base pair analog in a homoduplex. This results in the lower melting temperature at the site of a mismatched base of a heteroduplex compared to a homoduplex.
- a heteroduplex can be formed by annealing of two nearly complementary sequences.
- hybridization refers to a process of heating and cooling a double stranded DNA (dsDNA) sample, e.g., heating to 95°C followed by slow cooling.
- the heating process causes the DNA strands to denature.
- the strands re-combine, or anneal, into duplexes.
- IP-RP-HPLC when performed at an elevated temperature which is sufficient to denature that portion of a DNA fragment domain which contains a heteromutant site, then heteroduplexes separate from homoduplexes.
- IP-RP-HPLC when performed at a temperature which is sufficient to partially denature a heteroduplex, is referred to as DHPLC.
- DHPLC is also referred to in the art as "Denaturing Matched Ion Polynucleotide Chromatography" (DMIPC).
- the determination of a mutation is preferably made by hybridizing the homozygous sample with the known wild type fragment and performing a DHPLC analysis at a partially denaturing temperature. If the sample contained only wild type fragments then a single peak would be seen in the DHPLC analysis since no heteroduplexes could be formed.
- the determination of a mutation can be made by hybridizing the homozygous sample with the corresponding wild type fragment and performing a DHPLC analysis. If the sample contained only wild type fragments then a single peak would be seen in the DHPLC analysis since no heteroduplexes could be formed. If the sample contained homozygous mutant fragments or was heterozygous for the mutation, then analysis by DHPLC can be used to detect the separation of homoduplexes and heteroduplexes.
- mutant separation profile is defined herein to include a DHPLC separation chromatogram which shows the separation of heteroduplexes from homoduplexes. Such separation profiles are characteristic of samples which contain mutations or polymorphisms and have been hybridized prior to being separated by DHPLC.
- the DHPLC separation chromatogram 102 shown in FIG. 1 exemplifies a mutation separation profile as defined herein.
- “Mutation standards” are defined herein to include mixtures of DNA species that when hybridized and analyzed by DHPLC, produce previously characterized mutation separation profiles which can be used to evaluate the performance of the chromatography system. Mutation standards can be obtained commercially (e.g. a WAVE® System Low Range Mutation Standard, part no. 560077, GCH338 Mutation Standard (part no. 700215), and HTMS219
- the 209 base pair mutation standard comprises a 209-bp fragment from the human Y chromosome locus DYS217 (GenBank accession number S76940)).
- FIG. 1 Analysis of a 209bp Mutation Standard (Transgenomic) is illustrated in FIG. 1.
- the mutation standard Prior to injection of the mixture onto the separation column, the mutation standard is preferably hybridized as shown in the scheme 100.
- the hybridization process created two homoduplexes and two heteroduplexes.
- the hybridization product was separated using DHPLC.
- the two lower retention time peaks represent the two heteroduplexes and the two higher retention time peaks represent the two homoduplexes.
- the two homoduplexes separate because the A-T base pair denatures at a lower temperature than the C-G base pair.
- the results are consistent with a greater degree of denaturation in one duplex and/or a difference in the polarity of one partially denatured heteroduplex compared to the other, resulting in a difference in retention time on the reverse-phase separation column.
- PCR polymerase chain reaction
- Stationary phases for carrying out the separation include reverse-phase supports composed of alkylated base materials, such as silica, polyacrylamide, alumina, zirconia, polystyrene, and styrene-divinyl copolymers.
- Styrene-divinyl copolymer base materials include copolymers composed of i) a monomer of styrene such as styrene, alkyl-substituted styrenes, ⁇ -methylstyrene, or alkyl substituted ⁇ -methylstyrenes and ii) a divinyl monomer such as divinylbenzene or divinylbutadiene.
- the surface of the base material is alkylated with hydrocarbon chains containing from about 4-18 carbon atoms.
- the stationary support is composed of beads from about 1-100 microns in size.
- a suitable column based on a polymeric stationary support is the DNASep ® column (Transgenomic).
- An example of a suitable column based on a silica stationary support is the Microsorb Analytical column (Varian and Rainin).
- Monolithic columns including capillary columns, can also be used, such as disclosed in U.S. Pat. No. 6,238,565; U.S. Patent Application No. 09/562,069 filed May 1 , 2000; the PCT application WOOO/15778; and by Huber et al (Anal. Chem. 71 :3730-3739 (1999)).
- the length and diameter of the separation column, as well as the system mobile phase pressure and temperature, and other parameters, can be varied as is known in the art.
- Size-based separation of DNA fragments can also be performed using batch methods and devices as disclosed in U.S. Pat. Nos. 6,265,168; 5,972,222; and 5,986,085.
- the mobile phase contains an ion-pairing agent (i.e. a counter ion agent) and an organic solvent.
- Ion-pairing agents for use in the method include lower primary, secondary and tertiary amines, lower trialkylammonium salts such as triethylamm ⁇ nium acetate and lower quaternary ammonium salts.
- the ion-pairing reagent is present at a concentration between about 0.05 and 1.0 molar.
- Organic solvents for use in the method include solvents such as methanol, ethanol, 2-propanol, acetonitrile, and ethyl acetate.
