WO1994016107A1

WO1994016107A1 - DNA SEQUENCING WITH Bst POLYMERASE

Info

Publication number: WO1994016107A1
Application number: PCT/US1994/000562
Authority: WO
Inventors: Darwin Johnson Prockop; James Joseph Earley; Geraradus Cornelus Tromp; Sisko Helena Kuivaniemi
Original assignee: Thomas Jefferson University
Priority date: 1993-01-12
Filing date: 1994-01-12
Publication date: 1994-07-21

Abstract

A method of sequencing DNA comprising adding a nucleic acid template and primer to an effective amount of a polymerase, wherein said polymerase is Bst polymerase in a dried down state. The present invention also provides a method of using polymerase in a DNA sequencing method wherein said polymerase is Bst polymerase in a dried down state.

Description

DNA SEQUENCING WITH Bst POLYMERASE

REFERENCE TO GOVERNMENT GRANTS

This work was supported by research grants from the National Institutes of Health, grant numbers AR 38188 and HL 45996. The United States Government may have certain rights in this invention.

FIELD OF THE INVENTION

The present invention is directed to sequencing nucleic acids by the dideoxynucleotide sequencing method.

BACKGROUND OF THE INVENTION

The dideoxynucleotide chain termination method is an efficient process for DNA sequencing. It comprises a set of simple reactions that can be performed in a few minutes and can yield a few hundred nucleotides of DNA sequence. Performing many sequencing reactions, however, very quickly becomes tedious and leads to operator errors since optimal results require consistent timing and precise pipetting of small volumes (0.5 to 10 μl) .

Performing multiple sequencing reactions in parallel such as in multiwell format with multichannel pipets improves throughput and reduces the tedium. The multichannel format is suitable for increasing throughput, not only with manual pipetting, but also with robotic automation. Nonetheless, it is difficult to manually pipet small volumes precisely and reproducibly with a multichannel pipet, since it is easy for one of the channels to fill partially if the pipet is not aligned perfectly with the wells. The problem is compounded in the sequencing protocols, both for manual as well as robotic pipetting, because the small volumes are frequently pipetted from sources of which the volumes are only fractionally larger than the desired volume. Published European Patent Application 0 298 669 discloses the use of dried down enzymes including restriction enzymes; nucleic acid polymerases DNA polymerase I (Klenow fragment) and Tag DNA polymerase; and nucleic acid modification enzymes. The present invention discloses the use of particular dried down enzymes in DNA sequencing. To overcome the limitation of pipetting small volumes, the present invention provides sequencing reagents which have been dried down in multiwell format. As a result, it is possible to pipet volumes that are double or more the volumes used in the standard, non- dried down protocols.

SUMMARY OF THE INVENTION

A method of sequencing DNA comprising the addition of a nucleic acid template and primer to an effective amount of a DNA polymerase and of other sequencing reagents, wherein said DNA polymerase is Bst DNA polymerase and the Bst DNA polymerase and some or all of the other sequencing reagents are in a dried-down state. The present invention also provides a method of using DNA polymerase and sequencing reagents in a DNA sequencing method wherein said polymerase is Bst DNA polymerase and the DNA polymerase and sequencing reagents are in a dried- down state.

BRIEF DESCRIPTION OF THE FIGURES

Figure 1 is an autoradiograph of sequences obtained with Sequenase in the dried-down format. Sequencing reactions were performed as described and the fragments were separated by electrophoresis through a 6% polyacrylamide DNA sequencing gel. Sequences from eight sets of sequencing reactions (loaded G, A, T, C) are shown. The reagents were dried down on a microtiter plate. Termination reagents were dried slowly whereas the labeling reagents and Sequenase were freeze-dried. All non- enzyme reagents were identical for all sets of reactions. As indicated, one half (four) of the icrotiter plate wells that received labeling reagents and enzymes, received one unit of enzyme whereas the other four wells received two units of enzyme. The lanes with less enzyme show a marked lack of signal intensity as well as almost total premature termination (bands in all lanes) about half way up the gel. The lanes with more (two units) enzyme show satisfactory signal but still show signs of premature termination.

Figure 2 is an autoradiograph of sequences obtained with Tag DNA polymerase in the dried-down format. Four sets of reactions (loaded G, A, T, C) are shown. All reagents included non-ionic detergents and were dried down according to the protocol that included applying vacuum in two steps. Sequences were of acceptable quality.

Figure 3 is an autoradiograph of sequences obtained with Tag DNA polymerase in the dried-down format demonstrating the effect of additional DTT on the quality of sequences. All reagents included non-ionic detergents and were dried down according to the protocol that applied vacuum in two stages. Six sets of reactions (loaded G, A, T, C) are shown and the presence of additional DTT to 3 mM is shown. There is no apparent difference due to the presence or absence of additional DTT and sequences were of acceptable quality.

Figure 4 is an autoradiograph of sequences obtained with Bst DNA polymerase in the dried-down format. Reagents for sequencing with Bst DNA polymerase were dried down according to the protocol that included applying vacuum in two stages. All reagents were identical except that the numbers of units of enzyme dried down were as indicated. Eleven sets of reactions (loaded G, A, T, C) are shown. Bst DNA polymerase generated sequences of good quality with as few as 0.25 U of enzyme per set of reactions. Figure 5 is an autoradiograph of sequences obtained with Tag and Bst DNA polymerases in the dried-down format. Reagents were dried down according to the protocol that included applying vacuum in two stages. The reagents for both enzymes were dried simultaneously under identical conditions. Twelve sets of reactions (loaded G, A, T, C) are shown. The number of units of the polymerases that were dried down were as indicated. The results obtained with Tag DNA polymerase are an example of the variability that was observed but occurred sporadically and could not be resolved by the addition of more enzyme. It contrasted starkly with the stability of Bst DNA polymerase. Figure 6 is an autoradiograph demonstrating the effect of additional DTT as well as storage conditions on Bst DNA polymerase in the dried-down format. Plates with Bst DNA polymerase were prepared as described except that DTT to 3 Mm was added to some wells as indicated. Plates were stored overnight at -20°C(A) or at room temperature (B) . Twelve sets of reactions (loaded G, A, T, C) are shown. In contrast to Tag DNA polymerase, Bst DNA polymerase appeared to be sensitive to additional DTT in that the signal intensity as well as extension (processivity) was decreased. The enzyme appeared to be stable at room temperature in the dried-down format.

