US20120135414A1 - Chemically-enhanced primer compositions, methods and kits - Google Patents

Chemically-enhanced primer compositions, methods and kits Download PDF

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US20120135414A1
US20120135414A1 US13/284,839 US201113284839A US2012135414A1 US 20120135414 A1 US20120135414 A1 US 20120135414A1 US 201113284839 A US201113284839 A US 201113284839A US 2012135414 A1 US2012135414 A1 US 2012135414A1
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primer
chemically
nuclease
sequencing
enhanced
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Linda Lee
Sam Lee Woo
Peter Ma
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Life Technologies Corp
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Life Technologies Corp
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Priority to US13/397,626 priority patent/US8703925B2/en
Assigned to Life Technologies Corporation reassignment Life Technologies Corporation ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: LEE, LINDA, MA, PETER, WOO, SAM LEE
Assigned to Life Technologies Corporation reassignment Life Technologies Corporation ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: MA, PETER, LEE, LINDA, WOO, SAM
Publication of US20120135414A1 publication Critical patent/US20120135414A1/en
Priority to US14/053,571 priority patent/US9410192B2/en
Priority to US14/198,308 priority patent/US9708650B2/en
Priority to US15/230,834 priority patent/US20170051342A1/en
Priority to US15/652,224 priority patent/US10221449B2/en
Priority to US16/247,267 priority patent/US11104944B2/en
Priority to US17/399,449 priority patent/US20220049289A1/en
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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
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/686—Polymerase chain reaction [PCR]
    • 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
    • C12Q1/6869—Methods for sequencing
    • C12Q1/6874—Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation
    • 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
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/6853—Nucleic acid amplification reactions using modified primers or templates
    • 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
    • C12Q1/6869—Methods for sequencing
    • 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
    • C12Q2525/00—Reactions involving modified oligonucleotides, nucleic acids, or nucleotides
    • C12Q2525/10—Modifications characterised by
    • C12Q2525/113—Modifications characterised by incorporating modified backbone
    • 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
    • C12Q2525/00—Reactions involving modified oligonucleotides, nucleic acids, or nucleotides
    • C12Q2525/10—Modifications characterised by
    • C12Q2525/125—Modifications characterised by incorporating agents resulting in resistance to degradation

Definitions

  • the present teachings pertain to chemically modified oligonucleotide sequence primer compositions and methods for sequencing DNA and fragment analysis.
  • the teachings also relate to compositions for preparing, fragment analysis and sequencing of nucleic acids such as cDNA and DNA.
  • a standard polymerase chain reaction (PCR)/sequencing workflow generally includes five steps requiring reagent addition: an initial PCR step, a PCR clean-up step, a sequencing step, a sequencing cleanup step, and electrophoresis.
  • the PCR step involves amplification of a template polynucleotide using amplification primers and a thermo-stable DNA polymerase enzyme.
  • the PCR cleanup step is commonly done by the addition of exonuclease I and alkaline phosphatase, followed by incubation, and subsequent heat-inactivated to inactivate the enzymes.
  • FIG. 1A A standard PCR/sequencing workflow is illustrated in FIG. 1A .
  • a typical PCR reaction uses an excess of amplification primers, some primers remain unincorporated upon completion of the PCR reaction. This necessitates removal of the excess primers before proceeding to a sequencing reaction, because the excess amplification primers will interfere with the subsequent sequencing reaction.
  • the PCR reaction furthermore contains an excess of dNTPs that can interfere with the subsequent sequencing reaction.
  • the hydrolytic properties of exonuclease I which degrades single-stranded DNA present in the PCR mixture allows the amplification product (amplicon) to be used more efficiently in subsequent sequencing applications.
  • the enzyme activity of alkaline phosphatase dephosphorylates free dNTPs remaining from the PCR reaction.
  • exonuclease I and alkaline phosphatase enzymes are heat inactivated before adding sequencing primer, dNTPs, and dye-labeled ddNTPs; otherwise the enzymes would degrade these reagents and the sequencing reaction products.
  • the present teachings provide a composition for a chemically-enhanced primer.
  • the primer can comprise a negatively charged moiety, an oligonucleotide sequence and a nuclease-resistant linkage.
  • the primer can be used in fragment analysis, sequencing nucleic acid and for improving resolution, PCR through sequencing workflows with POP-7TM polymer on capillary electrophoresis instruments such as those manufactured by Applied Biosystems (Foster City, Calif.).
  • the present teachings provide a composition for sequencing nucleic acid.
  • the composition can comprise a composition comprising a chemically-enhanced primer comprising an oligonucleotide sequence, a negatively charged moiety (NCM) and at least one nuclease-resistant linkage.
  • the composition can further comprise a polymerase, a nuclease, deoxynucleotide triphosphates (dNTPs), and dideoxynucleotide triphosphates (ddNTPs) and at least one dye-label.
  • the composition can be added in one step directly to a PCR reaction product, without first removing excess PCR amplification primers from the PCR reaction product.
  • the present teachings relate to a method of preparing DNA for sequencing, a method of sequencing DNA, and a composition for sequencing DNA.
  • the teachings provide a method of PCR/sequencing (including cycle sequencing) that can be quicker and simpler, and require fewer steps, than traditional methods.
  • the methods of the present teachings utilize a chemically-enhanced primer in combination with nuclease, which can reduce sequence noise and remove undesired sequence priming.
  • the present teachings further provide a composition for DNA sequencing that can be used with such a method.
  • the present teachings disclose a method of preparing DNA for sequencing.
  • the DNA preparation method can eliminate at least one reagent addition step used in conventional PCR/cycle sequencing, thereby reducing the number of processing steps.
  • a method of preparing DNA for sequencing can comprise amplifying DNA under conditions to produce amplification reaction products, the amplification reaction products comprise excess amplification primer, and contacting the amplification reaction products with a reaction mixture comprising a nuclease and a chemically-enhanced sequencing primer, under conditions in which the excess amplification primer is degraded by the nuclease.
  • the chemically-enhanced primer is essentially non-degraded under such conditions.
  • the excess amplification primer can comprise inter-nucleotide phosphodiester bonds that are susceptible to nuclease cleavage.
  • the chemically-enhanced primer can comprise at least one inter-nucleotide nuclease-resistant linkage, including but not limited to at least one phosphorothioate bond that is not susceptible to nuclease cleavage.
  • a DNA sequencing method can comprise adding a sequencing reaction mix directly to a completed PCR amplification reaction, without first performing a separate cleanup step; that is, without first removing excess PCR amplification primers by the addition of a nuclease and completing a nuclease inactivation step, followed by a second addition of sequencing primers and reagents.
  • a method of sequencing DNA can comprise amplifying DNA in a first reaction mixture comprising nuclease-sensitive amplification primers to form amplified DNA, contacting the first reaction mixture with a second reaction mixture comprising a nuclease and a chemically-enhanced primer under conditions in which the nuclease-sensitive amplification primers are degraded by the nuclease, inactivating the nuclease, and causing the amplified DNA to serve as template in a sequencing reaction under conditions in which the chemically-enhanced primer primes the sequencing reaction.
  • the present teachings further provide a system for sequencing DNA that can comprise amplifying DNA in a first reaction mixture comprising nuclease sensitive amplification primers to form amplified DNA, contacting said first reaction mixture of the amplifying step with a second reaction mixture comprising a nuclease and a chemically-enhanced primer, under conditions in which the nuclease sensitive amplification primers are degraded by the nuclease; inactivating the nuclease and causing the amplified DNA to react in a sequencing reaction under conditions in which the chemically-enhanced primer primes said sequencing reaction; and identifying a nucleotide base sequence of the amplified DNA by mobility-dependent separation of sequencing reaction products.
  • kits comprises a chemically-enhanced primer comprising a negatively charged group, an oligonucleotide sequence and a nuclease resistant moiety.