- the mobile phase for carrying out the separation of the present invention contains less than about 40% by volume of an organic solvent and greater than about 60% by volume of an aqueous solution of the ion-pairing agent.
- elution is carried out using a binary gradient system.
- At least partial denaturation of heteroduplex molecules can be carried out several ways including the following. Temperatures for carrying out the separation method of the invention are typically between about 40° and 70°C, preferably between about 55°-65°C. In a preferred embodiment, the separation is carried out at 56° C. Alternatively, in carrying out a separation of GC-rich heteroduplex and homoduplex molecules, a higher temperature (e.g., 64°C) is preferred.
- a wide variety of liquid chromatography systems are available that can be used for conducting DHPLC. These systems typically include software for operating the chromatography components, such as pumps, heaters, mixers, fraction collection devices, injector. Examples of software for operating a chromatography apparatus include HSM Control System (Hitachi), ChemStation (Agilent), VP data system (Shimadzu), Millennium32 Software (Waters), Duo-Flow software (Bio-Rad), and ProStar Biochromatography HPLC System (Varian).
- the operating temperature and the mobile phase composition can be determined by trial and error. However, these parameters are preferably obtained by using software.
- Computer software that can be used in carrying out DHPLC is disclosed in the following patents and patent applications: U.S. Pat. No. 6,287,822; 6,197,516; U.S. Patent Application no. 09/469,551 filed Dec. 22, 1999; and in WO0146687 and WO0015778. Examples of software for predicting the optimal temperature for DHPLC analysis are disclosed by Jones et al. in Clinical Chem. 45:113-1140 (1999) and in the website having the address of http://insertion.stanford.edu/melt.html. And example of a commercially available software includes WAVEMaker® software and Navigator® software (Transgenomic, Inc.).
- Non-ionic polymeric detergents refers to surface-active agents that have no ionic charge and which can stabilize a polymerase enzyme herein at a pH range of from about 3.5 to about 9.5, preferably from 4 to 8.5.
- the polymerae enzyme herein can be stored in a buffer that contains one or more non-ionic polymeric detergents.
- the PCR buffers described herein can include one or more non-ionic detergents.
- Such detergents are generally those that have a molecular weight in the range of approximately 100 to 250,000, preferably about 4,000 to 200,000 daltons and stabilize the enzyme at a pH of from about 3.5 to about 9.5, preferably from about 4 to 8.5.
- Examples of such detergents include those specified on pages 295-298 of McCutcheon's Emulsifiers & Detergents, North American edition (1983), published by the McCutcheon Division of MC Publishing Co., 175 Rock Road, Glen Rock, N.J.
- the detergents are selected from the group comprising ethoxylated fatty alcohol ethers and lauryl ethers, ethoxylated alkyl phenols, octylphenoxy polyethoxy ethanol compounds, modified oxyethylated and/or oxypropylated straight-chain alcohols, polyethylene glycol monooleate compounds, polysorbate compounds, and phenolic fatty alcohol ethers.
- the detergent can be selected from the group consisting of a polyoxyethylated sorbitan monolaurate, an ethoxylated nonyl phenol, ethoxylated fatty alcohol ethers, laurylethers, ethoxylated alkyl phenols, octylphenoxy polyethoxy ethanol compounds, modified oxyethylated and/or oxypropylated straight chain alcohols, polyethylene glycol monooleate compounds, polysorbate compounds, and phenolic fatty alcohol ethers or a combination thereof.
- the detergent can be a polyoxyethylated sorbitan monolaurate, an ethoxylated nonyl phenol or a combination thereof.
- Tween 20 from ICI Americas Inc., Wilmington, Del., which is a polyoxyethylated (20) sorbitan monolaurate, lconol.TM. NP-40, from BASF Wyandotte Corp. Parsippany, N.J., which is an ethoxylated alkyl phenol (nonyl), and Triton® X-100 (t- octylphenoxypolyethoxyethanol available from Sigma-Aldrich, catalogue no. T9284), Nonidet P-40, or a combination thereof.
- the present invention involves nucleic acid amplification procedures, such as PCR, which involve chain elongation by a DNA polymerase.
- PCR nucleic acid amplification procedures
- DNA polymerase enzymes such as Taq polymerase.
- PCR Protocols A Guide to Methods and Applications. (Innis, M, Gelfand, D., Sninsky, J. and White, T., eds.), Academic Press, San Diego (1990) for detailed description of PCR methodology. PCR is also described in detail in U.S. Patent No.
- a target nucleic acid In a typical PCR protocol, a target nucleic acid, two oligonucleotide primers (one of which anneals to each strand), nucleotides, polymerase and appropriate salts are mixed and the temperature is cycled to allow the primers to anneal to the template, the DNA polymerase to elongate the primer, and the template strand to separate from the newly synthesized strand. Subsequent rounds of temperature cycling allow exponential amplification of the region between the primers.
- Oligonucleotide primers useful in the present invention may be any oligonucleotide of two or more nucleotides in length.
- PCR primers are about 15 to about 30 bases in length, and are not palindromic (self- complementary) or complementary to other primers that may be used in the reaction mixture.