Figure 7 is a layout of a Master and Target microtiter plate during dispensing of reagents. Reagent stocks were placed in five wells (12B through 12F) of the master plate. Seven microliters were transferred successively to rows of wells (five wells at a time) on the target plate. The reagents were dispensed to the target plate such that the wells 2A through 2F contained the labeling reagents and enzyme, 3A through 3H contained the guanosine termination mix, 4A through 4H contained the adenosine termination mix, 5A through 5H contained the thymidine termination mix and wells 6A through 6H contained the cytosine termination mix. Symbols: L-labeling reagents and enzyme; G-guanosine termination mix; A-adenosine termination mix; T-thymidine termination mix; C-cytosine termination mix; 1-8- reagents transferred simultaneously (same number) using a multichannel pipet; arrows-direction of transfer. DETAILED DESCRIPTION OF THE INVENTION The present invention is directed to a method of DNA sequencing using dried-down polymerase and reagents. The present invention is also directed to a method of using dried- down reagents, particularly sequencing reagents, in DNA sequencing. The methods of the present invention may be especially useful for sequencing in a multiwell format. For purposes of the present invention, DNA sequencing includes, and is not limited to, the use of one or more radiolabeled deoxynucleotide(s) . Alternatively, radiolabeled primers, fluorescently-labeled primers or dideoxynucleotides, biotin- labeled primers or deoxynucleotides may be used.

Reactions may also be performed in the absence of label and detection achieved by hybridization of short oligonucleotide primers that may be labeled with radioisotopes or other components that allow for use of signal-producing enzymes such as luciferase.

For purposes of the present invention, polymerases for use in DNA sequencing include and are not limited to, DNA polymerases such as Bst DNA polymerase. Particularly, the present invention is directed to the method of DNA sequencing wherein the DNA polymerase is dried-down Bst DNA polymerase; and the use of dried-down Bst DNA polymerase in DNA sequencing. Other sequencing reagents include, and are not limited to, pH buffers, EDTA for example; non-ionic detergents, one or more of Brij-35, NP-40, Triton X-100®, Tween® or a mixture of equal parts of these detergents for example; a dye such as xylene cyanol, Fuchsin S, brilliant green, bro ophenol blue, methyl blue, methylene blue or toluidine blue; deoxynucleotides; dideoxynucleotides; a primer, such as M13 universal primers, forward and reverse, for 3-galactosidase-containing vectors, and primers for promoters of SP6, T3, and T7 RNA polymerases; and control DNA.

The dideoxynucleotide method of sequencing DNA is an enzymatic chain termination method which is detailed in Sa brook et al. , Molecular Cloning: A Laboratory Manual , second edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 1989. Briefly, a short oligonucleotide primer is annealed to template DNA and DNA is synthesized enzymatically by extending the annealed primer with a DNA polymerase, usually Sequenase®, Tag DNA polymerase or Bst DNA polymerase. A collection of randomly terminated fragments is generated by specific incorporation, four separate reactions of the four dideoxynucleotides (ddA, ddC, ddG and ddT) that prevent further extension of the DNA chains. Conventional templates may be used in accordance with the present invention. The templates include and are not limited to bacteriophage M13 vectors such as M13mpl8 or M13mpl9, phagemid vector which may be single or double stranded, plasmid vectors, and polymerase chain reaction (PCR) products which may be single or double stranded. Primers, which anneal to vector sequences flanking the target DNA, may be about 15 to about 29 nucleotides in length. The length of the primer is determined by the nature of its DNA sequence as well as the template used. The collection of randomly terminated DNA fragments are then separated according to size (length) by electrophoresis on a denaturing polyacrylamide gel and the sequence is determined by the ladder of fragments differing by a single base in length that are produced from the four dideoxynucleotide reactions.

As set forth in the present invention, "dried-down" refers to desiccation (removal of water) of DNA sequencing reagents and is not limited to a two stage vacuum drying such that in the first stage, the reagents are exposed to a pressure of about 125 Pascals (Pa) to about 375 Pa for about 10 minutes to about 15 minutes; preferably a pressure of about 125 Pa for about 10 minutes. In the second stage, the reagents are exposed to a pressure of about 25 Pa to about 50 Pa for about 20 minutes to about 30 minutes; preferably a pressure of about 25 Pa for about 30 minutes.

The preferred enzyme for the purposes of the present invention is Bst DNA polymerase, a thermostable DNA polymerase from Bacillus stearothermophilus . The Bst DNA polymerase is dried down prior to use in the present invention. About 0.7 units to about 1.3 units, preferably about 1.0 unit of the Bst DNA polymerase is used in a method of DNA sequencing. The advantages of using a thermostable DNA polymerase for sequencing are that a microtiter plate with all the reagents can be heated during the denaturation step without loss of enzyme activity and that the extension and termination reactions occur at elevated temperatures so that -GC- rich templates can be sequenced with greater resolution. The standard microtiter plates with the dried down sequencing reagents for sequencing with Bst DNA polymerase can be used with standard laboratory robots to automate DNA sequencing. All the components are present on one plate which may be manipulated in its entirety for all steps. Because the enzyme is thermally stable, the entire plate with all 96 wells can be heated as a single entity, and therefore it can easily be used with laboratory automation equipment designed to manipulate whole, intact 96-well plates. The volumes that need to be pipetted are in the precise range provided by standard laboratory pipets and robots.