  • the kit can have at least one of a instructions for use, a nuclease, a sufficient quantity of enzyme for sequencing or fragment analysis, buffer to facilitate the sequencing or fragment analysis, dNTPs, modified dNTPs, dNTP analogs and 7-Deaza-dGTP for strand extension during sequencing or fragment analysis, ddNTPs, a dye-label, loading solution for preparation of the sequenced or fragment analyzed material for electrophoresis, genomic DNA as a template control, a size marker to insure that materials migrate as anticipated in the separation medium, and a protocol and manual to educate the user and limit error in use.
  • FIG. 1 is a diagrammatic representation of a standard PCR/cycle sequencing workflow; with five steps in FIG. 1A and four steps in FIG. 1B , the disclosed improved workflow.
  • FIG. 2 illustrates an exonuclease 1-resistant oligonucleotide having a nuclease-resistant linkage at the terminal 3′ end, according to various embodiments.
  • FIG. 3A illustrates a chemically-enhanced primer consisting of (C3) 10 -M13*(Forward).
  • FIG. 3B illustrates a chemically-enhanced primer consisting of (C3) 8 -M13 (Forward).
  • FIG. 3C illustrates a chemically-enhanced primer consisting of (C3) 9 -M13 (Forward).
  • FIG. 3D illustrates a chemically-enhanced primer consisting of (C3) 5 -M13 (Forward).
  • FIG. 3E illustrates a chemically-enhanced primer consisting of (C3) 6 -trebler-M13 (Forward).
  • FIG. 3F illustrates a chemically-enhanced primer consisting of (C3) 3 -Long trebler-M13 (Forward).
  • FIG. 3G illustrates a chemically-enhanced primer consisting of (C 3 ) 8 -treb-M13 (Forward).
  • FIG. 3H illustrates a chemically-enhanced primer consisting of (C3) 15 -M13* (Forward), * indicates a phosphorothioate linkage.
  • FIG. 3I illustrates a chemically-enhanced primer consisting of (C3) 15 -M13* (Forward), * indicates a phosphorothioate linkage.
  • FIG. 3J illustrates a chemically-enhanced primer consisting of (C3) 18 -M13* (Forward), * indicates a phosphorothioate linkage
  • FIG. 4A-4B illustrates a chemically-enhanced primer consisting of (C3) 15 -gene specific primer oligonucleotide sequence* (Forward) or a universal primer oligonucleotide sequence* (Forward), respectively, indicates a phosphorothioate linkage.
  • FIG. 4C illustrates a chemically-enhanced primer consisting of (C3) 15 -oligonucleotide sequence (Forward).
  • PCR/cycle sequencing refers to a method for determining a nucleotide sequence of DNA by PCR amplifying the DNA, followed by sequencing reactions repeated (or cycled) several times. This cycling is similar to PCR because the sequencing reaction is allowed to proceed at 42° C.-55° C., then stopped at 95° C., and started again at 42° C.-55° C., and uses a thermostable DNA polymerase.
  • phosphorothioate linkage refers to an inter-nucleotide linkage comprising a sulfur atom in place of a non-bridging oxygen atom within the phosphate linkages of a sugar phosphate backbone.
  • the term phosphorothioate linkage refers to both phosphorothioate intra-nucleotide linkages and phosphorodithioate inter-nucleotide linkages.
  • a “phosphorothioate linkage at a terminal 3′ end” refers to a phosphorothioate linkage at the 3′ terminus, that is, the last phosphate linkage of the sugar phosphate backbone at the 3′ terminus.
  • a phosphorothioate linkage at a terminal 3′ end is illustrated in FIG. 2 .
  • phosphodiester linkage refers to the linkage—PO 4 — which is used to link nucleotide monomers. Phosphodiester linkages as contemplated herein are linkages found in naturally-occurring DNA.
  • nuclease-resistant linkage refers to an oligonucleotide sequence, such as a primer, that is resistant to digestion in the 3′ to 5′ direction by nuclease.
  • Phosphorothioate and boronophosphate linkages are two examples of nuclease-resistant linkages. The examples are not to be construed as limited to just these examples.
  • the term “primer” refers to an oligonucleotide, typically between about 10 to 100 nucleotides in length, capable of selectively binding to a specified target nucleic acid or “template” by hybridizing with the template.
  • the primer can provide a point of initiation for template-directed synthesis of a polynucleotide complementary to the template, which can take place in the presence of appropriate enzyme(s), cofactors, substrates such as nucleotides and oligonucleotides and the like.
  • the term “chemically-enhanced primer” refers to a primer that can have a negatively charged moiety at a terminal 5′ end of the primer or within the primer.
  • the primer can also include a nuclease-resistant linkage at the last phosphate linkage of the sugar phosphate backbone at the 3′ terminus.
  • sequencing primer refers to an oligonucleotide primer that is used to initiate a sequencing reaction performed on a nucleic acid.
  • sequencing primer refers to both a forward sequencing primer and to a reverse sequencing primer.
  • extension primer refers to an oligonucleotide, capable of annealing to a nucleic acid region adjacent a target sequence, and serving as an initiation primer for elongation of the oligonucleotide by using the target sequence as the complementary template for nucleotide extension under suitable conditions well known in the art.
  • a sequencing reaction employs at least one extension primer or a pair of extension primers. The pair would include an “upstream” or “forward” primer and a “downstream” or “reverse” primer, which delimit a region of the nucleic acid target sequence to be sequenced.
  • amplification primer refers to an oligonucleotide, capable of annealing to an RNA or DNA region adjacent a target sequence, and serving as an initiation primer for nucleic acid synthesis under suitable conditions well known in the art.
  • a PCR reaction employs a pair of amplification primers including an “upstream” or “forward” primer and a “downstream” or “reverse” primer, which delimit a region of the RNA or DNA to be amplified.
  • the term “tailed primer” or “tailed amplification primer” refers to a primer that includes at its 3′ end a sequence capable of annealing to an RNA or DNA region adjacent a target sequence, and serving as an initiation primer for DNA synthesis under suitable conditions well known in the art.
  • the primer includes its 5′ end a sequence capable of annealing to a sequencing primer, for example, an oligonucleotide sequence, an universal sequencing primer, a gene-specific primer, primer and the like.
  • amplifying refers to a process whereby a portion of a nucleic acid is replicated. Unless specifically stated, “amplifying” refers to a single replication or to an arithmetic, logarithmic, or exponential amplification.
  • target amplicon refers to an amplification product having the target sequence of interest and resulting form an amplification reaction, e.g., a polymerase chain reaction (PCR).
  • PCR polymerase chain reaction
  • extend As used herein, the terms “extend”, “extension” and “extending” are used interchangeably and refer to a process whereby an oligonucleotide is increased in length at the 3′ end according to a template target nucleic acid sequence. Unless specifically stated, “extend” refers to a single expansion or to a plurality of parallel or multiple expansions of a target or multiple target nucleic acid target sequences.
  • determining a nucleotide base sequence or the term “determining information about a sequence” encompasses “sequence determination” and also encompasses other levels of information such as eliminating one or more possibilities for a sequence. It is noted that performing sequence determination of a polynucleotide typically yields equivalent information regarding the sequence of a perfectly complementary (100% complementary) polynucleotide and thus is equivalent to sequence determination performed directly on a perfectly complementary polynucleotide.
  • nucleic acid sequence can refer to the nucleic acid material itself and is not restricted to the sequence information (i.e. the succession of letters chosen among the five base letters A, C, G, T, or U) that biochemically characterizes a specific nucleic acid, for example, a DNA or RNA molecule. Nucleic acids shown herein are presented in a 5′ ⁇ 3′ orientation unless otherwise indicated.
  • mobility-dependent separation can refer to the separation of nucleic acid fragments due to the charge and size associated with the fragment.
  • fluorescent dye refers to moieties that absorb light energy at a defined excitation wavelength and emit light energy at a different wavelength.
  • the fluorescent dyes selected for use are spectrally resolvable.
  • spectrally resolvable means that the dyes can be distinguished on the basis of their spectral characteristics, particularly fluorescence emission wavelength, under conditions of operation. For example, the identity of the one or more terminal nucleotides can be correlated to a distinct wavelength of maximum light emission intensity, or perhaps a ratio of intensities at different wavelengths.
