Enzyme-pore Constructs

Abstract

The invention relates to constructs comprising a transmembrane protein pore subunit and a nucleic acid handling enzyme. The pore subunit is covalently attached to the enzyme such that both the subunit and enzyme retain their activity. The constructs can be used to generate transmembrane protein pores having a nucleic acid handling enzyme attached thereto. Such pores are particularly useful for sequencing nucleic acids. The enzyme handles the nucleic acid in such a way that the pore can detect its component nucleotides by stochastic sensing.

Description

FIELD OF THE INVENTION

[0001] The invention relates to constructs comprising a transmembrane protein pore subunit and a nucleic acid handling enzyme. The pore subunit is covalently attached to the enzyme such that both the subunit and enzyme retain their activity. The constructs can be used to generate transmembrane protein pores having a nucleic acid handling enzyme attached thereto. Such pores are particularly useful for sequencing nucleic acids. The enzyme handles the nucleic acid in such a way that the pore can detect each of its component nucleotides by stochastic sensing.

BACKGROUND OF THE INVENTION

[0002] Stochastic detection is an approach to sensing that relies on the observation of individual binding events between analyte molecules and a receptor. Stochastic sensors can be created by placing a single pore of nanometer dimensions in an insulating membrane and measuring voltage-driven ionic transport through the pore in the presence of analyte molecules. The frequency of occurrence of fluctuations in the current reveals the concentration of an analyte that binds within the pore. The identity of an analyte is revealed through its distinctive current signature, notably the duration and extent of current block (Braha, O., Walker, B., Cheley, S., Kasianowicz, J. J., Song, L., Gouaux, J. E., and Bayley, H. (1997) Chem. Biol. 4, 497-505; and Bayley, H., and Cremer, P. S. (2001) Nature 413, 226-230).

[0003] Engineered versions of the bacterial pore forming toxin .alpha.-hemolysin (.alpha.-HL) have been used for stochastic sensing of many classes of molecules (Bayley, H., and Cremer, P. S. (2001) Nature 413, 226-230; Shin, S., H., Luchian, T., Cheley, S., Braha, O., and Bayley, H. (2002) Angew. Chem. Int. Ed. 41, 3707-3709; and Guan, X., Gu, L.-Q., Cheley, S., Braha, O., and Bayley, H. (2005) ChemBioChem 6, 1875-1881). In the course of these studies, it was found that attempts to engineer .alpha.-HL to bind small organic analytes directly can prove taxing, with rare examples of success (Guan, X., Gu, L.-Q., Cheley, S., Braha, O., and Bayley, H. (2005) ChemBioChem 6, 1875-1881). Fortunately, a different strategy was discovered, which utilized non-covalently attached molecular adaptors, notably cyclodextrins (Gu, L.-Q., Braha, O., Conlan, S., Cheley, S., and Bayley, H. (1999) Nature 398, 686-690), but also cyclic peptides (Sanchez-Quesada, J., Ghadiri, M. R., Bayley, H., and Braha, O. (2000) J. Am. Chem. Soc. 122, 11758-11766) and cucurbiturils (Braha, O., Webb, J., Gu, L.-Q., Kim, K., and Bayley, H. (2005) ChemPhysChem 6, 889-892). Cyclodextrins become transiently lodged in the .alpha.-HL pore and produce a substantial but incomplete channel block. Organic analytes, which bind within the hydrophobic interiors of cyclodextrins, augment this block allowing analyte detection (Gu, L.-Q., Braha, O., Conlan, S., Cheley, S., and Bayley, H. (1999) Nature 398, 686-690).

[0004] There is currently a need for rapid and cheap DNA or RNA sequencing technologies across a wide range of applications. Existing technologies are slow and expensive mainly because they rely on amplification techniques to produce large volumes of nucleic acid and require a high quantity of specialist fluorescent chemicals for signal detection. Stochastic sensing has the potential to provide rapid and cheap DNA sequencing by reducing the quantity of nucleotide and reagents required.