Bst DNA polymerase is more stable after drying down, in that the sequencing results generated with it are more consistent from batch to batch of plates prepared. Experiments with plates containing Tag DNA polymerase which produced poor results demonstrated that the Tag enzyme could be replaced with new enzyme to produce good results. Replacement of Tag DNA polymerase in half the wells of a plate generated good results with the new Tag DNA polymerase and poor results with the dried-down Tag DNA polymerase and therefore confirmed the variability of the Tag DNA polymerase.

Multiple reactions in parallel using multichannel pipets have routinely been used to improve the throughput of DNA sequencing. Because of the limitations inherent in using multichannel pipets with small volumes, it was apparent that modification of the reactions to accommodate larger volumes was necessary. Drying reagents down allows larger volumes to be transferred between steps. Particularly, in the present invention, the initial reaction volume during the denaturation (at about 65°C for about 5 minutes) and annealing (at about room temperature for about 5 minutes) steps of DNA sequencing may be about 45 μl (microliters) to about 50 μl; preferably about 47 μl. There is a loss of about 6 μl due to evaporation at the elevated temperature during denaturation and annealing. The entire volume is successively transferred to the wells containing dNTPs (that may include a radiolabeled dNTP) and to the wells containing DNA polymerase. The reaction is incubated at about 63°C to about 67°C, preferably about 65°C for about 4.5 minutes to about 5.5 minutes; preferably about 5 minutes. Due to the approximate 6 μl lost to evaporation, about 35 μl remains. The reaction is then divided into 4 termination reactions by transferring about 6 μl to about 8 μl; preferably about 7 μl to each of the columns of wells containing the dideoxynucleotide reagent mixes. The reactions are incubated for about 4.5 minutes to about 5.5 minutes, preferably about 5 minutes at about 63°C to about 67°C, preferably about 65°C, to incorporate the dideoxynucleotides.

Successful application of a dry-down protocol to sequencing yields improved results with manual multichannel pipetting. The procedure is also ideally suited to robotic automation since the plate can be manipulated in its entirety at all times because the dried enzyme is stable at the temperature used to denature the template. Three different DNA polymerases have been analyzed to define a sequencing protocol using reagents that are dried onto microtiter plates. The dry-down procedure was first attempted with

Sequenase®, a T7 bacteriophage DNA polymerase conventionally used in DNA sequencing, modified such that 3' - 5' exonuclease activity is eliminated. Sequenase® was dried down on microtiter plates and sequences were obtained (Figure 1) . Sequenase®, however, is known to be labile and the results obtained with the dried enzyme demonstrated a detectable loss of activity in terms of decreased incorporation (as detected by decreased band intensity) or inability to continue extension. The loss of activity was compensated for by increasing the number of units of enzyme dried down per well (Figure 1) . The loss of enzyme activity was attributed to denaturation of some of the enzyme molecules during the drying process. Results from using plates with dried reagents together with non-dried enzyme (conventional format in solution) were comparable to those of conventional sequencing reactions. An inherent limitation of using Sequenase® for the dried down format is that the enzyme cannot be heated to the temperature used to denature the template. Therefore, an additional set of steps to denature the template is required and the plate cannot be heated and manipulated in its entirety. While these limitations make dried down Sequenase® unsuitable for automation, DNA sequencing using dried down Sequenase® by manual operation remains possible.

Another candidate enzyme for the drying method was Tag DNA polymerase from Thermus aguaticus . Tag DNA polymerase is thermally stable and is also conventionally used for DNA sequencing. Initial experiments demonstrated that the well-known stability of Tag DNA polymerase appeared to produce results equal to and better than those obtained with Sequenase®. Tag DNA polymerase survived the drying down better than Sequenase® and generated sequences of good quality. Further experimentation revealed that there was variability in incorporation and extension achieved after drying. The instability in the Tag DNA polymerase was often the cause of variability.

Tag DNA polymerase is supplied in a buffer that contains dithiothreitol (DTT) . Therefore, the possibility that the enzyme was adversely affected by oxidation during the drying was investigated. Inclusion of additional DTT in the enzyme dilution buffer had no adverse effect. Enzyme lots stored (at -20°C) for about 7 days to about two months in the laboratory were more likely to yield poor results after drying. However, Tag DNA polymerase from the same tube still functioned well in the polymerase chain reaction (PCR) .

Another thermally stable enzyme candidate, the DNA polymerase Bst from Bacillus stearothermophilus has properties that make it extremely suitable for DNA sequencing. It is extremely stable in solution as it may be incubated for 14 days at room temperature without loss of activity. Bst DNA polymerase generated excellent sequences after drying and yielded reproducible results.

Bst DNA polymerase was remarkably well suited to the dry-down method. Few experiments were necessary to define conditions for drying and sequencing that yielded reproducible results of excellent quality. In contrast to Tag DNA polymerase which appeared to be unaffected by additional DTT, Bst DNA polymerase was inhibited such that the reactions did not extend as far as reactions in the absence of additional DTT. The enzyme generated good quality sequences after drying, even when using as few as about 0.25 units of enzyme per reaction. It was remarkably robust as exemplified by generation of good quality sequences over a range of Mg²⁺ concentrations as well as when plates were left out at room temperature overnight.

Increasing the throughput of sequences generated in a laboratory using the current dideoxynucleotide DNA sequencing chemistry is possible if the reactions are carried out in parallel, either with automation, manually or the like. Automation imposes a number of restrictions as to the physical format and arrangement of the reagents. General purpose laboratory robots and workstations typically employ 96-well microtiter plates, such as Falcon® flexible U-bottom PVC microtiter plates available from Thomas Scientific (Swedesboro, NJ) . Such complete, unattended automation requires the plate to be manipulated in its entirety. Another constraint imposed by the robots and workstations is the volume pipetted precisely and reproducibly. Drying reagents in microtiter plate wells allows a larger volume to be transferred to the well containing the dried down reagents or enzymes. Therefore, the dry-down method circumvents the volume limitation of robots and workstations and also reduces the probability of volume errors when multichannel pipets are used manually.