- Oligonucleotide primers are oligonucleotides used to hybridize to a region of a target nucleic acid to facilitate the polymerization of a complementary nucleic acid.
- any primer may be synthesized by a practitioner of ordinary skill in the art or may be purchased from any of a number of commercial venders (e.g., from Boehringer Mannheim Corp., Indianapolis, Ind.; New England Biolabs, Inc., Beverley, Mass.; Pharmacia LKB Biotechnology, Inc., Piscataway, N.J.). It will be recognized that the PCR primers can include covalently attached groups, such as fluorescent tags. U.S. Pat. No. 6,210,885 describes the use of such tags in mutation detection by DHPLC. It is to be understood that a vast array of primers may be useful in the present invention, including those not specifically disclosed herein, without departing from the scope or preferred embodiments thereof.
- the PCR process is limited in its ability to replicate DNA strands by the specificity of the DNA polymerase used, as well as other features of the reaction.
- the primers may bind to portions of a DNA strand which are only partially complementary. Such nonspecific primer binding will produce products with an undesired sequence.
- the first and second primers may also bind to complementary portions of each other, producing primer dimers.
- the specificity of DNA polymerases varies with the reaction conditions employed as well as with the type of enzyme used. No enzyme affords completely error-free extensions of a primer. A non-complementary base will be introduced from time to time.
- Such polymerase related errors produce double stranded DNA products which are not exact copies of the original DNA sample, that is, the products contain PCR induced mutations.
- Other PCR process variables which may influence the accuracy or fidelity of DNA replication include reaction temperature, primer annealing temperature, enzyme concentration, dNTP concentration, Mg ++ concentration, source of the polymerase and combinations thereof.
- PCR product profile as used herein is defined to include the data generated by DHPLC as applied to the product of a PCR process.
- the DHPLC data can distinguish the expected product and other components of the reaction mixture from one another. These components comprise desired product(s), byproducts and reaction artifacts.
- the PCR product profile can be in the form of a visual display, a printed representation of the data or the original data stream.
- the degree of fidelity of replication of DNA fragments by PCR depends on many factors which have long been recognized in the art. Some of these factors are interrelated in the sense that a change in the PCR product profile caused by an increase or decrease in the quantity or concentration of one factor can be offset, or even reversed by a change in a different factor. For example, an increase in the enzyme concentration may reduce the fidelity of replication, while a decrease in the reaction temperature may increase the replication fidelity. An increase in magnesium ion concentration or dNTP concentration may result in an increased rate of reaction which may have the effect of reducing PCR fidelity.
- Buffering agents and salts are used in the PCR buffers and storage solutions of the present invention to provide appropriate stable pH and ionic conditions for nucleic acid synthesis, e.g., for DNA polymerase activity, and for the hybridization process.
- buffers and salt solutions and modified buffers are known in the art that may be useful in the present invention, including agents not specifically disclosed herein.
- Preferred buffering agents include, but are not limited to, TRIS, TRICINE, BIS-TRICINE, HEPES, MOPS, TES, TAPS, PIPES, CAPS.
- Preferred salt solutions include, but are not limited to solutions of; potassium acetate, potassium sulfate, ammonium sulfate, ammonium chloride, ammonium acetate, magnesium chloride, magnesium acetate, magnesium sulfate, manganese chloride, manganese acetate, manganese sulfate, sodium chloride, sodium acetate, lithium chloride, and lithium acetate.
- the invention provides methods and compositions for high sensitivity mutation detection by DHPLC analysis.
- the invention involves the use of Pho polymerase for preparing DNA fragments for analysis by DHPLC.
- the invention involves testing PRC reaction buffers for compatibility for analysis DHPLC.
- PCR amplification comprises steps such as primer design, choice of DNA polymerase enzyme, the number of amplification cycles and concentration of reagents. Each of these steps, as well as other steps involved in the PCR process affects the purity of the amplified product.
- PCR induced mutations wherein a non-complementary base is added to a template, are often formed during sample amplification. Such PCR induced mutations make mutation detection results ambiguous, since it may not be clear if a detected mutation was present in the sample or was produced during the PCR process.
- Pho DNA polymerase in preparing amplifying DNA samples for analysis by DHPLC.
- This aspect of the invention is based in part on Applicants surprisingly discovery that Pho DNA polymerase yields lower rates of misincorporation of bases in PCR as compared to a wide variety of other polymerases.
- Pho DNA polymerase is produced by the hyper-thermophilic archaebacterim, Pyrococcus horikoshii OT3 (Kawarabayasi et al. DNA
- the recombinant polymerase protein can be purified by conventional methods. For example, purification of the recombinant polymerase can be facilitated by including histidine residues on the amino or carboxy terminus as known in the art (U.S. Pat. Nos. 5,310,63; 4,887,830; 5,047,513; and 5,284,933; and Current Protocols in Molecular Biology, Ausubel et al, eds, Supplement 24 CPMB pp. 10.11.8-1-.11.22 (1992)) which purification utilizes a Ni 2+ -NTA resin (available from Novagen (part no. 70666-5)).