SUMMARY OF THE INVENTION

[0005] The inventors have surprisingly demonstrated that covalent attachment of a transmembrane protein pore subunit to a nucleic acid handling enzyme results in a construct that is capable of both forming a pore and handling nucleic acids. The inventors have also surprisingly demonstrated that the construct can be used to generate a transmembrane protein pore that is capable of both handling a nucleic acid and sequencing the nucleic acid via stochastic sensing. The fixed nature and close proximity of the enzyme to the pore means that a proportion of the nucleotides in a target nucleic acid will interact with the pore and affect the current flowing through the pore in a distinctive manner. As a result, transmembrane protein pores comprising such constructs are useful tools for stochastic sensing and especially for sequencing nucleic acids.

[0006] Accordingly, the invention provides a construct comprising a transmembrane protein pore subunit and a nucleic acid handling enzyme, wherein the subunit is covalently attached to the enzyme, wherein the subunit retains its ability to form a pore and wherein the enzyme retains its ability to handle nucleic acids. The invention also provides: [0007] a polynucleotide sequence which encodes a construct of the invention; [0008] a modified pore for use in sequencing nucleic acids, comprising at least one construct of the invention; [0009] a kit for producing a modified pore for use in sequencing nucleic acids, comprising:

[0010] (a) at least one construct of the invention; and

[0011] (b) any remaining subunits needed to form a pore; [0012] a kit for producing a modified pore for use in sequencing nucleic acids, comprising:

[0013] (b) at least one polynucleotide of the invention; and

[0014] (c) polynucleotide sequences encoding any remaining subunits needed to form a pore; [0015] a method of producing a construct of the invention, comprising:

[0016] (a) covalently attaching a nucleic acid handling enzyme to a transmembrane protein pore subunit; and

[0017] (b) determining whether or not the resulting construct is capable of forming a pore and handling nucleic acids; [0018] a method of producing a modified pore of the invention, comprising:

[0019] (a) covalently attaching a nucleic acid handling enzyme to a transmembrane protein pore; and

[0020] (b) determining whether or not the resulting pore is capable of handling nucleic acids and detecting nucleotides; [0021] method of producing a modified pore of the invention, comprising:

[0022] (a) allowing at least one construct of the invention to form a pore with other suitable subunits; and

[0023] (b) determining whether or not the resulting pore is capable of handling nucleic acids and detecting nucleotides. [0024] a method of purifying a transmembrane pore comprising at least one construct of the invention, comprising:

[0025] (a) providing the at least one construct and the other subunits required to form the pore;

[0026] (b) oligomerising the at least one construct and other subunits on synthetic lipid vesicles; and

[0027] (c) contacting the vesicles with a non-ionic surfactant; and

[0028] (d) recovering the oligomerised pore; [0029] a method of sequencing a target nucleic acid sequence, comprising:

[0030] (a) contacting the target sequence with a pore of the invention, which comprises an exonuclease, such that the exonuclease digests an individual nucleotide from one end of the target sequence;

[0031] (b) contacting the nucleotide with the pore so that the nucleotide interacts with the adaptor;

[0032] (c) measuring the current passing through the pore during the interaction and thereby determining the identity of the nucleotide; and

[0033] (d) repeating steps (a) to (c) at the same end of the target sequence and thereby determining the sequence of the target sequence; and

[0034] a method of sequencing a target nucleic acid sequence, comprising:

[0035] (a) contacting the target sequence with a pore of the invention so that the enzyme pushes or pulls the target sequence through the pore and a proportion of the nucleotides in the target sequence interacts with the pore; and

[0036] (b) measuring the current passing through the pore during each interaction and thereby determining the sequence of the target sequence.

DESCRIPTION OF THE FIGURES

[0037] FIG. 1 shows how exonuclease enzymes catalyse the hydrolysis of phosphodiester bonds. Within the active site of the exonuclease, a water molecule is enabled to react with the phosphate of the 3' end of the polynucleotide (DNA). Cleavage of the bond between the phosphate and the sugar towards the 5' end releases a monophosphate (deoxy)nucleoside.