  • polynucleotide refers to a linear polymer of nucleosides (including deoxyribonucleosides, ribonucleosides, or analogs thereof) joined by inter-nucleosidic linkages.
  • a polynucleotide such as an oligonucleotide is represented by a sequence of letters, such as “ATGCCTG,” it will be understood that the nucleotides are in 5′ ⁇ 3′ order from left to right and that “A” denotes deoxyadenosine, “C” denotes deoxycytidine, “G” denotes deoxyguanosine, and “T” denotes deoxythymidine, unless otherwise noted.
  • the letters A, C, G, and T can be used to refer to the bases themselves, to nucleosides, or to nucleotides comprising the bases, as is standard in the art.
  • inter-nucleoside linkage is typically a phosphodiester bond, and the subunits are referred to as “nucleotides.”
  • Oligonucleotide primers comprising other inter-nucleoside linkages, such as phosphorothioate linkages, are used in certain embodiments of the teachings. It will be appreciated that one or more of the subunits that make up such an oligonucleotide primer with a non-phosphodiester linkage can not comprise a phosphate group.
  • nucleotide As used herein, and nucleic acids comprising one or more inter-nucleoside linkages that are not phosphodiester linkages are still referred to as “polynucleotides”, “oligonucleotides”, etc.
  • sequence determination includes determination of partial as well as full sequence information. That is, the term includes sequence comparisons, fingerprinting, and like levels of information about a target polynucleotide, as well as the express identification and ordering of each nucleoside of the target polynucleotide within a region of interest.
  • sequence determination comprises identifying a single nucleotide, while in other embodiments more than one nucleotide is identified. Identification of nucleosides, nucleotides, and/or bases are considered equivalent herein. It is noted that performing sequence determination on a polynucleotide typically yields equivalent information regarding the sequence of a perfectly complementary polynucleotide and thus is equivalent to sequence determination performed directly on a perfectly complementary polynucleotide.
  • kits refers to any delivery system for delivering materials.
  • delivery systems include systems that allow for the storage, transport, or delivery of reaction reagents (e.g., oligonucleotides, enzymes, primer set(s), etc. in the appropriate containers) and/or supporting materials (e.g., buffers, written instructions for performing the assay etc.) from one location to another.
  • reaction reagents e.g., oligonucleotides, enzymes, primer set(s), etc.
  • supporting materials e.g., buffers, written instructions for performing the assay etc.
  • kits can include one or more enclosures (e.g., boxes) containing the relevant reaction reagents and/or supporting materials.
  • fragment kit refers to a delivery system comprising two or more separate containers that each contain a subportion of the total kit components.
  • the containers may be delivered to the intended recipient together or separately.
  • a first container may contain an enzyme for use in an assay, while a second container contains oligonucleotides.
  • any delivery system comprising two or more separate containers that each contains a subportion of the total kit components are included in the term “fragmented kit.”
  • a “combined kit” refers to a delivery system containing all of the components of a reaction assay in a single container (e.g., in a single box housing each of the desired components).
  • kit includes both fragmented and combined kits.
  • references to templates, oligonucleotides, primers, etc. generally mean populations or pools of nucleic acid molecules that are substantially identical within a relevant region rather than single molecules.
  • a “template” generally means a plurality of substantially identical template molecules;
  • a “primer” generally means a plurality of substantially identical primer molecules, and the like.
  • Cycle sequencing involves adding to a target nucleic acid or an amplification product thereof, sequencing primer, deoxynucleotide triphosphates (dNTPs), dye-labeled chain terminating nucleotides (e.g., dideoxynucleotide triphosphates (ddNTPs-dyes)), and DNA polymerase, followed by thermal cycle sequencing.
  • dNTPs deoxynucleotide triphosphates
  • dye-labeled chain terminating nucleotides e.g., dideoxynucleotide triphosphates (ddNTPs-dyes)
  • DNA polymerase e.g., dideoxynucleotide triphosphates (ddNTPs-dyes)
  • Standard cycle sequencing procedures are well established. Cycle sequencing procedures are described in more detail, for example, in U.S. Pat. No. 5,741,676, and U.S. Pat. No. 5,756,285, each herein incorporated by reference in its entirety
  • cycle sequencing comprises dNTPS, a sequencing primer (labeled or not), ddNTPs (labeled or not) and DNA polymerase as known to one of skill in the art. It is noted that a labeled sequencing primer can provide fragment analysis information and/or determination of the sequence of a target nucleic acid or amplification product thereof.
  • a chemically-enhanced primer comprising an oligonucleotide sequence, a negatively charged moiety (NCM) and at least one nuclease-resistant linkage.
  • NCM negatively charged moiety
  • the at least one nuclease-resistant linkage includes but is not limited to at least one phosphorothioate linkage (PS) or at least one boronophosphate linkage.
  • the nuclease-resistant linkage is not present in the chemically-enhanced primer.
  • the primer can be used to prime a target nucleic acid in a sequencing reaction, herein referred to as a chemically-enhanced sequencing primer or for fragment analysis, herein referred to as a chemically-enhanced extension primer.
  • the oligonucleotide sequence can be a universal primer or a gene specific nucleotide sequence.
  • Examples of universal primers include but are not limited to M13 (P/N 402071 and 402072, Applied Biosystems), US1 (UNISEQ, PLoS Medicine 3(10)e431 (2006)), T7 (P/N 402126, but without dye, Applied Biosystems), SP6 (P/N 402128, but without dye, Applied Biosystems), and T3 (P/N 402127, but without dye, Applied Biosystems). See the ABI PRIMS® 377 DNA Sequence 96-Lane Upgrade User's Manual for primer sequences.
  • the oligonucleotide sequence can also contain a dye-label such as a fluorescent label.
  • the NCM can be located at the terminal 5′ end of the oligonucleotide sequence or within the oligonucleotide sequence.
  • NCM include but are not limited to phosphoramidite, a (C)n spacer wherein n can be from 1-9 (available from Glen Research), the amino acids aspartic acid and glutamic acid as well as nucleotides and nucleotide analogs (dATP, dCTP, dGTP and dTTP).
  • the NCM can contain only one negatively charged monomer or a plurality of negatively charged moieties, for example at least five, ten, 12, 15, 18, 20, 24 or more repeat units of the spacer, for example, (Cn) x , where x is any integer between 1 and at least 11, at least 12, at least 15, at least 18, at least 20, at least 24 or more Cn spacers where “n” is 3 or 6, e.g., C3 spacers, C6 spacers or a combination of C3 and C6 spacers in a linear arrangement or a branched arrangement.
  • the C3 and C6 spacers individually or in combination can also form a branched NCM by forming a doubler or a trebler such as, for example, (C3) 3 -treb-M13 or [(C3) 2 -treb]-treb-M13, where the NCM is represented by (C3) 3 -treb or [(C3) 2 -treb]-treb and M13 represents the oligonucleotide sequence, as would be known to one of skill in the art.
  • the NCM can also contain a dye-label such as a fluorescent label.
  • At least none, at least one, at least two or more phosphorothioate linkages can be at a terminal 3′ end of the oligonucleotide sequence.
  • the presence of at least one nuclease-resistant linkage provides resistance to digestion by 3′-5′ nucleases such as Exonuclease I (P/N MO293S New England Biolabs, Ipswich, Mass.), Exo III (P/N MO206S, New England Biolabs, Ipswich, Mass.), Pfu (Promega, P/N M7741, Madison, Wis.), and DNA pol I (P/N M0209S, New England Biolabs, Ipswich, Mass.).
  • the resistance of the chemically-enhanced primer to nuclease digestion offers the advantage of eliminating a PCR clean-up step in the PCR to sequencing protocol. Removal of the extra non-nuclease resistant amplification primers left over from the PCR step can be accomplished in the sequencing reaction mixture. A brief exposure of the PCR amplification reaction to the nuclease within the sequencing reaction mixture degrades the non-nuclease resistant amplification primers followed by an inactivation of the nuclease. The chemically-enhanced primer remains available for the sequencing reaction while the non-nuclease resistant amplification primers and the nuclease have been removed and inactivated, respectively.