- Genomic DNA containing the gene for Pho polymerase was provided by Professor Bernard Connelly (University of Newcastle), and the gene was amplified and cloned into plasmid pQIS130R2. Site directed mutagenesis was performed on the plasmid to correct mutations occurring within the coding sequence. When this had been completed and confirmed by sequencing the coding sequence was put into an expression vector (pET 14b, CN Biosciences). The vector was expressed in E. Coli, and the resulting Pho polymerase was extracted.
- Pho polymerase is available commercially (OptimaseTM polymerase, Transgenomic).
- PCR is carried out using a polymerase preparation that is both compatible with the DHPLC system and that has the highest possible fidelity during amplification.
- EXAMPLE 2 by comparing the fidelity of PCR using a series of polymerase enzymes commonly used for PCR, Applicants surprisingly discovered that Pho polymerase gave the highest fidelity of any polymerase tested.
- DHPLC analysis showed the presence of two distinct forms of DNA fragment (FIG. 2).
- FIG. 2 eight different polymerases were compared. The major component of each PCR product was found to be homoduplex DNA observed as a peak with a retention time of approximately 4 minutes. In addition to this major component a second peak was observed indicating the presence of heteroduplex DNA resulting from polymerase induced base misincorporations. The size of the heteroduplex peak was found to be consistent for each polymerase but varied over a considerable range between different polymerases.
- FIG. 3 provides another illustration of the effect of base misincorporations during PCR on peak profiles obtained using DHPLC.
- the PCR product profile 130 from analysis of amplification by Pho polymerase shows a small "bump" 132 prior to the well defined main peak 134, indicative of high quality PCR with few misincorporations.
- the PCR product profile 136 from analysis of amplified products of Herculase polymerase (Stratagene) shows a distinct "shoulder" 138 prior to the main peak indicating a higher level of misincorporation than for Pho. Polymerases that induce the incorporation of high numbers of errors during amplification can have a detrimental effect on data analysis.
- PCR product profiles obtained for Pho polymerase 134 and Herculase 136 showed heteroduplex formation in 7.3% and 22.1 % of PCR products, respectively.
- the affect of these misincorporations is clearly visible and at high levels of misincorporations the quality of data acquired using DHPLC can be impaired.
- FIG. 4 shows the percentage of total PCR product found to form heteroduplex DNA, indicating the presence of misincorporated bases.
- the data in FIG. 4 and TABLE 1 correlate well with the relative error incorporation rates that have been shown for these polymerases in other studies (Cline et al. Nucleic Acids Research. 24:3546-3551 (1996); Mattila, et al. Nucleic Acids Research 19:4967-4973 (1991 ); Cha, et al. R. S. & Thilly, W. G. PCR Methods and Applications 3:S18-S29 (1993); Cariello, et al. Nucleic Acids Research 19:4193-4198 (1991); Keohavong, et al.
- PCR- induced mutations are the result of "PCR infidelity", which is a well-known characteristic of PCR in general. Any and all mutation-derived mismatches within the final PCR products will give rise to heteroduplices, whether the mutation originates from the genomic DNA sequence or are introduced in the PCR.
- FIG. 5 illustrates the signal processing procedure for performing background signal measurements, and shows the area due to homoduplex 120, the area due to heteroduplex 122, the corrected baseline 124, the heteroduplex peak 126, and the heteroduplex peak height 128.
- the background peak area was determined by calculating the heteroduplex area's percentage of the total area after baseline-correction, while background peak height was determined by calculating the heteroduplex height's percentage of the total height after baseline-correction.
- the instant invention is also based in part on Applicant's surprising discovery that Pho polymerase exhibits a more reproducible rate of misincorporation of bases (infidelity) as compared to other DNA polymerases. This was demonstrated in an experiment in which a sequence within pBR322 was amplified using various DNA polymerases (EXAMPLE 4), and the PCR products were analyzed using DHPLC. As shown in TABLE 2, the standard deviation of the mean for Pho polymerase was lower than for the other polymerases.
- TABLE 2 shows the variation in the relative amount of misincorporations introduced by different thermostable polymerases, measured as peak area and peak height (the chromatographs for Taq, Pfu and Pho are shown in FIGs. 6-8).
- Taq P ⁇ represent three replicate determinations for a different Taq polymerase ("Platinum” Taq) for the amplification of the ras exon 1 alleles (EXAMPLE 3).
- the present invention also concerns providing a PCR buffer, or other solution, for use in PCR that does not interfere with analysis of the PCR products by DHPLC.
- This aspect of the invention is based in part on the discovery by Applicants that certain components commonly included in PCR buffers and storage solutions are often incompatible with analysis of PCR products by DHPLC. Applicants have found that a number of commercially available PCR buffers and polymerase preparations, such as provided in PCR kits, are not compatible with analysis by DHPLC because of interference with the elution of DNA fragments from the separation column.
- FIG. 9 illustrates the effect of multiple injections of a PCR buffer obtained in the Pfu polymerase kit sold by Stratagene on the performance of a separation column as measured by the retention time of heteroduplex DNA in the 209bp Mutation Standard mixture of homoduplex and heteroduplex molecules.
- the retention time of the heteroduplex peak decreased after multiple injections of the PCR buffer tested.
- a washing procedure was used to regenerate the separation column.