[0038] FIG. 2 shows the crystal structures of exonucleases used in the Example, N and C-terminus and active sites are shown for each. i) Adapted form of EcoExoIII; ii) EcoExoI; iii) TthRecJ-cd; and iv) Lambda exo.

[0039] FIG. 3 shows a cartoon of an exonuclease equipped .alpha.-HL pore. The exonuclease is genetically fused to one of the seven monomers of the heptamer, with linker arms sufficiently long to enable correct protein folding of the exonuclease moiety and the .alpha.-HL moiety.

[0040] FIG. 4 shows generic image of the protein construct generated shows the BspEI insertion point(s) in the .alpha.-HL gene. Ligation AfuExoIII, bounded by two stretches of DNA encoding a (serine/glycine).sub.x5 repeat (shown hatched) generates a fusion protein in which a 64.5 kDa protein will be generated, under the transcriptional control of the T7 promoter shown.

[0041] FIG. 5 shows the oligomerisation of .alpha.-HL Loop 1 fusion constructs with wild-type .alpha.-HL at different protein ratios. i) HL-wt-EcoExoIII-L1-H6; ii) HL-RQC-EcoExoI-L1-H6; and iii) HL-RQC-TthRecJ-L1-H6.

[0042] FIG. 6 shows the control of homo and heteroheptamer generation by different monomer ratios. HL-RQ subunits are shown in white and fusion subunits in black. Increasing the ratio of fusion subunits to wild-type subunits increases the generation of 2:5, 1:6 and 0:7 hetero and homo-heptamers. Similarly increasing the concentration of HL-RQ monomer increases the generation of 6:1 and 5:2 heteroheptamers.

[0043] FIG. 7 shows the oligomerisation of HL-RQC-EcoExoIII-L1-H6 fusion proteins that contain a stiff polyproline EcoExoIII C-terminus linker. IVTT expressed proteins mixed in a 5:1 wild-type to fusion protein ratio in the presence of purified rabbit red blood cell membranes. i) HL-RQC-EcoExoIII-L1-{SG} 5+{SG} 5-H6; ii) HL-RQC-EcoExoIII-L1-{SG}5+5P-H6; iii) HL-RQC-EcoExoIII-L1-4SG+5P-H6; and iv) HL monomers.

[0044] FIG. 8 shows the Loop 2 region of a single .alpha.-hemolysin subunit with the mature heptamer. Subunit 1 shown in white, subunits 2-7 shown in grey and the loop 2 region of subunit 1 shown in black.

[0045] FIG. 9 shows the oligomerisation of alternative Loop 2 EcoExoIII fusion proteins. i) HL-(RQ).sub.7; ii) HL-(RQ).sub.6(RQC-EcoExoIII-L2a-H6).sub.1; iii) HL-(RQ).sub.6(RQC-EcoExoIII-L2a-8P-H6).sub.1; iv) HL-(RQ).sub.6(RQC-EcoExoIII-L2-H48.DELTA.-H6).sub.1; v) HL-(RQ).sub.6(RQC-EcoExoIII-L2-D45.DELTA.-H6).sub.1; vi) HL-(RQ).sub.6(RQC-EcoExoIII-L2-D45-K46.DELTA.-H6).sub.1; and vii) HL-(RQ).sub.6(RQC-EcoExoIII-L2-D45-N47.DELTA.-H6).sub.1.

[0046] FIG. 10 shows the oligomerisation of alternative Loop 2 EcoExoIII fusion proteins. i) HL-(RQ).sub.7; ii) HL-(RQ).sub.6(RQC-EcoExoIII-L2a-H6).sub.1; iii) HL-(RQ).sub.6(RQC-EcoExoIII-L2-D45-N47.DELTA.-H6).sub.1; iv) HL-(RQ).sub.6(RQC-EcoExoIII-L2-D46-K56.DELTA.-H6).sub.1; v) HL-(RQ).sub.6(RQC-EcoExoIII-L2-D46.DELTA.-H6).sub.1; vi) HL-(RQ).sub.6(RQC-EcoExoIII-L2-D46-N47.DELTA.-H6).sub.1; vii) HL-(RQ).sub.6(RQC-EcoExoIII-L2-A1-S16.DELTA./D46-N47.DELTA.-H6).sub.1; viii) HL-(RQ).sub.6(RQC-EcoExoIII-L2-F42-D46.DELTA.-H6).sub.1; and ix) HL-(RQ).sub.6(RQC-EcoExoIII-L2143-D46.DELTA.-H6).sub.1.