  • the chemically-enhanced sequencing primer is able to run with POP-7 polymer having an electrophoretic run time as short as 65 minutes to generate 700 high quality bases starting from the first base using a 3500 Genetic Analyzer (Applied Biosystems). In contrast, it took 135 minutes with POP-6 polymer to produce only 600 high quality bases.
  • the primer of the present teachings in conjunction with the POP-7 polymer provided a 52% throughput increase compared to the electrophoresis time with the POP-6 polymer. The throughput was increased as well as reducing hands-on-time by eliminating a separate PCR clean-up step prior to initiation of the sequencing reaction. ( FIG. 1A and FIG. 1B ).
  • HLA Human Leukocyte Antigens
  • the HLAs are used for tissue and organ typing as well as tissue and organ cross-matching for transplantation matching and evaluation of rejection.
  • the SeCore® HLA-DRB1 (Invitrogen, Carlsbad, Calif.) primer set and group specific sequencing primers (GSSP) were used on 34 DNA samples. Sequencing reactions were performed with traditional sequencing primers and with the chemically-enhanced sequencing primers.
  • the sequencing reaction products were electrophoresed on an Applied Biosystems 3500xlTM Genetic Analyzer using POP7 polymer (Applied Biosystems). Comparison of 5′ resolution and basecalling accuracy and quality was made between the two primers. On average the traditional sequencing primers with POP7 polymer yielded high quality readable bases by 25 bases after the sequencing primer while the chemically-enhanced sequencing primers yielded high quality bases by base 5 and by base 1 in many cases and also resulted in increased basecalling accuracy and a 40% decrease in overall workflow time. Table 1 provides examples of the improved sequencing quality obtained with the chemically-enhanced primers.
  • Table 1 illustrate the relative basecalling accuracy between the SeCore® HLA Sequence and the chemically-enhanced sequencing primer when sequenced in both directions of exon 2 from HLA-DRB1, DQB1 and DPB1 in 34 different samples.
  • uTYPE® HLA Sequencing Software Invitrogen aligned the forward and reverse traces to a reference sequence and a HLA library. Basecalling accuracy was assessed by how many base positions required manual edits to resolve discrepancies between the forward, reverse and reference sequence.
  • the chemically-enhanced sequencing primer equaled or slightly outperformed the existing method by requiring fewer manual edits (17) and provided a simplified workflow and faster electrophoresis time vs.
  • the chemically-enhanced sequencing primer also improved 5′ mobility seen as 5′ C/A and A/G in DPB1, resolved shoulder problems in HLA-DQB1, and reduced C nucleotide compression routinely observed in HLA-DRB-1 sequences to substantially improve primary mixed basecalling (data not shown).
  • the chemically-enhanced sequencing primer and improved workflow improved polymorphism detection and more efficient use of allele specific sequencing primers for heterozygous ambiguity resolution resulting in significant time savings for obtaining data that was superior in quality to existing methods.
  • a composition for sequencing nucleic acid can comprise a polymerase, a nuclease, a chemically-enhanced sequencing primer, dNTPs, and a chain terminator (e.g., ddNTPs).
  • the polymerase can comprise Taq polymerase, for example AmpliTaq Gold polymerase.
  • the nuclease can comprise exonuclease I.
  • the chemically-enhanced sequencing primer can comprise at least one phosphorothioate linkage. In other embodiments, the chemically-enhanced sequencing primer can comprise a terminal 3′ end phosphorothioate linkage.
  • the ddNTPs can comprise ddNTPs-dyes, for example fluorescent dye-labeled ddNTPs.
  • the chemically-enhanced sequencing primer can comprise a dye, for example a fluorescent dye-labeled oligonucleotide and/or at least one fluorescently dye-labeled NCM moiety within the NCM compound.
  • the composition for sequencing nucleic acid can comprise a polymerase, for example a DNA polymerase, in an amount of from about 0.01 Unit to about 20 Units, for example, from about 0.1 Unit to about 1.0 Unit, or about 0.8 Unit.
  • the composition can comprise polymerase in an amount within a range having an upper limit of from about 10 Units to about 20 Units and a lower limit of from about 0.01 Unit to about 0.05 Unit.
  • the composition can comprise a nuclease, for example exonuclease I, in an amount of from about 1 Unit to about 40 Units, for example, from about 2 Units to about 15 Units, or about 10 Units.
  • the composition can comprise nuclease in an amount within a range having an upper limit of from about 10 Units to about 40 Units, and a lower limit of from about 1 Unit to about 2 Units.
  • the composition for sequencing nucleic acid can comprise a chemically-enhanced sequencing primer, in an amount of from about 0.1 ⁇ M to about 20 ⁇ M, for example about 1.0 ⁇ M.
  • the composition can comprise a chemically-enhanced sequencing primer in an amount within a range having an upper limit of from about 10 ⁇ M to about 20 ⁇ M and a lower limit of from about 0.05 ⁇ M to about 0.1 ⁇ M.
  • the composition can comprise dNTPs in an amount of from about 20 ⁇ M to about 5000 ⁇ M, for example, about 500 ⁇ M.
  • the composition can comprise dNTPs in an amount within a range having an upper limit of from about 2000 ⁇ M to about 5000 ⁇ M and a lower limit of from about 20 ⁇ M to about 50 ⁇ M. According to various embodiments, the composition can comprise ddNTPs in an amount of from about 0.03 ⁇ M to about 10 ⁇ M, for example about 3 ⁇ M. The composition can comprise ddNTPs in an amount within a range having an upper limit of from about 5 ⁇ M to about 10 ⁇ M and a lower limit of from about 0.01 ⁇ M to about 0.05 ⁇ M. All molar amounts are based on final concentrations of the final volume.
  • the composition can comprise a non-nuclease-resistant amplification primer in an amount of from about 0.1 ⁇ M to about 20 ⁇ M, for example about 1.0 ⁇ M.
  • the composition can comprise a non-nuclease-resistant amplification primer in an amount within a range having an upper limit of from about 10 ⁇ M to about 20 ⁇ M and a lower limit of from about 0.05 ⁇ M to about 0.1 ⁇ M. All molar amounts are based on final concentrations of the final volume.
  • the composition for sequencing nucleic acid can further comprise a PCR amplification product.
  • the PCR amplification product can comprise an amplified DNA target sequence.
  • the PCR amplification product can comprise non-nuclease-resistant amplification primer(s).
  • the non-nuclease-resistant amplification primer can comprise, for example, phosphodiester linkages that are sensitive to degradation by exonuclease.
  • the PCR amplification product can comprise a target specific amplicon that incorporates nucleic acid sequence capable of annealing to a universal primer.
  • a method of preparing a nucleic acid for sequencing can comprise a step of amplifying the nucleic acid under conditions to produce amplification reaction products.
  • the nucleic acid can be amplified using, for example, polymerase chain reaction (PCR).
  • PCR polymerase chain reaction
  • the nucleic acid can also be amplified using other methods such as, for example, multiple strand displacement amplification, helicase displacement amplification, nick translation, Q beta replicase amplification, rolling circle amplification, and other isothermal amplification methods.
  • the nucleic acid to be amplified can comprise, for example, RNA, DNA, cDNA, genomic DNA, viral DNA, plasmid DNA, recombinant DNA, amplicon DNA, synthetic DNA or the like.
  • Template molecules can be obtained from any of a variety of sources.
  • DNA as a template molecule can be isolated from a sample, which can be obtained or derived from a subject.
  • sample is used in a broad sense to denote any source of a template on which sequence determination is to be performed.
  • the phrase “derived from” is used to indicate that a sample and/or nucleic acids in a sample obtained directly from a subject comprising nucleic acid can be further processed to obtain template molecules.