In order for the dry-down sequencing method to be successful, the DNA polymerase should withstand drying and reproducibly generate sequences of good quality. The constraint imposed by automation, that the plate should be manipulated in its entirety, also means that the enzyme should be stable enough in its dried form to withstand the heating during the denaturation step. Bst DNA polymerase meets the criteria and appears to be extremely well suited to the dry- down method; it may be dried down on microtiter plates and generates sequences of good quality. It is robust in the dried form; it is stable for more than a week at -20°C and at least overnight at room temperature.

The dried down Bst is useful in DNA sequencing methods; particularly the dideoxynucleotide methods; more particularly a multiwell format.

Conventional DNA sequencing reactions currently comprise two major steps: a single extension reaction in the absence of dideoxynucleotides that extends the primer and usually incorporates labeled DNTP, and four separate termination reactions during which dideoxynucleotides (one per reaction) are incorporated causing the termination of DNA synthesis. The volume of the extension reaction is at least four times the volume of the termination reactions. Prior to extension, the template is heat-denatured and annealed to the primer. The dried down Bst DNA polymerase reaction can be divided into the following steps: Heat denaturation of the template, annealing of primer to the template, extension of the primer and four termination reactions. Prior to heat denaturation, primer, template DNA, water and buffer are added to each of the wells in a column of wells. The starting volume is in the range of about 45 μl to about 50 μl, preferably about 47 μl. For the preferred starting volume of 47μl, the concentrations of the components are as follows: control DNA template (M13mpl8) , 17 ng/ml; primer, 21.3 nM (21.3 fmol/μl) ; MgCl₂, 10.2 mM; Tris-HCl pH 8.8 at room temperature, 34.0 mM. To denature the DNA template, the plate is heated to between about 63°C to about 67°C, preferably to about 65°C, for about 4.5 minutes to about 5.5 minutes, preferably about 5 minutes. To anneal the primer to the template, the plate is transferred to about room temperature, about 20°C to about 23°C, preferably about 21°C. During the denaturation and annealing steps, about 6 μl are lost due to evaporation, therefore, the concentrations of the reagents are about: control DNA, 19.5 ng/μl; primer, 24.3 nM (24.3 fmol/μl) ; MgCl₂, 11.7 mM; Tris-HCl pH 8.0 at room temperature, 39.0 mM. The entire volume is transferred to one or more wells to reconstitute dried down reagents that include Bst DNA polymerase. The dried reagents contribute the following when dissolved in 41 μl: EDTA 0.025 Mm; bovine serum albumin, 0.025 μg/ml; xylene cyanol, 0.00085%; non-ionic detergents which these include but are not limited to equal parts of Brij-35 (dodecylpoly(oxyethelene glycol ether)_n where n=23) , NP-40 (ethyl phenyl polyethylene glycol) , Triton X-100® (polyethylene glycol tert-octylphenyl ether) and Tween-20® (polyoxyethylene sorbitanmonolaurate) , 0.0074%; dNTPS other than the radiolabeled dNTP, 0.147 μM; radiolabeled dNTP, 0.196 μM; Bst DNA polymerase, 0.024 U/μl; and Tris-HCl pH 7.0 at room temperature, 0.25 mM.

For the extension reaction the plate is incubated at about 63°C to about 67°C, preferably about 65°C, for about 4.5 minutes to about 5.5 minutes, preferably about 5 minutes. At the elevated temperature there is again loss of about 6 μl due to evaporation and as a result the volume is about 35 μl at the end of the 5 minute extension reaction. The concentrations of the reagent at the after extension are about as follows: MgCl₂, 13.7 mM; EDTA, 0.029 mM; BSA, 0.029 μg/ml; xylene cyanol, 0.001%; non-ionic detergents, 0.009%, Bst DNA polymerase, 0.029 U/μl; and Tris-HCl pH 8.8 at room temperature, 39.25 mM. Due to the nature of the reaction, the concentrations of dNTPS, primer and free template cannot be determined after extension.

To initiate termination, about 6 μl to about 8 μl, preferably 7 μl of the extension reaction volume is transferred to teach of four wells containing the dideoxynucleotide termination reagents. The deoxy- and dideoxy- nucleotides are dried down in a buffer that, when resuspended in 7 μl, contributes: EDTA, 0.125 mM; bovine serum albumin, 0.125 μg/ml; xylene cyanol, 0.043%; non-ionic detergents, 0.37% and Tris-HCl pH 7.0 at room temperature, 1.25 mM. All four deoxynucleotides (dATP, dCTP, dGTP and dTTP) are present at about 13.5 μM in each of the four termination reactions. Each termination reaction contains only one dideoxynucleotide and because Bst DNA polymerase incorporates each of the dideoxynucleotides with different efficiencies, their concentrations are not the same. In the A termination reaction, the concentration of ddATP is about 200 μM to about 400 μM, preferably about 314 μM. In the C termination reaction, the concentration of ddCTP is about 450 μM to about 850 μM, preferably about 650 μM. In the G termination reaction, the concentration of ddGTP is about 340 μM to about 630 μM, preferably about 485 μM. In the T termination reaction, the concentration of ddTTP is about 80 μM to about 150 μM, preferably about 114 μM. The overall concentration of buffer reagents is about as follows: MgCl₂, 13.7 μM; EDTA, 0.154 mM; bovine serum albumin, 0.154 μg/ml; xylene cyanol, 0.005%; non-ionic detergents, 0.046%; Tris-HCl pH 8.8 at room temperature, 47.25 mM. The termination reactions are incubated at about 63°C to about 67°C, preferably about 65°C, for about

4.5 minutes to about 5.5 minutes; preferably about 5 minutes.