[0047] FIG. 11 shows the oligomerisation of EcoExoI C-terminus fusion proteins. a) denotes both hemolysin and enzyme-fusion protein monomers are radiolabelled, b) denotes only the fusion protein monomer is radiolabelled. i) HL-(RQ).sub.6(RQC-EcoExoI-Cter-{SG}8-H6).sub.1; ii) HL-(RQ).sub.6(RQC-EcoExoI-Cter-DG{SG}8-H6).sub.1; iii) HL-(RQ).sub.6(RQC-EcoExoI-Cter-WPV{SG}8-H6).sub.1; iv) HL-(RQ).sub.6(RQC-EcoExoI-Cter-DGS {P}12-H6).sub.1; and v) HL-(RQ).sub.6(RQC-EcoExoI-Cter-WPV {P}12-H6).sub.1.

[0048] FIG. 12 shows the effect of different surfactants on EcoExoIII activity. Left graph--Sodium dodecyl sulphate (SDS): a; 0%, b; 0.1%, c; 0.5%. Right graph--n-Dodecyl-D-maltopyranoside (DDM): a; 0%, b; 0.1%, c; 0.25%, d; 0.5%.

[0049] FIG. 13 shows the oligomerisation of E. coli BL21 (DE3) pLysS expressed .beta.-hemolysin monomers for formation and purification of preferentially 6:1 heteroheptamers. His-tag purification is used to select between heteroheptamers and wild-type homoheptamer to give a large excess of 6:1 heteroheptamer.

[0050] FIG. 14 shows the exonuclease activity of monomer and heteroheptamer fusion proteins. Left graph--Activity of Wild-type and fusion monomers: a, 10.sup.-'2 dilution HL-RQC-EcoExoIII-L1-H6; b, 10.sup.-'4 dilution HL-RQC-EcoExoIII-L1-H6; c, 10.sup.-'6 dilution HL-RQC-EcoExoIII-L1-H6; d, 10.sup.-'2 dilution HL-RQ. Right graph--Activity of HL-(RQ).sub.6(RQC-EcoExoIII-L1-H6).sub.1: a, DDM crude extract; b, Ni-NTA purified; c, Ni-NTA purified and buffer exchange.

[0051] FIG. 15 shows base detection by the HL-(RQ).sub.6(RQC-EcoExoIII-L2-D46-N47.DELTA.-H6).sub.1 heteroheptamer. The top trace was obtained from a heteroheptamer with a covalently attached am.sub.6-amPDP.sub.1-.beta.CD adapter molecule. Further blocking events can be seen and ascribed to individual mono-phosphate nucleosides for base discrimination. The bottom graph shows the corresponding histograms of dNMP events from the top trace. Peaks, from left to right, correspond to G, T, A, C respectively. Data acquired at 400/400 mM KCl, 180 mV and 10 .mu.M dNMPs.

DESCRIPTION OF THE SEQUENCE LISTING

[0052] SEQ ID NO: 1 shows the polynucleotide sequence encoding one subunit of wild-type .alpha.-hemolysin (.alpha.-HL).