  • the source of a sample can be of any viral, prokaryotic, archaebacterial, or eukaryotic species or a synthetic species.
  • the source can be a human.
  • the sample can comprise, for example, embryonic, cultured cells, tissues or organs, bone, tooth, organ, tissue, preserved, e.g., formalin-fixed paraffin embed (PFPE) organ or tissue, degraded, mummified, or tissue including blood or another body fluid containing cells, such as sperm, a biopsy sample, or the like.
  • PFPE formalin-fixed paraffin embed
  • Mixtures of nucleic acids from different samples and/or subjects can be combined. Samples can be processed in any of a variety of ways. Nucleic acids can be isolated, purified, and/or amplified from a sample using known methods.
  • Amplifying nucleic acid can typically result in a reaction product that comprises excess amplification primer and an amplicon (also referred to as an amplification product) that comprises a target nucleic acid.
  • a method of preparing nucleic acid for sequencing can comprise removing excess amplification primer from the reaction product.
  • the amplification primer can be removed, for example, by adding a nuclease enzyme and providing appropriate conditions for the nuclease to degrade the amplification primer.
  • the amplification primer can be removed by contacting the amplification reaction product with a reaction mixture comprising a nuclease enzyme.
  • nucleases suitable for use in the subject methods preferentially degrade single-stranded polynucleotides over double-stranded polynucleotides, thus destroying excess primers while leaving intact double-stranded amplicons available for sequencing in subsequent steps.
  • the nuclease enzyme can comprise, for example, exonuclease I. Exonuclease I can be obtained from various commercial suppliers, for example from USB Corp., Cleveland, Ohio. Appropriate reaction conditions can include, for example, optimal time, temperature, and buffer parameters to provide for nuclease enzyme activity.
  • excess amplification primer can be degraded by adding exonuclease I to the amplification reaction product and incubating at about 37° C. for about 10 to about 30 min.
  • Exonuclease I can hydrolyze single-stranded DNA in a 3′ ⁇ 5′ direction.
  • a reaction mixture can further comprise a chemically-enhanced sequencing primer.
  • the chemically-enhanced sequencing primer can be essentially non-degraded by a reaction mixture comprising a nuclease, for example, exonuclease I, under reaction conditions at which excess amplification primer can be degraded by the nuclease.
  • essentially non-degraded it is intended that any degradation that takes place of the chemically-enhanced sequencing primer is not of a level that significantly interferes with the process employed to generate sequencing and/or fragment analysis data in the subsequent sequencing reactions or fragment analysis reactions.
  • the chemically-enhanced sequencing primer can comprise an oligonucleotide sequence.
  • the chemically-enhanced sequencing primer can comprise one of more nuclease-resistant internucleotide linkage(s).
  • the internucleotide linkage may be a phosphorothioate linkage.
  • the chemically-enhanced sequencing primer can comprise a nuclease-resistant internucleotide linkage at a terminal 3′ end, at a terminal 5′ end, and/or at one or more internal linkage sites.
  • the nuclease resistant internucleotide linkage is at least one phosphorothioate linkage.
  • Chemically-enhanced sequencing primers were synthesized having one or two phosphorothioate linkages on the terminal 3′ end to protect the chemically-enhanced sequencing primers from exonuclease I digestion.
  • the Sp stereoisomer can protect the primer from exonuclease I digestion but the Rp stereoisomer was found to provide no protection from exonuclease I digestion (data not shown).
  • the chemically-enhanced primer can comprise a negatively charged group/compound/molecule (NCM).
  • NCM can be located at the terminal 5′ end of the oligonucleotide sequence or within the oligonucleotide sequence. Examples of NCM are disclosed above ( FIGS. 3A-3J , 4 A- 4 C).
  • the NCM can be attached to both a non-dye-labeled oligonucleotide sequence which functions as the primer sequence as well as to a dye-labeled oligonucleotide sequence which function as the primer sequence.
  • the dye can be attached to a nucleotide or nucleotide analog of the oligonucleotide sequence or to the NCM as would be known to one of skill in the art.
  • FIGS. 3A-3J , 4 A- 4 C illustrate exemplary M13 oligonucleotide sequence primers and gene-specific primers with various NCMs.
  • the chromatograms illustrating the results of sequencing reactions with the exemplary NCM+oligonucleotide sequence primer structures with a variety of templates can be found in FIGS. 3-12 and 16 of U.S. Ser. No. 61/407,899, filed Oct. 28, 2011 and U.S. Ser. No. 61/408,553, filed Oct. 29, 2011).
  • analogs in reference to nucleosides/tides and/or polynucleotides comprise synthetic analogs having modified nucleobase portions, modified pentose portions and/or modified phosphate portions, and in the case of polynucleotides, modified internucleotide linkages, as described generally elsewhere (e.g., Scheit, Nucleotide Analogs (John Wiley, New York, (1980); Englisch, Angew. Chem. Int. ed. Engl. 30:613-29 (1991); Agrawal, Protocols for Polynucleotides and Analogs , Humana Press (1994)).
  • modified phosphate portions comprise analogs of phosphate wherein the phosphorous atom is in the +5 oxidation state and one or more of the oxygen atoms is replaced with a non-oxygen moiety e.g., sulfur.
  • exemplary phosphate analogs include but are not limited to phosphorothioate, phosphorodithioate, phosphoroselenoate, phosphorodiselenoate, phosphoroanilothioate, phosphoranilidate, phosphoramidate, boronophosphates, including associated counterions, e.g., H + , NH 4 + , Na + , if such counterions are present.
  • Exemplary modified nucleobase portions include but are not limited to 2,6-diaminopurine, hypoxanthine, pseudouridine, C-5-propyne, isocytosine, isoguanine, 2-thiopyrimidine, and other like analogs.
  • Particularly preferred nucleobase analogs are iso-C and iso-G nucleobase analogs available from Sulfonics, Inc., Alachua, Fla. (e.g., Benner, et al., U.S. Pat. No. 5,432,272).
  • modified pentose portions include but are not limited to 2′- or 3′-modifications where the 2′- or 3′-position is hydrogen, hydroxy, alkoxy, e.g., methoxy, ethoxy, allyloxy, isopropoxy, butoxy, isobutoxy and phenoxy, azido, amino or alkylamino, fluoro, chloro, bromo and the like.
  • Modified internucleotide linkages include phosphate analogs, analogs having achiral and uncharged intersubunit linkages (e.g., Sterchak, E.
  • P., et al., Organic Chem, 52:4202 (1987)), and uncharged morpholino-based polymers having achiral intersubunit linkages e.g., U.S. Pat. No. 5,034,506.
  • a particularly preferred class of polynucleotide analogs where a conventional sugar and internucleotide linkage has been replaced with a 2-aminoethylglycine amide backbone polymer is peptide nucleic acid (PNA) (e.g., Nielsen et al., Science, 254:1497-1500 (1991); Egholm et al., J. Am. Chem. Soc., 114: 1895-1897 (1992)).
  • PNA peptide nucleic acid
  • the chemically-enhanced primer can comprise a universal primer, selected from US1, M13, T7, SP6, T3, or other sequencing primers as would be known to one of skill in the art.
  • a universal primer selected from US1, M13, T7, SP6, T3, or other sequencing primers as would be known to one of skill in the art.
  • an M13 universal forward primer an M13 universal reverse primer, or the like.
  • the chemically-enhanced primer can comprise an oligonucleotide sequence or a specific gene specific oligonucleotide sequence, to the target nucleic acid sequence for which the nucleic acid sequence was to be determined.
  • the oligonucleotide primer sequence can be the identical primer sequence as the sequence of the amplification primer used to generate the PCR amplification product having the amplified nucleic acid target sequence and/or DNA target sequence.
  • embodiments of a method for preparing nucleic acid for sequencing can comprise using a phosphorothioated sequencing primer, and the teachings disclosed herein exemplify using a sequence primer having a NCM at or near the terminal 5′ end and a phosphorothioated terminal 3′ end of an oligonucleotide sequence, other types of chemically-enhanced primers can be utilized within the scope of the present teachings.