Reactions are terminated by the addition of about 6 μl to about 8 μl, preferably about 7 μl of STOP buffer consisting of 95% forma ide, 20 mM EDTA pH 8.0, 0.05% bromophenol blue and 0.05% xylene cyanol. The final volume, with the addition of 7 μl of STOP buffer, is about 8 to 9 μl due to evaporation. Reactions may also be terminated by cooling the plate, e.g., by placing the plate on ice or at 4°C, prior to the addition of STOP buffer. The present invention is further described in the following examples. These examples are not to be construed as limiting the scope of the appended claims.

EXAMPLE 1 General dry down procedure Several parameters were investigated to expedite the drying process while minimizing damage to the enzymes. These parameters included the effect of the magnitude of vacuum used to dry the reagents, the interval necessary to dry the reagents, and the effect of surface tension (adherence of reagents to the plates) .

Addition of the dye, xylene cyanol, to a final concentration of 0.005% to all the reagents, was extremely useful for determining if the reagents were dried down and adhering to the plate. Thus, technical problems in seeing the dried reagents were overcome. Not detecting the dried reagents makes it difficult to determine whether sequencing failures were due to loss of reagents or due to problems with the enzyme. It may also be difficult to determine if reagents were lost during the drying process or after drying. In subsequent experiments xylene cyanol was shown to have no adverse effect on the sequences. Alternatively, other dyes which may also be used to stain the dried reagents include and are not limited to bromophenol blue, fuchsin S, brilliant green, crystal violet, methyl blue, methylene blue, and toluidine blue.

The first attempts at drying the reagents simulated freeze-drying. Microtiter plates containing reagents were placed on dry ice. After freezing, the plates were placed in a vacuum chamber and vacuum of about 25 Pa for about 30 minutes was applied. The dried plates contained tiny flakes in the wells. The flakes were easily disturbed by air currents as well as electrostatic charges. To overcome these problems, drying was attempted without first freezing the reagents. The applied vacuum, of about 25 Pa to about 50 Pa, for about 20 to about 30 minutes continued to result in freezing with similar consequences. A two-stage drying procedure that avoided freezing of the reagents by ensuring that the initial vacuum was in the range of from about 60 to about 90 Pa (500 to 750 millitorr) for about 10 to about 15 minutes was adopted. After the reagents appeared to be dry, the vacuum was changed to about 25 Pa for 20 minutes. The above two-stage drying protocol prevented the formation of flakes but resulted in crystalline deposits that did not adhere tightly to the plate at the bottoms of the wells. To obtain a better distribution and adsorption of the reagents to the bottoms of the wells, the effect of surfactants were investigated. Because it was known that Tag DNA polymerase is not affected by non-ionic detergents such as Triton X-100®, Tween-20®, NP-40 and Brij-35, one or more of these were added to the reagents to a final concentration of 0.05%. Initial experiments indicated that the non-ionic detergent did not have an adverse effect on the chemistry and in subsequent experiments, the concentration was raised to 0.075%. Inclusion of non-ionic detergents produced a more uniform distribution of the reagents at the bottoms of the wells. Additionally, the reagents adhered tightly to the plate such that the flakes were difficult to disturb by air currents or electrostatic charge. One consequence of including surfactants was the need to modify the two-stage dry-down such that the first stage served to de-gas the reagents to prevent bubbles rising above the wells. For this purpose, the first- stage vacuum was held between about 125 Pa and about 375 Pa (1,000 to 3,000 millitorr) for about 10 minutes to about 15 minutes; more preferably about 125 Pa for about 10 minutes. The second stage remained at about 25 Pa for about 20 minutes. A second consequence of including surfactants was that bubbles were generated during the sequencing reactions when mixing and dissolving the dried reagents by pipetting the solution up and down rapidly. The bubbles had no detectable effect on the sequences. The inclusion of the surfactants, however, resulted in more rapid resuspension and dissolution of the reagents.

EXAMPLE 2 Preparation of stock solutions

Sequenase® enzyme dilution buffer (SEP)

The buffer provided in the kit was diluted four-fold and xylene cyanol was added to give final concentrations of: 2.5 mM Tris-HCl pH 7.5, 1.25 mM DTT, 125 μg/ml BSA and 0.005% xylene cyanol.

10% Non-Ionic Detergent Solution C10% NIP)

Equal parts of 10% stock solutions of Brij-35, NP-40,

Triton X-100®, and Tween-20®, were mixed to prepare the 10% NID.

Enzyme Dry Down Buffer fE-DD)

The 10X concentration buffer consisted of: 15 mM

Tris-HCl pH 8.0, 1.5 mM EDTA, 1.5 mg/ml acetylated BSA, 0.05% xylene cyanol and 0.75% NID. Nucleotide Dry Down Buffer (N-DD)

The buffer was identical in composition to E-DD buffer except that the pH was 7.0.

Labeling Deoxynucleotide Solution (LDN)

Initial experiments with Sequenase® and Tag DNA polymerase were performed with the labeling mixes provided in the kits. For subsequent experiments and for experiments with

Bst DNA polymerase the labeling solution was prepared. The solution contained the non-radioactive deoxynucleotide triphosphates for the extension and labeling reaction. The stock solutions of dCTP, dITP (Sequenase® and Tag DNA polymerase) , 7-deaza dGTP {Bst DNA polymerase) , and dTTP, were diluted to 75 μM each in 0.1 mM EDTA and 10 mM Tris HCl (pH

7.0) .

Sequencing Templates Any template suitable for DNA sequencing may potentially be used. M13mpl8 was used as a control template to develop the system. Single-stranded DNA produced by asymmetrical PCR with primers specific for the particular PCR products has also been used. Termination Mixes

Labeling deoxynucleotide solution was used as a stock such that the concentration each of the deoxynucleotides was 13.7 μM for all four termination mixes. The optimal ratio of i the dideoxynucleotide/deoxynucleotide (ddNTP/dNTP) for each base was determined empirically for Tag and Bst DNA polymerases. The final concentrations of the deoxynucleotides and dideoxynucleotides used with Bst DNA polymerase were as shown in Table 1.