[0053] SEQ ID NO: 2 shows the amino acid sequence of one subunit of wild-type .alpha.-HL. Amino acids 2 to 6, 73 to 75, 207 to 209, 214 to 216 and 219 to 222 form .alpha.-helices. Amino acids 22 to 30, 35 to 44, 52 to 62, 67 to 71, 76 to 91, 98 to 103, 112 to 123, 137 to 148, 154 to 159, 165 to 172, 229 to 235, 243 to 261, 266 to 271, 285 to 286 and 291 to 293 form .beta.-strands. All the other non-terminal amino acids, namely 7 to 21, 31 to 34, 45 to 51, 63 to 66, 72, 92 to 97, 104 to 111, 124 to 136, 149 to 153, 160 to 164, 173 to 206, 210 to 213, 217, 218, 223 to 228, 236 to 242, 262 to 265, 272 to 274 and 287 to 290 form loop regions. Amino acids 1 and 294 are terminal amino acids.

[0054] SEQ ID NO: 3 shows the polynucleotide sequence encoding one subunit of .alpha.-HL M113R/N139Q (HL-RQ).

[0055] SEQ ID NO: 4 shows the amino acid sequence of one subunit of .alpha.-HL M113R/N139Q (HL-RQ). The same amino acids that form .alpha.-helices, .beta.-strands and loop regions in wild-type .alpha.-HL form the corresponding regions in this subunit.

[0056] SEQ ID NO: 5 shows the pT7 .alpha.-HL BspEI knockout polynucleotide sequence (pT7-SC1_BspEI-KO). The .alpha.-HL encoding sequence is between nucleotides 2709 and 3593. The BspEI remnant is at nucleotides 3781 and 3782.

[0057] SEQ ID NO: 6 shows the polynucleotide sequence encoding one subunit of wild-type .alpha.-hemolysin containing a BspEI cloning site at position 1 (L1).

[0058] SEQ ID NO: 7 shows the polynucleotide sequence encoding one subunit of wild-type .alpha.-hemolysin containing a BspEI cloning site at position 2 (L2a).

[0059] SEQ ID NO: 8 shows the polynucleotide sequence encoding one subunit of wild-type .alpha.-hemolysin containing a BspEI cloning site at position 2 (L2b).

[0060] SEQ ID NO: 9 shows the codon optimized polynucleotide sequence derived from the xthA gene from E. coli. It encodes the exonuclease III enzyme from E. coli.

[0061] SEQ ID NO: 10 shows the amino acid sequence of the exonuclease III enzyme from E. coli. This enzyme performs distributive digestion of 5' monophosphate nucleosides from one strand of double stranded DNA (dsDNA) in a 3'-5' direction. Enzyme initiation on a strand requires a 5' overhang of approximately 4 nucleotides. Amino acids 11 to 13, 15 to 25, 39 to 41, 44 to 49, 85 to 89, 121 to 139, 158 to 160, 165 to 174, 181 to 194, 198 to 202, 219 to 222, 235 to 240 and 248 to 252 form .alpha.-helices. Amino acids 2 to 7, 29 to 33, 53 to 57, 65 to 70, 75 to 78, 91 to 98, 101 to 109, 146 to 151, 195 to 197, 229 to 234 and 241 to 246 form .beta.-strands. All the other non-terminal amino acids, 8 to 10, 26 to 28, 34 to 38, 42, 43, 50 to 52, 58 to 64, 71 to 74, 79 to 84, 90, 99, 100, 110 to 120, 140 to 145, 152 to 157, 161 to 164, 175 to 180, 203 to 218, 223 to 228, 247 and 253 to 261, form loops. Amino acids 1, 267 and 268 are terminal amino acids. The enzyme active site is formed by loop regions connecting .beta..sub.1-.alpha..sub.1, .beta..sub.3-.beta..sub.4, .beta..sub.5-.beta..sub.6, .beta..sub.III-.alpha..sub.I, .beta..sub.IV-.alpha..sub.II and .beta..sub.V-.beta..sub.VI (consisting of amino acids 8-10, 58-64, 90, 110-120, 152-164, 175-180, 223-228 and 253-261 respectively). A single divalent metal ion is bound at residue E34 and aids nucleophilic attack on the phosphodiester bond by the D229 and H259 histidine-aspartate catalytic pair.