- FIG. 5 illustrates the effect of multiple injections of a PCR buffer in the Herculase polymerase kit sold by Stratagene on the performance of a separation column as measured by the retention time of heteroduplex DNA in the 209bp Mutation Standard mixture of homoduplex and heteroduplex molecules.
- the retention time of the heteroduplex peak decreased after multiple injections of the PCR buffer tested.
- a washing procedure was not effective in regenerating the separation column.
- This PCR buffer was determined to contain BSA.
- Applicants have herein devised a method for testing PCR buffers, and other solutions that are to be used in PCR, for compatibility with analysis by DHPLC.
- the concentrations of the ingredients in the PCR buffer can be manipulated such that the buffer is operable during PCR and is also compatible with the separation of the PCR products using DHPLC.
- Another aspect of the instant invention provides a method for quantifying the compatibility of a buffer or other solution that is to be analyzed by DHPLC.
- the calculation of a "DHPLC Incompatibility Index" is illustrated in FIG. 11 and described in EXAMPLE 5. Briefly, a Mutation Standard (i.e. a mixture of known homoduplex and heteroduplex fragments) is injected onto the separation column and eluted at a temperature which partially denatures at a site of mismatch and a chromatogram is recorded. The retention time of the earliest eluting heteroduplex peak in the chromatograph is obtained. After multiple injections of the solution being characterized, e.g.
- the Mutation Standard is again injected, and the retention time of the first eluting heteroduplex peak is compared to the retention time of the first eluting heteroduplex peak prior to the multiple injections.
- the DHPLC Incompatibility Index is calculated as described in EXAMPLE 5.
- PCR buffers or other solutions that are characterized by a DHPLC Incompatibility Index of no greater than 0.1 can be operable for use in DHPLC analysis, while values no greater than 0.05 are more preferred, and values no greater than 0.01 are most preferred.
- this Index allows one to test whether a PCR buffer, or any other solution, will be compatible with the DHPLC system. It will be appreciated, that by the use of this Index, PCR buffers and other solutions can be designed to select components and component concentrations in order to minimize interference with analysis by DHPLC. For example, in use, this method can be used to test a mixture that includes a preparation of a proofreading DNA polymerase combined with a PCR buffer, but without PCR primers or template, in order to simulate the conditions present during a PCR.
- PCR buffers interfere with DHPLC analysis and exhibit a DHPLC Incompatibility Index of about 0.1 or more.
- DHPLC Incompatibility Index of about 0.1 or more.
- a PCR buffer at its working concentration includes one or more non-ionic detergents at a concentration in the range of about 0.001 % to about 0.01% volume/total volume of buffer. Preferably, the concentration is less than or equal to about 0.01 %.
- the concentration of the non-ionic detergent in the PCR buffer is operably less than about 1 % (volume/volume of buffer), preferably no greater than about 0.095%, more preferably no greater than about 0.05%, and most preferably no greater than about 0.01%.
- the non-ionic detergent can be present in the range of about 0.05% to about 0.001%, and preferably in the range of about 0.02% to about 0.001%.
- the PCR buffer can include salts, buffering agent, magnesium, and other compounds as indicated hereinabove.
- An example of a suitable PCR buffer (1x) is as follows: KCI (75mM), Tris (pH 8.8, 10mM), MgSO 4 (1.5mM), Triton X-100 (0.01 %).
- FIG. 12 illustrates the effect of multiple injections of this PCR buffer on the performance of a separation column as measured by the retention time of heteroduplex DNA in the 209bp Mutation Standard mixture of homoduplex and heteroduplex molecules.
- PCR buffers are substantially free of, and more preferably are devoid of, these interfering agents.
- PCR buffers that are preferably devoid of, or which contain minimal concentrations of, components that can interfere with DHPLC analysis.
- inhibitors can include one or more of the following: unidentified "proprietary” ingredients such as “stabilizers”, “enhancers” or “additives”; Bovine serum albumin (BSA); autoclaved water; mineral oil; formamide; Proteinase K; high molecular weight stabilizers such as polyethylene glycol (PEG); detergents such as Triton X-100, NP40, Tween 20, sodium dodecyl sulfate; sodium lauryl sulfate.
- BSA Bovine serum albumin
- PEG high molecular weight stabilizers
- detergents such as Triton X-100, NP40, Tween 20, sodium dodecyl sulfate; sodium lauryl sulfate.
- reagents such as those commonly used in the purification of DNA, such as proteases, solvents, nucleases, phenol, guanidinium, etc., are inhibitors of DNA polymerase activity and also may show incompatibility with the reverse phase column. If these reagents are used, it is preferred to carry out a final ethanol precipitation and wash step to remove most of these contaminants prior to PCR. Excess EDTA, isopropanol, or iso-amyl alcohol can inhibit the PCR, and are preferably removed prior to PCR.
- Certain compounds may be present in the PCR mixture, but preferably do not exceed concentrations (as shown in parentheses) that minimize interference with DHPLC analysis: glycerol (2%), DMSO (10%), betaine (1.25- 2.5M).
- the DHPLC Incompatibility Index can be used to devise other PCR solutions, such as storage buffers for DNA polymerases.