  • a nuclease resistant sequencing primer can comprise an alkyl phosphonate monomer, RO—P( ⁇ O)(—Me)(—OR), such as dA-Me-phosphonamidite, and/or a triester monomer, RO—P( ⁇ O)(—OR′)(—OR), such as dA-Me-phosphoramidite (available from Glen Research, Sterling, Va.), and/or a locked nucleic acid monomer (available from Exiqon, Woburn, Mass.), and/or a boranophosphate monomer, RO—P(—BH 3 )( ⁇ O) (—OR), as described by Shaw, Barbara Ramsey, et al., in “Synthesis of Boron-Containing ADP and GDP Analogues: Nucleoside 5′-(P-Boranodisphosphates)”, Perspectives in Nucleoside and Nucleic Acid Chemistry, pg. 125-130, (2000), or the like.
  • the amplification reaction products can comprise a target amplicon.
  • the target amplicon can comprise a result of PCR amplification from amplification primers.
  • the target amplicon can comprise double stranded DNA.
  • the target amplicon can comprise single stranded DNA.
  • the amplification primers can comprise tailed primers.
  • the tailed primers can be used, for example, to generate a target specific amplicon that incorporates nucleic acid sequence capable of annealing to a universal primer or a gene specific primer.
  • a method for preparing nucleic acid for sequencing can comprise inactivating a nuclease after excess primer is degraded by the nuclease.
  • the nuclease can be inactivated by heating.
  • the nuclease can be heat-inactivated by heating to a temperature of from about 80° C. to about 90° C. for about 15 minutes.
  • the inactivation of the nuclease can occur within the vesicle and in the same reaction step as the sequencing reaction as shown in FIG. 1B in the Cycle Seq. (cycle sequencing) step.
  • templates to be sequenced can be synthesized by PCR in individual aqueous compartments (also called “reactors”) of an emulsion.
  • the compartments can each contain a particulate support such as a bead having a suitable first amplification primer attached thereto, a first copy of the template, a second amplification primer, and components needed for a PCR reaction (for example nucleotides, polymerase, cofactors, and the like).
  • a particulate support such as a bead having a suitable first amplification primer attached thereto, a first copy of the template, a second amplification primer, and components needed for a PCR reaction (for example nucleotides, polymerase, cofactors, and the like).
  • a method for sequencing nucleic acid can comprise amplifying nucleic acid in a first reaction mixture comprising nuclease sensitive amplification primers to form amplified nucleic acid, contacting the first reaction mixture with a second reaction mixture comprising a nuclease and a chemically-enhanced primer, under conditions in which the nuclease sensitive amplification primers are degraded by the nuclease, and inactivating the nuclease and causing the amplified nucleic acid to react in a sequencing reaction under conditions in which the chemically-enhanced primer primes the sequencing reaction.
  • results can be obtained based on the sequencing reaction and a nucleotide base sequence of the amplified nucleic acid can be determined based on the results.
  • the nucleotide base sequence can be determined by a mobility-dependent separation of the sequencing reaction products.
  • the amplifying can be by polymerase chain reaction amplification.
  • the second reaction mixture can further comprise dNTPs, ddNTPs, a dye-label, and a thermo-stable DNA polymerase.
  • each of the ddNTPs can be labeled with a different fluorescent dye (ddNTP-dye).
  • the ddNTPs can comprise BigDye ddNTPs, available from Applied Biosystems, Foster City, Calif.
  • the chemically-enhanced primer can be labeled with a fluorescent dye. The label can be attached to the oligonucleotide sequence and/or the NCM region of the chemically-enhanced primer.
  • the thermo-stable DNA polymerase can comprise, for example, a DNA polymerase known to one of skill in the art.
  • the sequencing reaction can comprise a thermal cycle sequencing reaction.
  • nucleic acid polymerases may be used in the methods described herein.
  • the nucleic acid polymerizing enzyme can be a thermostable polymerase or a thermally degradable polymerase.
  • Suitable thermostable polymerases include, but are not limited to, polymerases isolated from Thermus aquaticus, Thermus thermophilus, Pyrococcus woesei, Pyrococcus furiosus, Thermococcus litoralis , and Thermotoga maritima .
  • Suitable thermodegradable polymerases include, but are not limited to, E. coli DNA polymerase I, the Klenow fragment of E.
  • coli DNA polymerase I examples include T7, T3, SP6 RNA polymerases and AMV, M-MLV and HIV reverse transcriptases.
  • Non-limiting examples of commercially available polymerases that can be used in the methods described herein include, but are not limited to, TaqFS®, AmpliTaq® CS (Applied Biosystems), AmpliTaq FS (Applied Biosystems), AmpliTaq Gold® (Applied Biosystems), Kentaq1 (AB Peptide, St. Louis, Mo.), Taquenase (ScienTech Corp., St.
  • ThermoSequenase (Amersham), Bst polymerase, Vent R (exo ⁇ ) DNA polymerase, ReaderTMTaq DNA polymerase, VENTTM DNA polymerase (New England Biolabs), DEEPVENTTM DNA polymerase (New England Biolabs), PFUTurboTM DNA polymerase (Stratagene), Tth DNA polymerase, KlenTaq-1 polymerase, SEQUENASETM 1.0 DNA polymerase (Amersham Biosciences), and SEQUENASE 2.0 DNA polymerase (United States Biochemicals).
  • the nuclease can comprise exonuclease I.
  • the exonuclease I can be sensitive to heat inactivation and can be essentially 100 percent deactivated by heating, for example, heating at about 80° C. for about 15 minutes.
  • Other heat inactivated nucleases may be used in the subject methods and compositions including but not limited to Exo III, Pfu or DNA pol I.
  • the chemically-enhanced primer comprises at least one phosphorothioate linkage. In some embodiments, the chemically-enhanced primer comprises at least one terminal 3′ end phosphorothioate linkage. In some embodiments, as described above, the chemically-enhanced primer comprises a NCM and an oligonucleotide sequence 5′ of the phosphorothioate linkage.
  • the sequencing reaction products can be analyzed on a sieving or non-sieving medium.
  • the PCR products can be analyzed by electrophoresis; e.g., capillary electrophoresis, as described in H. Wenz et al. (1998), G ENOME R ES. 8:69-80 (see also E. Buel et al. (1998), J. F ORENSIC S CI. 43:(1), pp. 164-170)), or slab gel electrophoresis, as described in M. Christensen et al. (1999), S CAND . J. C LIN . L AB . I NVEST.
  • a system for sequencing DNA can comprise amplifying DNA in a first reaction mixture comprising nuclease sensitive amplification primers to form amplified DNA; contacting said first reaction mixture of the amplifying step with a second reaction mixture comprising a nuclease and a chemically-enhanced primer, under conditions in which the nuclease sensitive amplification primers are degraded by the nuclease; inactivating the nuclease and causing the amplified DNA to react in a sequencing reaction under conditions in which the chemically-enhanced primer primes said sequencing reaction; and identifying a nucleotide base sequence of the amplified DNA by mobility-dependent separation of sequencing reaction products.
  • the system for sequencing DNA is selected from separation by charge and separation by size, wherein the separation by size plus charge is selected from gel electrophoresis and capillary electrophoresis and separation by size is by a liquid gradient, and a denaturing gradient medium.
  • kits that utilize the chemically-enhanced primer composition and methods described above.
  • a basic kit can comprise a container having one or more chemically-enhanced primers.
  • a kit can also optionally comprise instructions for use.
  • kits can also comprise other optional kit components, such as, for example, one or more of a nuclease, a sufficient quantity of enzyme for sequencing or fragment analysis, buffer to facilitate the sequencing reaction or fragment analysis reaction, dNTPs, modified dNTPs, dNTP analogs and 7-Deaza-dGTP for strand extension during sequencing reaction or fragment analysis reaction, ddNTPs, a dye-label, loading solution for preparation of the sequenced or fragment analyzed material for electrophoresis, genomic DNA as a template control, a size marker to insure that materials migrate as anticipated in the separation medium, and a protocol and manual to educate the user and limit error in use.