Table 1 Termination Mix

AT CT GT TT ddA(μM) 314.0 ddC 651.0 ddG 485.0 ddT 114.0 dNTPS (μM) 13.5 13.5 13.5 13.5 dNTPS = equal concentrations of dATP, dCTP, dGTP, dTTP. The concentration of each dNTP is equal to the amounts indicated in Table 1.

EXAMPLE 3 Preparation of Microtiter Plates

Typically plates were prepared in batches of six or multiples thereof. A total of six solutions (enzyme in appropriate dilution buffer, Sequenase® in SED (Sequenase® dilution buffer) and Bst or Tag DNA polymerase in E-DD (Enzyme dry down buffer) , LDN and the four termination mixes AT, CT, GT, TT) were prepared and kept on ice. For experiments with Bst or Tag DNA polymerase, the enzyme was diluted in IX E-DD buffer. To simplify the pipetting, all reagents were made up so that it was possible to use a constant volume of 7 μl to dispense the six different solutions. First, the master mixes were dispensed into a single master plate that was kept on ice. To reduce the unrecoverable volume lost, the master mixes were placed in as few wells as possible. The typical arrangement of a master plate and a target plate is shown in FIGURE 7. A well in a column of wells (see FIGURE 7) on the master plate received 200 μl of the appropriate solution. The reagents in a column of wells were sufficient for three target plates. Empty target plates were placed on the bench, six at a time, at room temperature and the solutions were rapidly dispensed. After a batch of six plates were completed, the plates were stored at 4°C until the solutions were dispensed to all batches of plates.

When all reagents were dispensed, the plates were placed in a vacuum chamber (Speed-Vac with rotor removed) , and vacuum was applied. As described above, vacuum was a parameter that was varied in the experiments. The final protocol was a two-stage application of vacuum as follows: an initial vacuum that was held between 125 and 375 Pa (1,000 to 3,000 millitorr) for 10 minutes followed by 20 min at 25 Pa.

EXAMPLE 4 Sequenase® Initial experiments were performed with Sequenase® because it is a conventional DNA polymerase widely used for sequencing and because it provides consistent results in the conventional DNA sequencing format.

Sequencing kits for Sequenase® (Modified T7 DNA polymerase; Sequenase® Version 2.0) as well as M13 universal primer (-40) and M13mpl8 template DNA were obtained from United States Biochemical Corporation, USB (Cleveland, OH) . Acetylated BSA was obtained from Promega (Madison, WI) . Glycerol and xylene cyanol were obtained from Sigma (St. Louis, MI) . Falcon® flexible U-bottom PVC microtiter plates and lids were obtained from Thomas Scientific (Swedesboro, NJ) . Heating blocks with sculpted surfaces that match the U-bottom microtiter plates were obtained from USA Scientific Plastics (Ocala, FL) . A Titertek multichannel pipet for the range from 5 to 50 μl was obtained from Flow Laboratories, ICN (Costa Mesa, CA) . The ³⁵S-dATP (500 Ci/mmol) used as label was obtained from Du Pont NEN Research Products (Boston MA) . To determine the effect of drying on the enzyme, the components of the Sequenase® kit (USB) , were dried down on a PVC microtiter plate. Sequenase® for several reaction wells - about 0.25 μl (about 3.25 U) for each reaction well - was diluted with 1.75 μl SED (Sequenase enzyme dilution buffer) as recommended by the supplier. The enzyme was further diluted by adding 5 μl water for each reaction well. Therefore, a volume of 7 μl of diluted Sequenase® was pipetted to the third column of a PVC microtiter plate. A solution of the labeling mix (dNTPs) from the kit, DTT from the kit and S-dATP was prepared such that 1 μl of the labeling mix, 0.5 μl of the ³⁵S-dATP (20 nM, 500 Ci/mmol) and 1 μl of 0.1 M DTT per well was diluted with water to 7 μl per well. Seven μl of the labeling solution was pipetted to each well in column two of the PVC microtiter plate. Similarly, the four termination mixes from the kit were diluted with water to a volume of 7 μl per well. For the termination mixes 3.5 μl of the kit reagents were diluted with 3.5 μl of water. The four termination mixes were dispensed to columns 4 - 7 of the microtiter plate. The plate was kept on ice during the time that the reagents were dispensed.

The reagents, labeling, solution, diluted enzyme, and termination mixes were dried down by the application of vacuum. As described, in initial experiment, the plate with reagents was frozen on dry ice prior to applying vacuum. In subsequent experiments, the plate was exposed to vacuum without freezing.

For purposes of comparison, enzyme was dried down in four of the eight wells in a column. When the sequencing reactions were performed, enzyme in the conventional format (in solution) was added to the wells that did not have any enzyme dried down.

After drying the reagents for each reaction well, 4 μl (0.8 μg) of single-stranded M13mpl8 template in the presence of 1 μl (1 pmol) primer and 7 μl of Sequenase® reaction buffer, was denatured at about 65°C for 5 minutes in a microcentrifuge tube and the primer was annealed by allowing the tube to cool to room temperature. Template primer (42 μl) and 3.25 U of Sequenase® (2 μl of enzyme diluted according to manufacturer's recommendations) were added to all eight wells in a column. Sequencing reactions were performed under standard conditions for Sequenase® (labeling at room temperature, termination at 37°C) using a multichannel pipet to transfer the columns of reagents from well to well.