[0062] SEQ ID NO: 11 shows the codon optimized polynucleotide sequence derived from the sbcB gene from E. coli. It encodes the exonuclease I enzyme (EcoExoI) from E. coli.

[0063] SEQ ID NO: 12 shows the amino acid sequence of exonuclease I enzyme (EcoExoI) from E. coli. This enzyme performs processive digestion of 5' monophosphate nucleosides from single stranded DNA (ssDNA) in a 3'-5' direction. Enzyme initiation on a strand requires at least 12 nucleotides. Amino acids 60 to 68, 70 to 78, 80 to 93, 107 to 119, 124 to 128, 137 to 148, 165 to 172, 182 to 211, 213 to 221, 234 to 241, 268 to 286, 313 to 324, 326 to 352, 362 to 370, 373 to 391, 401 to 454 and 457 to 475 form .alpha.-helices. Amino acids 10 to 18, 28 to 26, 47 to 50, 97 to 101, 133 to 136, 229 to 232, 243 to 251, 258 to 263, 298 to 302 and 308 to 311 form .beta.-strands. All the other non-terminal amino acids, 19 to 27, 37 to 46, 51 to 59, 69, 79, 94 to 96102 to 106, 120 to 123, 129 to 132, 149 to 164, 173 to 181, 212, 222 to 228 233, 242, 252 to 257, 264 to 267, 287 to 297, 303 to 307, 312, 325, 353 to 361, 371, 372, 392 to 400455 and 456, form loops. Amino acids 1 to 9 are terminal amino acids. The overall fold of the enzyme is such that three regions combine to form a molecule with the appearance of the letter C, although residues 355-358, disordered in the crystal structure, effectively convert this C into an O-like shape. The amino terminus (1-206) forms the exonuclease domain and has homology to the DnaQ superfamily, the following residues (202-354) form an SH3-like domain and the carboxyl domain (359-475) extends the exonuclease domain to form the C-like shape of the molecule. Four acidic residues of EcoExoI are conserved with the active site residues of the DnaQ superfamily (corresponding to D15, E17, D108 and D186). It is suggested a single metal ion is bound by residues D15 and 108. Hydrolysis of DNA is likely catalyzed by attack of the scissile phosphate with an activated water molecule, with H181 being the catalytic residue and aligning the nucleotide substrate.

[0064] SEQ ID NO: 13 shows the codon optimized polynucleotide sequence derived from the recJ gene from T. thermophilus. It encodes the RecJ enzyme from T. thermophilus (TthRecJ-cd).

[0065] SEQ ID NO: 14 shows the amino acid sequence of the RecJ enzyme from T. thermophilus (TthRecJ-cd). This enzyme performs processive digestion of 5' monophosphate nucleosides from ssDNA in a 5'-3' direction. Enzyme initiation on a strand requires at least 4 nucleotides. Amino acids 19 to 33, 44 to 61, 80 to 89, 103 to 111, 136 to 140, 148 to 163, 169 to 183, 189 to 202, 207 to 217, 223 to 240, 242 to 252, 254 to 287, 302 to 318, 338 to 350 and 365 to 382 form .alpha.-helices. Amino acids 36 to 40, 64 to 68, 93 to 96, 116 to 120, 133 to 135, 294 to 297, 321 to 325, 328 to 332, 352 to 355 and 359 to 363 form .beta.-strands. All the other non-terminal amino acids, 34, 35, 41 to 43, 62, 63, 69 to 79, 90 to 92, 97 to 102, 112 to 115, 121 to 132, 141 to 147, 164 to 168, 184 to 188203 to 206, 218 to 222, 241, 253, 288 to 293, 298 to 301, 319, 320, 326, 327, 333 to 337, 351 to 358 and 364, form loops. Amino acids 1 to 18 and 383 to 425 are terminal amino acids. The crystal structure has only been resolved for the core domain of RecJ from Thermus thermophilus (residues 40-463). To ensure initiation of translation and in vivo expression of the RecJ core domain a methionine residue was added at its amino terminus, this is absent from the crystal structure information. The resolved structure shows two domains, an amino (2-253) and a carboxyl (288-463) region, connected by a long .alpha.-helix (254-287). The catalytic residues (D46, D98, H122, and D183) co-ordinate a single divalent metal ion for nucleophilic attack on the phosphodiester bond. D46 and H120 proposed to be the catalytic pair; however, mutation of any of these conserved residues in the E. coli RecJ was shown to abolish activity.