  • kit components such as, for example, one or more of a nuclease, a sufficient quantity of enzyme for sequencing or fragment analysis, buffer to facilitate the sequencing reaction or fragment analysis reaction, dNTPs, modified dNTPs, dNTP analogs and 7-Deaza-dGTP for strand extension during sequencing reaction or fragment analysis reaction, ddNT
  • kits can be varied depending upon a number of factors, such as the optimum sensitivity of the process. It is within the scope of these teachings to provide test kits for use in manual applications or test kits for use with automated detectors or analyzers.
  • compositions and methods of the present teachings are shown below. These examples are not limiting of the present teachings, and those of ordinary skill in the art will recognize that the components used in the reactions may be readily substituted with equivalent reagents known in the art.
  • the following Examples illustrate the ability of the chemically-enhance primer to provide higher resolution of a sequencing reaction and in less time with POP7 polymer and variants thereof, the stability of the chemically-enhance primer to exonuclease I, the incorporation of the chemically-enhance primer as a substrate for DNA polymerase, the compatibility of exonuclease I with the sequencing reagents, and the susceptibility of non-phosphorothioate primer to exonuclease I digestion.
  • the Examples further illustrate the use of tailed amplification primers along with universal phosphorothioate primers for sequencing.
  • the oligonucleotide was cleaved off the support with NH 4 OH and purified by HPLC using an ABI RP-300 (C-8) column (4.6 ⁇ 220 mm) using a flow rate of 1.5 ml/min. and a solvent gradient of 0.1M triethylammonium acetate-water pH 7.0 and acetonitrile, the trityl group was removed and the product was isolated by ethanol precipitation.
  • Protocol for oligo labeled with a 5′ phosphate An 18 base oligonucleotide labeled with a phosphate group at the 5′ position. This was made on an ABI model 394 DNA synthesizer using standard phosphoramidite chemistry. The phosphate group was generated using a phosphoramidite obtained from Glen Research (P/N 10-1922-90) The labeled 18mer was made from a one micromole column and on completion of the synthesis the oligonucleotide was cleaved off the support with NH 4 OH and purified by HPLC using an ABI RP-300 (C-18) column (4.6 ⁇ 220 mm) using a flow rate of 1.5 ml/min. and a solvent gradient of 0.1M triethylammonium acetate-water pH 7.0 and acetonitrile. The product was then isolated by ethanol precipitation.
  • Protocol for oligo labeled with dual branching (doubler) linker labeled with one or more C3 spacers An 18 base oligonucleotide labeled with a dual branching linkage followed by one or more C3 spacers at the 5′ position was made on an ABI model 394 DNA synthesizer using standard phosphoramidite chemistry.
  • the dual (doubler) branching (P/N 10-1920-90) and C3 spacer (P/N 10-1913-90) phosphoramidites were obtained from Glen Research.
  • the labeled 18mer was made with the trityl group intact using a one micromole synthesis column.
  • the oligonucleotide was cleaved off the support with NH 4 OH and purified by HPLC using an ABI RP-300 (C-18) column (4.6 ⁇ 220 mm) using a flow rate of 1.5 ml/min. and a solvent gradient of 0.1M triethylammonium acetate-water pH 7.0 and acetonitrile, the trityl group was removed and the product was isolated by ethanol precipitation.
  • Protocol for oligo labeled with trebler branching (trebler) linker labeled with one or more C3 spacers An 18 base oligonucleotide labeled with a trebler branching linkage followed by one or more C-3 spacers at the 5′ position was made on an ABI model 394 DNA synthesizer using standard phosphoramidite chemistry.
  • the trebler phosphoramidite (P/N 10-1922-90) and C-3 spacer (P/N 10-1913-90) phosphoramidites were obtained from Glen Research.
  • the labeled 18mer was made with the trityl group intact using a one micromole synthesis column.
  • the oligonucleotide was cleaved off the support with NH 4 OH and purified by HPLC using an ABI RP-300 (C-18) column (4.6 ⁇ 220 mm) using a flow rate of 1.5 ml/min. and a solvent gradient of 0.1M triethylammonium acetate-water pH 7.0 and acetonitrile, the trityl group was removed and the product was isolated by ethanol precipitation.
  • Protocol for oligo labeled with trebler branching linker end labeled with phosphates (3 total phosphates) An 18 base oligonucleotide labeled with a trebler branching linkage at the 5′ position followed by phosphorylation was made on an ABI model 394 DNA synthesizer using standard phosphoramidite chemistry.
  • the trebler branching (P/N 10-1922-90) and phosphorylating (P/N 10-1900-90) phosphoramidites were obtained from Glen Research.
  • the labeled 18mer was made using a one micromole synthesis column.
  • the oligonucleotide was cleaved off the support with NH 4 OH and purified by HPLC using an ABI RP-300 (C-18) column (4.6 ⁇ 220 mm) using a flow rate of 1.5 ml/min. and a solvent gradient of 0.1M triethylammonium acetate-water pH 7.0 and acetonitrile. The product was isolated by ethanol precipitation.
  • Protocol for oligo labeled with two generations of trebler branching linker end labeled with phosphates (9 total phosphates) An 18 base oligonucleotide labeled with 2 additions of trebler branching linkages at the 5′ position followed by phosphorylation was made on an ABI model 394 DNA synthesizer using standard phosphoramidite chemistry.
  • the trebler branching (P/N 10-1922-90) and phosphorylating (P/N 104900-90) phosphoramidites were obtained from Glen Research.
  • the labeled 18mer was made using a one micromole synthesis column.
  • the oligonucleotide was cleaved off the support with NH 4 OH and purified by HPLC using an ABI RP-300 (C-18) column (4.6 ⁇ 220 mm) using a flow rate of 1.5 ml/min. and a solvent gradient of 0.1M triethylammonium acetate-water pH 7.0 and acetonitrile. The product was isolated by ethanol precipitation.
  • Protocol for oligo labeled with one or more C-3 spacer containing a 3′ phosphorothioate linkage An 18 base oligonucleotide labeled with one or more C-3 spacers at the 5′ position was made on an ABI model 394 DNA synthesizer using standard phosphoramidite chemistry. The 3′ phosphorothioate linkage was made using standard methods with sulfurizing reagent (TETD P/N 401267 (Applied Biosystems, Foster City, Calif.). The C3 spacer phosphoramidite was obtained from Glen Research (P/N 10-1913-90). The labeled 18mer was made with the trityl group intact from a one micromole synthesis column.
  • the ol ig onucleotide was cleaved off the support with NH 4 OH and purified by HPLC using an ABI RP-300 (C-18) column (4.6 ⁇ 220 mm) using a flow rate of 1.5 ml/min. and a solvent gradient of 0.1M triethylammonium acetate-water pH 7.0 and acetonitrile, the trityl group was removed and the product was isolated by ethanol precipitation. Note: To synthesize more than one phosphorothioate linkage or to place this linkage anywhere in the 18-mer oligonucleotide chain, oxidize using the sulfurizing reagent at these position(s).
  • PCR reactions were carried out in the following 10 ⁇ L solution: to sequence amplicon RSA000013703, 1 ⁇ L 4 ng/ ⁇ L gDNA, M13-tagged primers (0.8 uM each): 1.5 ⁇ L of TGTAAAACGACGGCCAGTTTGATGGGCTCAGCAACAGGT (SEQ ID NO:1, gnl
  • PCR was carried out on a VeritiTM 96-well thermal cycler (P/N 4375786, Applied Biosystems). with the following thermal cycling conditions: 95° C. for 10 minutes, then 35 cycles of 96° C. for 3 seconds, 62° C. for 15 seconds, and 68° C. for 30 sec. followed by 72° C. for 2 min. and 4° C. hold.
  • a 10 ⁇ L sample was analyzed on an agarose gel. A band consistent with the expected 626 bp amplicon was observed.