Sequenase® appeared to be more stable when the drying was done in a manner similar to freeze-drying, i.e., rapid application of a vacuum with a pressure less than 25 Pa (about 200 millitorr) . However, under these conditions the reagents dried to the flaky deposits described above. Drying under a vacuum with a pressure greater than 25 Pa was detrimental to the enzyme and yielded more variable sequences. Yet, when the labeling and termination mixes were dried down in the absence of the enzyme and the enzyme was dried subsequently under its optimal conditions, the results were still variable. To address the variability, the possibility of an interaction between some of the enzyme molecules and the plastic surface of the microtiter plate resulting in the loss of activity was investigated. The addition of a buffering component, that stabilizes the enzyme against loss of activity, such as bovine serum albumin (BSA) appeared to stabilize the enzyme although variability was not completely eliminated.

EXAMPLE 5 Tag DNA polymerase Tag DNA polymerase (TAQuence® obtained from United

States Biochemical Corp. , Cleveland, Ohio) was substituted for Sequenase® in the dry-down protocol set forth in Example 1, in conjunction with the appropriate labeling and termination mixes. It was possible to obtain sequences of good quality using dried down Tag DNA polymerase, (See Figure 2) . After drying down, the TAQuence® reagents, 42 μl per reaction well consisting of 4 μl (0.8 μg) of M13mpl8 template in the presence of 1 μl (1 pmol) universal primer and 3.5 μl of Tag DNA polymerase buffer and 33.5 μl of water were added to each of the eight wells in a column. The template was denatured at about 65°C for 5 minutes by placing the U-bottom microtiter plate on a sculpted heat block. The plate was transferred to a block at 45°C and the primer was allowed to anneal for 5 minutes. The entire remaining volume of about 35 μl per well was successively transferred with a multichannel pipet to the wells containing the dried labeling mix and the wells contained the dried Tag DNA polymerase. Reagents were resuspended by rapid aspiration and dispensing with the multichannel pipet. The plate was incubated for 5 minutes at 45°C for the labeling/extension reaction. For each reaction, 7 μl of the reaction was pipetted to teach of the wells with the dried termination mixes using a multichannel pipet.

There was considerable variation in results, however, between experiments and between batches of plates. In an attempt to define more clearly the reason for the variability, microtiter plates from a batch that produced poor results were analyzed. The Tag DNA polymerase was removed from half (four of the eight wells) by rinsing the wells several times with about 100 μl of water. The enzyme was replaced with fresh enzyme and either dried down again or used in solution. For most assays, the control template M13mpl8 and the universal primer were used. In addition, products from asymmetrical PCRs with primers specific for those products were also used. The results demonstrated that the new enzyme generated sequences of excellent quality if it was used in solution. Dried down enzyme yielded variable results. Furthermore, batches of plates prepared with Tag DNA polymerase that had been stored in the laboratory for some time were more likely to yield poor or variable results.

A possible explanation for the loss of activity is denaturation of the enzyme during the drying because of interactions with the plastic surface similar to the loss of activity seen when enzymes are highly purified. To investigate the effect of stabilizing the enzyme during the drying, carrier protein in the form of BSA or gelatin was added to the enzyme solution prior to drying. Acetylated BSA did not seem to have adverse effects on the sequencing reactions and it dried down well in that the BSA-enzyme adhered well to the microtiter plates. In contrast, gelatin appeared to form a gel that did not quite dry. Inclusion of BSA did not, however, resolve the variability. As BSA did not appear to have an adverse effect and it was maintained in the drying protocol.

Another possible explanation for the variable results was that the drying protocol could expose the enzyme to oxidation. To investigate this possibility, DTT was added to a concentration of 3 mM in the enzyme dilution buffer. Sequences generated by enzyme dried down in the presence and in the absence of the added DTT were indistinguishable (Figure 3) .

EXAMPLE 6 Bst DNA polymerase

M13 universal primer (-40) and M13mpl8 template DNA were obtained from United States Biochemical Corporation, USB (Cleveland, OH) . Bst DNA polymerase was obtained from Bio-Rad Laboratories (New York, NY) . Deoxynucleotides and dideoxynucleotides were obtained as solutions from Boehringer Mannheim Biochemicals (Indianapolis, IN) . Acetylated BSA was obtained from Promega (Madison, WI) . Tris buffer, DTT, EDTA, MgCl₂, gelatin and xylene cyanol were obtained from Sigma (St.

Louis, MO) . Glycerol and xylene cyanol were obtained from

Sigma (St. Louis, MO) . Falcon® flexible U-bottom PVC microtiter plates and lids were obtained from Thomas Scientific

(Swedesboro, NJ) . Heating blocks with sculpted surfaces that match the U-bottom microtiter plates were obtained from USA Scientific Plastics (Ocala, FL) . A Titertek multichannel pipet for the range from 5 to 50 μl was obtained from Flow Laboratories, ICN (Costa Mesa, CA) . The ³⁵S-dATP (500 Ci/mmol) used as label was obtained from Du Pont NEN Research Products (Boston, MA) .

The stability of Bst DNA polymerase at room and elevated temperatures was investigated in its applicability to the dry-down protocol set forth in Example l. It appeared to be remarkably well suited to the dry down method. After preparing microtiter plates with dried down reagents, including enzyme, 47 μl per well of a mixture of 4 μl (0.8 μg) single- stranded M13mpl8 template in the presence of 1 μl (1 pmol) universal primer and 4 μl of Bst DNA polymerase reaction buffer, 38 μl of water was added to each of eight wells on a plate. The template was denatured at 65°C for 5 minutes. The plate was moved to room temperature and the primer was allowed to anneal for 5 minutes. The 41 μl that remained per well after evaporation was successively transferred with a multichannel pipet to the wells containing labeling mix and dried down enzyme. Reagents were resuspended by repetitive, rapid aspiration and dispensing. The plate was moved to a sculpted heat block at 65°C and incubated for 5 minutes. For each of the reactions, 7 μl of the remaining 35 μl was transferred to the wells containing the dried termination reagents. The termination reactions were carried out at 65°C for 5 minutes. Reactions were stopped by the addition of 7 μl of STOP buffer. The enzyme generated good quality sequences after drying, even when as few as 0.25 units of the enzyme were used per reaction (Figure 4) . Under identical conditions it was more suited to the dried-down format than Tag DNA polymerase (Figure 5) . It was also remarkably robust in that reactions performed with Mg²⁺ concentrations ranging from 5 to 20 mM generated sequences of good quality. To further assay the robustness of the enzyme, dried microtiter plates were left out overnight at room temperature. The sequences generated were indistinguishable from those of plates stored at -20°C (Figure 6) . The effect of adding DTT to the enzyme dilution buffer was also investigated. In contrast to Tag DNA polymerase, which appeared to be unaffected by additional DTT, Bst DNA polymerase was inhibited (Figure 6) . The reactions including DTT did not extend as far as reactions in the absence of additional DTT.