[0066] SEQ ID NO: 15 shows the codon optimized polynucleotide sequence derived from the bacteriophage lambda exo (redX) gene. It encodes the bacteriophage lambda exonuclease.

[0067] SEQ ID NO: 16 shows the amino acid sequence of the bacteriophage lambda exonuclease. The sequence is one of three identical subunits that assemble into a trimer. The enzyme performs highly processive digestion of nucleotides from one strand of dsDNA, in a 3'-5' direction. Enzyme initiation on a strand preferentially requires a 5' overhang of approximately 4 nucleotides with a 5' phosphate. Amino acids 3 to 10, 14 to 16, 22 to 26, 34 to 40, 52 to 67, 75 to 95, 135 to 149, 152 to 165 and 193 to 216 form .alpha.-helices. Amino acids 100 to 101, 106 to 107, 114 to 116, 120 to 122, 127 to 131, 169 to 175 and 184 to 190 form .beta.-strands. All the other non-terminal amino acids, 11 to 13, 17 to 21, 27 to 33, 41 to 51, 68 to 74, 96 to 99, 102 to 105, 108 to 113, 117 to 119, 123 to 126, 132 to 134, 150 to 151, 166 to 168, 176 to 183, 191 to 192, 217 to 222, form loops. Amino acids 1, 2 and 226 are terminal amino acids. Lambda exonuclease is a homo-trimer that forms a toroid with a tapered channel through the middle, apparently large enough for dsDNA to enter at one end and only ssDNA to exit at the other The catalytic residues are undetermined but a single divalent metal ion appears bound at each subunit by residues D119, E129 and L130.

[0068] SEQ ID NO: 17 shows the polynucleotide sequence encoding HL-wt-EcoExoIII-L1-H6 used in the Example.

[0069] SEQ ID NO: 18 shows the amino acid sequence of one subunit of HL-wt-EcoExoIII-L1-H6 used in the Example.

[0070] SEQ ID NO: 19 shows the polynucleotide sequence encoding HL-RQC-EcoExoIII-L1-H6 used in the Example.

[0071] SEQ ID NO: 20 shows the amino acid sequence of one subunit of HL-RQC-EcoExoIII-L1-H6 used in the Example.

[0072] SEQ ID NO: 21 shows the polynucleotide sequence encoding HL-RQC-EcoExoI-L1-H6 used in the Example.

[0073] SEQ ID NO: 22 shows the amino acid sequence of one subunit of HL-RQC-EcoExoI-L1-H6 used in the Example.

[0074] SEQ ID NO: 23 shows the polynucleotide sequence encoding HL-RQC-TthRecJ-L1-H6 used in the Example.

[0075] SEQ ID NO: 24 shows the amino acid sequence of one subunit of HL-RQC-TthRecJ-L1-H6 used in the Example.

[0076] SEQ ID NO: 25 shows the polynucleotide sequence encoding HL-RQC-EcoExoIII-L2-D45-N47.DELTA.-H6 used in the Example.

[0077] SEQ ID NO: 26 shows the amino acid sequence of one subunit of HL-RQC-EcoExoIII-L2-D45-N47.DELTA.-H6 used in the Example.

[0078] SEQ ID NO: 27 shows the polynucleotide sequence encoding HL-RQC-EcoExoI-Cter-{SG}8-H6 used in the Example.

[0079] SEQ ID NO: 28 shows the amino acid sequence of one subunit of HL-RQC-EcoExoI-Cter-{SG}8-H6 used in the Example.

[0080] SEQ ID NO: 29 shows the polynucleotide sequence encoding HL-RQC-EcoExoI-Cter-DG{SG}8-H6 used in the Example.