  • Amplicon RSA000013703 SEQ ID NO:3 template ZC is shown below with primer binding sites for PCR forward primer, and PCR reverse primer (reverse complement) underlined.
  • the Sequencing primer contained a terminal 5′ Negatively Charged Moiety (NCM) and a terminal 3′ phosphorothioate group indicated by an asterisk: M13 forward primer (1 ⁇ M) (NCM-TGTAAAACGACGGCCAG*T) (SEQ ID NO:4) or M13 reverse primer (1 ⁇ M) (NCM-CAGGAAACAGCTATGAC*C) (SEQ ID NO:5).
  • FIG. 3H provides the structure of the NCM.
  • FIG. 11 is a electropherogram (see U.S. Ser. No. 61/407,899, filed Oct. 28, 2011 and U.S. Ser. No. 61/408,553, filed Oct. 29, 2011), of a chemically-enhanced primer ( FIG. 3H ) with a terminal 3′ PS linkage and ZC as the template.
  • the sequence of ZC shows high resolution at base 1 from the primer.
  • PCR reactions were carried out in the following 10 ⁇ L solution: to sequence amplicon RSA000317141 (Template Seq01, 545 bp), 1 ⁇ L 4 ng/ ⁇ L gDNA, M13-tagged primers (0.8 uM each): 1.5 ⁇ L of TGTAAAACGACGGCCAGTGCTGCCTCTGATGGCGGAC (SEQ ID NO:6, forward, gnl
  • PCR was carried out on a VeritiTM 96-well thermal cycler (P/N 4375786, Applied Biosystems). with the following thermal cycling conditions: 95° C. for 10 minutes, then 35 cycles of 96° C. for 3 seconds, 62° C. for 15 seconds, and 68° C. for 30 sec. followed by 72° C. for 2 min. and 4° C. hold.
  • a 10 ⁇ L sample was analyzed on an agarose gel. A band consistent with the expected 545 bp amplicon was observed.
  • Amplicon RSA000317141 SEQ ID NO:8, template Seq01 ( FIG. 3I ) is shown below with primer binding sites for PCR forward primer, and PCR reverse primer (reverse complement) underlined.
  • the Sequencing primer contained a terminal 5′ Negatively Charged Moiety (NCM) and a terminal 3′ phosphorothioate group indicated by an asterisk: M13 forward primer (1 ⁇ M) (NCM-TGTAAAACGACGGCCAG*T) (SEQ ID NO:4) or M13 reverse primer (1 ⁇ M) (NCM-CAGGAAACAGCTATGAC*C) (SEQ ID NO:5).
  • FIG. 16 (see U.S. Ser. No. 61/408,553, filed Oct. 29, 2011), provides a electropherogram of a chemically-enhanced primer with a terminal 3′ PS linkage and RSA000317141 as the template ( FIG. 3J ).
  • the sequence of RSA000317141 shows high resolution at base 1 from the primer.
  • PCR reactions were carried out in the following 10 ⁇ L solution: for example to sequence amplicon RSA0003176671 ⁇ L 10 ng/ ⁇ L gDNA, primers (0.8 uM each), 1.5 ⁇ L of TGTAAAACGACGGCCAGTGGCTCCTGGCACAAAGCTGG (gnl
  • PCR was carried using a Gold-plated 96-Well GeneAmp® PCR System 9700 (P/N 4314878, Applied Biosystems). Thermal cycling conditions: 96° C. 5 minutes, then 40 cycles of 94° C. 30 seconds, 60° C. 45 seconds, and 72° C. 45 sec. followed by 72° C. 2 min. and 4° C. hold. A 5 ⁇ L aliquot was analyzed on an agarose gel. A band consistent with the expected 630 bp amplicon was observed.
  • PCR clean-up The 10 ⁇ L of PCR amplification reaction was mixed with 2 ⁇ L of ExoSAP-IT® nuclease (P/N 78250, Affymetrix, Santa Clara, Calif.) and incubated on a Gold-plated 96-Well GeneAmp® PCR System 9700 (P/N 4314878, Applied Biosystems) at 37° C. 30 minutes followed by 80° C. for 15 minutes (inactivated the nuclease.
  • ExoSAP-IT® nuclease P/N 78250, Affymetrix, Santa Clara, Calif.
  • a sequencing reaction was prepared with the BigDye® Terminator v3.1 Cycle Sequencing Kit (24 reactions, P/N 4337454, Applied Biosystems): 2 ⁇ L of the PCR amplification reaction treated with ExoSAP-IT was mixed with 4 ⁇ L BigDye® Terminator v3.1 Cycle Sequencing Kit Master Mix (P/N 4337454, Applied Biosystems), 1 ⁇ L Sequencing primers chemically-enhanced with terminal 5′ NCM and with or without a terminal 3′ phosphorothioate linkage, (NCM-M13 forward and NCM-M13 reverse primer) and 3 ⁇ L water.
  • the cycle sequencing reaction was carried out at 96° C. 1 min. followed by 25 cycles, 96° C. 10 sec.
  • the sequencing primer is M13 forward primer (1 ⁇ M) containing a terminal 3′ phosphorothioate (PS) group indicated by an asterisk (NGM-TGTAAAACGACGGCCAG*T) (SEQ ID NO:4), M13 reverse primer (1 ⁇ M) (NGM-CAGGAAACAGCTATGAC*C) (SEQ ID NO:5) or without PS, M13 forward primer (1 ⁇ M) (NGM-TGTAAAACGACGGCCAGT) (SEQ ID NO:11), M13 reverse primer (1 ⁇ M) (NGM-CAGGAAACAGCTATGACC) (SEQ ID NO:12).
  • FIGS. 3A and 3F respectively
  • the sequences for RSA000317667 show high resolution at base 1 from the primer.
  • the amplified samples are analyzed by methods that resolve nucleobase sequences as would be known to one of skill in the art.
  • capillary electrophoresis can be used following the instrument manufactures directions.
  • BigDye XTerminator Purification Kit (Applied Biosystems, P/N 4376486) can be used in cycle sequencing clean up to prevent the co-injection of un-incorporated dye-labeled terminators, dNTPs and salts with dye-labeled extension products into a capillary electrophoresis DNA analyzer. Briefly, 13 ⁇ L sequencing reaction mixture was combined with 45 ⁇ L SAM Solution and 10 ⁇ L XTerminator Solution.
  • Capillary electrophoresis was performed on the current Applied Biosystems instruments, for example the Applied Biosystems 3500xl Genetic Analyzer, using the dye set Z as described the instrument's User Guide.
  • ShortReadSeq_BDX_POP7 RapidSeq_BDX_POP7
  • FastSeq_BDX_POP7 StdSeq_BDX_POP7 run modules.
  • BDxFastSeq50_POP7xl — 1 parameters were: oven temperature: 60 C, sample injection for 5 sec at 1.6 kV and electrophoresis at 13.4 kV for 2520 sec in Performance Optimized Polymer (POP-7TM polymer) with a run temperature of 60° C.
  • POP-7TM polymer Performance Optimized Polymer
  • detection techniques employed are generally not limiting. Rather, a wide variety of detection means are within the scope of the disclosed methods and kits, provided that they allow the presence or absence of an amplicon to be determined.

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US14/053,571 US9410192B2 (en) 2010-10-28 2013-10-14 Chemically-enhanced primer compositions, methods and kits
US14/198,308 US9708650B2 (en) 2010-10-28 2014-03-05 Chemically-enhanced primer compositions, methods and kits
US15/230,834 US20170051342A1 (en) 2010-10-28 2016-08-08 Chemically-enhanced primer compositions, methods and kits
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CN112175940A (zh) * 2019-07-03 2021-01-05 华大青兰生物科技(无锡)有限公司 一种基于外切酶的寡核苷酸纯化方法

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US20140377747A1 (en) 2014-12-25
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US20120270211A1 (en) 2012-10-25
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US20170051342A1 (en) 2017-02-23
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US10221449B2 (en) 2019-03-05
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US20140099645A1 (en) 2014-04-10

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