- DNA polymerase enzymes There are a variety of different DNA polymerase enzymes that can be used in this aspect of the invention, although proofreading polymerases are preferred.
- DNA polymerases useful in the present invention may be any polymerase capable of replicating a
- DNA polymerases are thermostable polymerases, which are especially useful in PCR.
- Thermostable polymerases are isolated from a wide variety of thermophilic bacteria, such as Thermus aquaticus (Taq),
- Thermus brockianus (Tbr), Thermus flavus (Tfl), Thermus ruber (Tru), Thermus thermophilus (Tth), Thermococcus litoralis (Tli) and other species of the
- Thermococcus genus Thermoplasma acidophilum (Tac), Thermotoga neapolitana (Tne), Thermotoga maritima (Tma), and other species of the Thermotoga genus, Pyrococcus furiosus (Pfu), Pyrococcus woesei (Pwo) and other species of the Pyrococcus genus, Bacillus sterothermophilus (Bst), Sulfolobus acidocaldarius (Sac) Sulfolobus solfataricus (Sso), Pyrodictium occultum (Poc), Pyrodictium abyssi (Pab), and Methanobacterium thermoautotrophicum (Mth), and mutants, variants or derivatives thereof.
- Bst Bacillus sterothermophilus
- Sulfolobus acidocaldarius Sulfolobus solfataricus
- thermostable DNA polymerase is selected from the group of Taq, Tbr, Tfl, Tru, Tth, Tli, Tac, Tne, Tma, Tih, Tfi, Pfu, Pwo, Kod, Bst, Sac, Sso, Poc, Pab, Mth, Pho, ES4, VENTTM, DEEPVENTTM, PFUTurboTM, AmpliTaq®, AccuTypeTM, or mixtures thereof, and active mutants, variants and derivatives thereof. It is to be understood that a variety of DNA polymerases may be used in certain aspects of the present invention, including DNA polymerases not specifically disclosed above, without departing from the scope or preferred embodiments thereof.
- Solutions for storing DNA polymerases can include one or more of the following components: buffering agents (e.g. Tris-HCI, HEPES), metal chelating agents (e.g. ethylenediamine tetraacetic acid (EDTA)), reducing agents (e.g. ⁇ - mercaptoethanol, dithiothreitol), non-ionic detergent (e.g. Triton X-100), gelatin, an ethoxylated nonyl phenol, a polyoxyethylated sorbitan monolaurate and glycerol, for example.
- buffering agents e.g. Tris-HCI, HEPES
- metal chelating agents e.g. ethylenediamine tetraacetic acid (EDTA)
- reducing agents e.g. ⁇ - mercaptoethanol, dithiothreitol
- non-ionic detergent e.g. Triton X-100
- gelatin an ethoxyl
- kits for use in detecting mutations in a double stranded DNA fragment may comprise one or more of the following: instructional material; a container that contains
- Pho DNA polymerase in a storage solution, wherein said storage solution is preferably characterized by having a DHPLC Incompatibility
- a container which contains PCR buffer a container which contains a PCR buffer wherein said buffer is characterized by having a DHPLC Incompatibility Index of no greater than 0.05; a container which contains a PCR buffer wherein said buffer comprises a non-ionic detergent, wherein said detergent is present at a concentration of no more than 0.01 % volume/volume of said buffer when said buffer is present in a PCR mixture.
- kits can also contain one or more of a separation column (e.g. a reverse phase separation column or an ion exchange separation column) for use in separating DNA molecules; a liquid chromatography system; software for operating the chromatography system; software for analyzing data generated from the liquid chromatographic analysis of the DNA molecules; and software for analyzing and modeling the melting properties of DNA molecules (i.e. primer design software).
- a separation column e.g. a reverse phase separation column or an ion exchange separation column
- cycling conditions that can be used as a starting point for PCR reactions.
- the conditions assume a reaction volume of 50 ⁇ L and a target fragment of 500 base pairs.
- the number of cycles used for PCR is a balance between the yield required from the reaction and the need to preserve optimum reaction conditions.
- the conditions in the reaction change because dNTPs are polymerized to form the PCR product.
- the polymerase is slowly denatured and the relative concentration of different components change.
- the absolute number of error incorporated in each cycle increases with increasing cycle number throughout the course of the PCR. Therefore it is preferable to use the minimum number of cycles required to achieve sufficient product yield.
- the example is for a typical Three-Step PCR reaction as well as Touchdown PCR. These methods are preferred as a starting point from which to optimize most reactions.
- the Unit of activity for Pho polymerase is defined as follows: the amount of enzyme that will incorporate 10 nmoles of dNTPs into acid insoluble material per 30 minutes at 74°C under defined reaction conditions.
- the concentration of the Pho polymerase in the PCR mixture (i.e. the working concentration) is preferably in the range of 0.01 units per ⁇ L to 0.05 units per ⁇ L.
