Stable compositions for nucleic acid amplification and sequencing

Abstract

The present invention is directed to compositions comprising mixtures of reagents, including thermostable enzymes (e.g., thermostable DNA polymerases), buffers, cofactors and other components, suitable for immediate use in nucleic acid amplification or sequencing techniques without dilution or addition of further components. The compositions contain no stabilizing agents (e.g., glycerol or serum albumin) and unexpectedly maintain activity for extended periods of time upon storage at temperatures above freezing. These compositions are useful, alone or in the form of kits, for nucleic acid amplification (e.g., by the Polymerase Chain Reaction) and sequencing (e.g., by dideoxy or “Sanger” sequencing), or for any procedure utilizing thermostable DNA polymerases in a variety of medical, forensic and agricultural applications. In particular, the compositions and methods are useful for amplifying and sequencing nucleic acid molecules that are larger than about 7 kilobases in size.

Description

CROSS REFERENCE TO RELATED APPLICATIONS[0001]This application is a continuation-in-part of U.S. application Ser. No. 08 / 801,720, filed Feb. 14, 1997, which is a continuation-in-part of U.S. application Ser. No. 08 / 689,815, filed Aug. 14, 1996 (now abandoned), the contents of both of which are fully incorporated herein by reference.FIELD OF THE INVENTION[0002]This invention is in the fields of molecular and cellular biology. The invention is particularly directed to reagent compositions for use in techniques whereby nucleic acids (DNA or RNA) are amplified or sequenced, and to methods of amplifying and sequencing long nucleic acid molecules, especially via the polymerase chain reaction (PCR).BACKGROUND OF THE INVENTIONDNA Polymerases[0003]During growth and reproduction of viruses and cellular organisms, the DNA containing the parental genetic information must be faithfully copied and passed on to the progeny. This highly regulated process of DNA replication is carried out in vivo by ...

AI Technical Summary

Benefits of technology

[0033]The invention is further directed to kits for DNA amplification or sequencing, said kits comprising a carrier means, such as a box, carton, tube or the like, having in close confinement therein one or more container means, such as vials, tubes, ampules, bottles or the like, wherein a first container means contains a composition comprising a mixture of reagents at working concentrations suitable for use without dilution and maintaining activity upon storage for extended time, said mixture consisting essentially of at least one thermostable DNA polymerase, buffer salts, magnesium salts and at least one nonionic detergent. In additional embodiments, the kits may optionally comprise one or more antibodies, in the first container means or in a separate container means, which specifically bind to one or more of the DNA polymerases present in the compositions of the kits, such as those antibodies described above. The first container means may also contain a mixture of dNTPs (for PCR applications) or ddNTPs (for sequencing applications). Alternatively, the dNTPs or ddNTPs may be included in a second container means also closely confined within the carrier means of the kit.

[0034]The invention is also directed to methods of amplifying or sequencing a nucleic acid molecule, comprising contacting the nucleic acid molecule to be amplified or sequenced, which is preferably larger than about 4-8 kilobases in size, more preferably larger than about 5-7 kilobases in size and most preferably larger than about 7 kilobases in size, with the compositions of the invention. The invention also provides nucleic acid molecules amplified by these methods.

[0035]The present invention is also directed more generally to compositions containing thermostable proteins or enzymes useful in molecular biology. These compositions comprise mixtures of reagents at working concentrations suitable for use with or without dilution which maintain the enzyme o

Problems solved by technology

The dual activity of certain DNA polymerases is, however, a drawback for some in vitro applications.

Unfortunately, the error rate (i.e., the rate at which incorrect dNTPs are incorporated into the new DNA strand by the enzyme) is somewhat higher for the Klenow fragment than for many other commonly used DNA polymerases, including E. coli DNA polymerases I and II and the polymerases from bacteriophages T4 and T7 (Kunkel, T. A., et al., J. Biol. Chem. 259:1539-1545, 1984; Tindall, K. R, and Kunkel, T. A., Biochemistry 27:6008-6013, 1988; Mattila, P., et al., Nucl.

This need for the addition of fresh enzyme at the beginning of each cycle increased the amount of time required for these processes, and increased the risk of operator error and contamination of the samples during reagent introduction, often leading to undesirable results.

The use of thermolabile DNA polymerases such as E. coli or T7 DNA polymerases in these approaches, however, is subject to the same limitations described above for their use in PCR.

The use of Taq and other thermostable polymerases in sequencing and PCR is not, however, without drawback.

These technical limitations are apparently related: it has been theorized that the Taq polymerase PCR length limitation is due to the low efficiency of elongation of the newly synthesized DNA strands at the sites of incorporation of mismatched bases in the parent strands (Barnes, Id.).

The 5′ to 3′ exonuclease activity present in most thermostable DNA polymerases can also degrade the 5′ ends of the oligonucleotide primers (also a complication with the 3′ to 5′ exonuclease activity which can degrade the 3′ ends of the primers), yielding undesirable results due to an early termination of the PCR process (See WO 92 / 06200; Barnes, Id.).

This need for high levels of ddNTPs can be prohibitively expensive, particularly when large DNA fragments are being sequenced.

Moreover, the solutions of enzymes had to be mixed with dNTPs or ddNTPs, cofactors (such as Mg++) and one or more detergents immediately prior to use in the sequencing or PCR processes, as it was believed that premixture and storage of these solutions would also deleteriously affect their stability.

In addition, dNTPs have traditionally been stored at temperatures below −20° C. and have also been thought to be unstable if stored otherwise (Maniatis, T., et al., Molecular Cloning, A Laboratory Manual, CRC Press, 1992).

Together, these limitations have made the use of compositions containing thermostable DNA polymerases in DNA sequencing and PCR more costly and time-consuming than would be desired.

However, as these enzymes also lack the 3′ to 5′ proofreading activity, their use subjects the PCR process to the increased error rates described above.

Thus, even with these mutant enzymes, high-fidelity PCR amplification of DNA fragments larger than 5-6 kilobases has proven exceedingly difficult.

Apparently, the low level of 3′ to 5′ exonuclease activity is sufficient to remove any mismatched bases incorporated by the majority polymerase, but is insufficient to significantly degrade the primers.

Despite its widespread use, however, conventional PCR can produce non-specific amplification fragments which range from small primer-dimer products to target fragments of various yields and of heterogeneous size.

These non-specific products not only obscure PCR results, but can also limit the sensitivity of PCR product detection and can also interfere with downstream processes such as DNA sequencing and cloning of PCR fragments.

These methods, however, are often cumbersome and are not used for routine or high throughput applications.

These monoclonal antibodies prevent the polymerization activity of the enzyme and result in inactivity of Taq DNA polymerase during the PCR setup and start of reactions.

Despite these successes in overcoming the ddNTP discrimination, length, fidelity, and artifact limitations, however, compositions comprising the reagents necessary for DNA sequencing or PCR capable of extended storage above freezing at working concentrations, without stabilizing agents, have not heretofore been reported.

Thus, the time and economic constraints to the use of solutions of thermostable enzymes in most applications have yet to be overcome.

Images