Other sequencing reagents for use in the present invention include and are not limited to pH buffers, such as 1.5 M Tris-HCl, 0.15 mM EDTA; stabilizers such as 0.15 mg/ml bovine serum albumin or acetylated bovine serum albumin; 0.075% non-ionic detergents (NID)/surfactants including one or more of Brij-35, NP-40, Triton X-100®, Tween 20® or a mixture of equal parts of these detergents in 1.5 mM Tris-HCl pH 8.0 at room temperature; 0.005% of a dye such as xylene cyanol, Fuchsin S, brilliant green, bromophenol blue, methyl blue, methylene blue or toluidine blue; deoxynucleotides in a buffer suitable for drying down, such as 0.15 mM EDTA, 0.15 mg/ml acetylated BSA, 0.075% non-ionic detergents such as those indicated above in 1.5 mM Tris-HCl pH 7.0 at room temperature; and dideoxynucleotides in a buffer suitable for drying down, such as 0.15 mM EDTA, 0.15 mg/ml acetylated BSA or 0.075% non-ionic detergents such as those indicated above in 1.5 mM Tris-HCl pH 7.0 at room temperature; DNA sequencing primers such as M13 universal primer and galactosidase-containing vectors which may be dried down, and control DNA such as single-stranded M13mpl8 DNA which may be dried down. Other reagents include and are not limited to, radiolabeled deoxynucleotides, primers for DNA sequencing (labeled or not labeled) , and fluorescently-labeled dideoxynucleotides template DNA for control reactions.

Various modifications of the invention in addition to those shown and described herein will be apparent to those skilled in the art from the foregoing description. Such modifications are also intended to fall within the scope of the appended claims.

Claims

CLAIMS What is claimed:

1. A method of sequencing DNA comprising adding a nucleic acid template and primer to an effective amount of DNA polymerase and one or more sequencing reagents, wherein said DNA polymerase and said sequencing reagents are in a dried down state.

2. The method of claim 1 wherein said DNA polymerase is Bst DNA polymerase, and said sequencing reagents are selected from the group consisting of pH buffers, stabilizers, non-ionic detergents, dye, deoxynucleotides, dideoxynucleotides, primer, and control DNA.

3. The method of claim 2 wherein said DNA sequencing is a dideoxynucleotide sequencing method.

4. The method of claim 2 wherein said pH buffer is selected from the group consisting of Tris and EDTA.

5. The method of claim 2 wherein said stabilizer is selected from the group consisting of acetylated BSA and BSA.

6. The method of claim 2 wherein said non-ionic detergent is selected from the group consisting of Brij-35, NP- 40, polyethylene glycol tert-octylphenyl ether and polyoxyethylene sorbitan onolaurate.

7. The method of claim 2 wherein said dye is selected from the group consisting of xylene cyanol, Fuchsin S, bromophenol blue, brilliant green, methyl blue, methylene blue, and toluidine blue.

8. The method of claim 2 wherein said primer is selected from the group consisting of M13 universal primers for

/3-galactosidase-containing vectors and primers for the promoters of RNA polymerases.

9. The method of claim 2 wherein control DNA selected from the group consisting of single stranded DNAs, vectors derived from bacteriophage M13 and β-galactosidase - containing plas id vectors is provided for one reaction set per plate.

10. A method of using DNA polymerase and one or more sequencing reagents in a DNA sequencing method wherein said DNA polymerase and said sequencing reagents are in a dried down state.

11. The method of claim 10 wherein said DNA polymerase is Bst DNA polymerase and said sequencing reagents are selected from the group consisting of pH buffer, stabilizers, non-ionic detergents, dye, deoxynucleotides, dideoxynucleotides, primer, and control DNA.

12. The method of claim 10 wherein said DNA sequencing method is a dideoxynucleotide sequencing method.

13. The method of claim 11 wherein said pH buffer is selected from the group consisting of Tris and EDTA.

14. The method of claim 11 wherein said stabilizers are selected from the group consisting of acetylated BSA and

BSA.

15. The method of claim 11 wherein said non-ionic detergent is selected from the group consisting of Brij-35, NP- 40, polyethylene glycol tert-octylphenyl ether and polyoxyethylene sorbitanmonolaurate.

16. The method of claim 11 wherein said dye is selected from the group consisting of xylene cyanol, Fuchsin S, bromophenol blue, brilliant green, methyl blue, methylene blue, and toluidine blue.

17. The method of claim 11 wherein said primer is selected from the group consisting of M13 universal primers for 3-galactosidase-containing vectors and primers for the promoters of RNA polymerases.

18. The method of claim 11 wherein control DNA selected from the group consisting of single stranded DNAs, vectors derived from bacteriophage M13 and β-galactosidase - containing plasmid vectors is provided for one reaction set per plate.

19. An apparatus for performing DNA sequencing comprising a plate with Bst DNA polymerase and one or more sequencing reagents in a dried down state.

20. The apparatus of claim 19 wherein said sequencing reagents are selected from the group consisting of pH buffers, stabilizers, non-ionic detergents, dye, deoxynucleotides, dideoxynucleotides, primer and control DNA.