- reaction buffer i.e. PCR buffer
- OptimaseTM polymerase (B) 0.5 to 1 ⁇ L (2.5 units) Forward Primer(A) 0.4 to 0.6 ⁇ M final concentration Reverse Primer(A) 0.4 to 0.6 ⁇ M final concentration PCR buffer(C) 5 ⁇ L of a 10X stock solution
- Template DNA(A) 100 to 150 ng (Human Genomic DNA) dNTPs(A) 200 ⁇ M final concentration of each dNTP
- Step 3 T a °C (A) 30 seconds to 1 minute(B)
- Step 4 72°C (B) 1 minute per 500 base pairs(A)
- Steps 2 to 4 repeat 25 to 30 times
- Step 4 72°C(B) 1 minute per 500 base pairs(A)
- Steps 2 to 4 repeat 13 times
- Step 6 T a °C(A) 1 minute(B)
- Step 7 72°C(B) 1 minute per 500 base pairs(A)
- the PCR buffer (1X) used with Pho polymerase contained the following components: KCI (75mM), Tris (pH 8.8, 10mM), MgSO 4 (1.5 ⁇ mM), Triton X-100 (0.01 %). Pho was maintained in a storage solution comprising: 40mM Tris-HCI (pH 7.5), 0.1 mM EDTA, 5mM ⁇ -mercaptoethanol, 0.1% (volume/total volume storage solution) Triton X-100, and 60% (volume/total volume storage solution) glycerol.
- a 500 bp fragment was amplified in a reaction consisting of 2.5 units of polymerase, 1 ⁇ M of each primer, PCR buffer and Mg 2+ to the manufacturers recommendations, approximately 1x10 5 copies of ⁇ DNA template, 200 ⁇ M of each dNTP and water to a final volume of 50 ⁇ L. Cycling conditions were as shown in TABLE 3, with a hot start step included as recommended by the manufacturer for those enzymes requiring this procedure.
- PCR products were then hybridized to ensure representative heteroduplex formation by heating at 95°C for 10 minutes followed by decreasing the temperature at a rate of 1.5°C per minute until a final temperature of 25°C was reached.
- Each PCR product was analyzed using DHPLC at a predicted optimum temperature of 62°C with a flow rate of 0.9mL/min and 10 ⁇ L injection volume.
- the separation column 50 x 4.6 mm ID
- a solvent gradient was generated by mixing eluent A (0.1 M TEAA pH 7.0) and B (0.1 M TEAA, 25% acetonitrile, pH 7.0) in a linear gradient running from 59 to 67% eluent B over 4 minutes.
- a 500-bp fragment was amplified from ⁇ phage genomic DNA with various polymerases with and without proofreading activity.
- Pho polymerase Transgenomic's Optimase Polymerase
- Pho polymerase results are shown in the bottom chromatogram. Due to the high yield obtained with Pho, chromatograms of PCR products for this polymerase were scaled by a factor of
- PCR buffers used in PCR were those provided with each of the commercial polymerases tested. All amplifications were performed under identical cycling conditions. The fidelity of polymerization was assessed at
- the amplifications used a 6-FAM-labeled, PAGE-purified forward primer CGCCCGCCGCCGCCCGCCGCCCGTCCCGCCATATAGTCACATTTTCATT ATTTTTATTATAAGG (SEQ ID NO: 1 ), non-template GC-clamp sequence italicized) and an unlabeled PAGE-purified reverse primer (AATTAGCTGTATCGTCAAGGCACTC) (SEQ ID NO: 2).
- Amplifications were performed by heat denaturation at 94°C for 1 minute, followed by 35 cycles of: 94°C for 15 seconds, 56°C for 15 seconds, 70°C for 15 seconds. Upon completion, a separate hybridization reaction was performed by heating to 95°C for three minutes, followed by cooling at -0.1 °C/second to 25°C.
- the amplified ras alleles were analyzed by injecting 10 ⁇ L of PCR product into the Wave® Fragment Analysis System. Fragment detection was achieved by tuning the fluorescence detector to 496 rim excitation/520 nm emission. Chromatographic eluent "A” was 0.1 M triethylammonium acetate, and eluent "B” was 0.1 M triethylammonium acetate, 25% (v/v) acetonitrile. The gradient is shown in TABLE 4, with a column temperature of 59°C. The end of each run was subjected to an automated column regeneration/clean-off with
- AAGTAGCGAAGCGAGCAGGACTGG (SEQ ID. NO: 4). Amplifications were performed by heat denaturation at 95°C for 3 minutes, followed by 25 cycles of: 95°C for 1 minute, 57°C for 1 minute, 72°C for 1 minute. A final extension step at 72°C was performed for 10 minutes. Upon completion, a hybridization step was performed by heating the products to 95°C for three minutes, followed by cooling at -0.1 °C/second to 25°C. Amplifications performed with Taq polymerase were further treated with 2 units of Klenow fragment for 15 minutes at 30°C, followed by inactivation of the Klenow fragment with 5 ⁇ L of 0.5M EDTA. This extra step ensured that any Tag-derived dATP overhangs were eliminated.
- the pBR322 amplification products were analyzed by injecting 10 ⁇ L of PCR product into the Wave® Fragment Analysis System. Fragment detection was achieved by tuning the UV absorbance detector to 260 nm. Chromatographic eluent "A” was 0.1 M triethylammonium acetate, and eluent "B” was 0.1 M triethylammonium acetate, 25% (v/v) acetonitrile. The gradient is shown in TABLE 5, with a column temperature of 65°C. The end of each run was subjected to an automated column regeneration/clean-off with 500 ⁇ L of 75% (v/v) acetonitrile. TABLE 5
- the DNA fragment used in the determination of the DHPLC Incompatibility Index comprises a mutant and a wild type 209-bp fragment.
- the mixture includes homoduplex and heteroduplex dsDNA as shown schematically in FIG. 1
- the 209bp Mutation Standard contains equal amounts of the double stranded sequence variants 168A and 168G of the 209 base pair fragment from the human Y chromosome locus DYS271 (GenBank accession Number S76940).
- the A-»G transition position 168 in the sequence was reported by Seielstad et al. (Human Molecular Genetics 3:2159-2161 (1994)) and the preparation of the variants has been described (Narayanaswami et al, Genetic Testing 5:9-16 (2001 )).
- the fragments are present at a total DNA concentration of 45 ⁇ g/mL and suspended in 10mM Tris-HCI, pH 8, 1mM EDTA.
- This Mutation Standard is available commercially from Transgenomic (WAVE® System Low Range Mutation Standard, part no. 560077) and a similar standard is available from Varian (Walnut Creek, CA).
- the Mutation Standard is hybridized by heating to 95°C for 12 min, then cooled to 25°C for 30 min.
- the chromatography system is the WAVE® DNA Fragment Analysis system (Transgenomic).
- the separation column is a 50 x 4.6 mm ID DNASep® column (Transgenomic) containing alkylated poly(styrene- divinylbenzene) beads.
- Eluents used for the separation are: Buffer A, 0.1 M triethylammonium acetate (TEAA), pH 7.0 (Transgenomic) in water; Buffer B, 0.1 M TEAA and 25% acetonitrile in water pH 7.0.
- the elution of DNA fragments is monitored with a UV detector at 254nm.
- the flow rate is 0.9 mL/min.
- the mobile phase gradient is as follows:
- a volume of 5 ⁇ L Mutation Standard is injected onto the separation column and eluted at 56°C, a temperature which partially denatures at a site of mismatch and a chromatogram is recorded. The resulting chromatogram is shown in FIG. 13. The retention time of the earliest eluting heteroduplex peak in the chromatograph is obtained, and if necessary, conditions are adjusted so that this retention time is about 3.3 min.
- PCR buffer storage buffer or other solution
- 5 ⁇ L of the PCR buffer (storage buffer or other solution) being tested is injected onto the separation column and eluted under the same conditions. This injection and elution is repeated 100 times and simulates the routine analysis of a PCR mixture.
- any PCR buffer, storage solution, or other solution being characterized is diluted to its "working concentration".
- the working concentration is the concentration that would be present in a PCR mixture during an actual PCR.
- An example of a PCR mixture is provided in the "Reaction Mix" in EXAMPLE 1.
- a PCR buffer is often provided, such as in a kit, as a 10-fold concentrated solution to be combined with DNA polymerase, template, NTPs, and other components.
- such a PCR buffer is diluted by a factor of 10, with double distilled water, prior to injection, in order to simulate actual concentrations present during PCR.
- the column is again tested by injecting the Mutation Standard. From the chromatogram 156, the retention time 158 of the earliest eluting heteroduplex peak 160 is determined (FIG. 11 ).
- the DHPLC Incompatibility Index is calculated according to the following equation:
- DHPLC Incompatibility Index (t - t')/t where t is the retention time 152 of the first eluting heteroduplex peak prior to the 100 injections of PCR buffer, and where t' is the retention time 158 of the first eluting heteroduplex peak after the 100 injections of PCR buffer.
- a storage solution for Pho polymerase was prepared which includes the following components in a 10X solution: 40mM Tris HCl (pH 7.5), 0.1 mM EDTA, 5mM ⁇ -mercaptoethanol, 0.1% (volume/volume total storage solution) Triton X-100, and 60% (volume/total volume storage solution) glycerol.
- the DHPLC Incompatibility Index of the storage solution is determined after a tenfold dilution in water and is found to be less than 0.05.
- a PCR buffer (1X) is prepared as follows: KCI (75mM), Tris (pH 8.8, 10mM), MgS0 4 (1.5mM), Triton X-100 (0.01% volume/total volume of buffer).
- the DHPLC Incompatibility Index of the PCR buffer is determined and is found to be less than 0.02.
Abstract
Description
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Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
DE102007057340A1 (en) | 2007-11-28 | 2009-06-04 | Eurogene Gmbh | Detecting mutations involving trinucleotide repeat sequences in genomic DNA comprises amplifying a section of the DNA and analyzing the product by denaturaing HPLC |
-
2002
- 2002-04-19 AU AU2002309588A patent/AU2002309588A1/en not_active Abandoned
- 2002-04-19 WO PCT/US2002/012583 patent/WO2002086444A2/en not_active Application Discontinuation
Also Published As
Publication number | Publication date |
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AU2002309588A1 (en) | 2002-11-05 |
WO2002086444A3 (en) | 2003-02-06 |
WO2002086444A2 (en) | 2002-10-31 |
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