[0081] SEQ ID NO: 30 shows the amino acid sequence of one subunit of HL-RQC-EcoExoI-Cter-DG{SG}8-H6 used in the Example.

[0082] SEQ ID NOs: 31 and 32 show the oligonucleotide sequences used in the exonuclease assay of the Example.

DETAILED DESCRIPTION OF THE INVENTION

[0083] It is to be understood that different applications of the disclosed products and methods may be tailored to the specific needs in the art. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments of the invention only, and is not intended to be limiting.

[0084] In addition as used in this specification and the appended claims, the singular forms "a", "an", and "the" include plural referents unless the content clearly dictates otherwise. Thus, for example, reference to "a construct" includes "constructs", reference to "a transmembrane protein pore" includes two or more such pores, reference to "a molecular adaptor" includes two or more such adaptors, and the like.

[0085] All publications, patents and patent applications cited herein, whether supra or infra, are hereby incorporated by reference in their entirety.

Constructs

[0086] The present invention provides constructs that are useful for sequencing nucleic acids. The constructs comprise a transmembrane protein pore subunit and a nucleic acid handling enzyme. The subunit is covalently attached to the enzyme. The constructs of the invention are useful tools for forming pores that are capable of sequencing nucleic acids by stochastic sensing. The constructs of the invention are particularly useful for generating transmembrane protein pores that can both handle a target nucleic acid sequence and discriminate between the different nucleotides in the target sequence. As described in more detail below, the enzyme handles a target nucleic acid in such a way that the pore can identify nucleotides in the target sequence and thereby sequence the target sequence.

[0087] The subunit retains its ability to form a pore. The ability of a construct to form a pore can be assayed using any method known in the art. For instance, the construct may be inserted into a membrane along with other appropriate subunits and its ability to oligomerize to form a pore may be determined. Methods are known in the art for inserting constructs and subunits into membranes, such as lipid bilayers. For example, constructs and subunits may be suspended in a purified form in a solution containing a lipid bilayer such that it diffuses to the lipid bilayer and is inserted by binding to the lipid bilayer and assembling into a functional state. Alternatively, constructs and subunits may be directly inserted into the membrane using the "pick and place" method described in M. A. Holden, H. Bayley. J. Am. Chem. Soc. 2005, 127, 6502-6503 and International Application No. PCT/GB2006/001057 (published as WO 2006/100484). The ability of a construct to form a pore is typically assayed as described in the Examples.

[0088] The enzyme retains its ability to handle nucleic acids. This allows the construct to form a pore that may be used to sequence nucleic acids as described below. The ability of a construct to handle nucleic acids can be assayed using any method known in the art. For instance, construct or pores formed from the constructs can be tested for their ability to handle specific sequences of nucleic acids. The ability of a construct or a pore to handle nucleic acids is typically assayed as described in the Examples.

[0089] A construct of the invention may form part of a pore. Alternatively, a construct may be isolated, substantially isolated, purified or substantially purified. A construct is isolated or purified if it is completely free of any other components, such as lipids or other pore monomers. A construct is substantially isolated if it is mixed with carriers or diluents which will not interfere with its intended use. For instance, a construct is substantially isolated or substantially purified if it present in a form that comprises less than 10%, less than 5%, less than 2% or less than 1% of other components, such as lipids or other pore monomers. A construct of the invention may be present in a lipid bilayer.

Attachment

[0090] The subunit is covalently attached to the enzyme. The subunit may be attached to the enzyme at more than one, such as two or three, points. Attaching the subunit to the enzyme at more than one point can be used to constrain the mobility of the enzyme. For instance, multiple attachments may be used to constrain the freedom of the enzyme to rotate or its ability to move away from the subunit.

[0091] The subunit may be in a monomeric form when it is attached to the enzyme (post expression modification). Alternatively, the subunit may be part of an oligomeric pore when it is attached to an enzyme (post oligomerisation modification).

[0092] The subunit can be covalently attached to the enzyme using any method known in the art. The subunit and enzyme may be produced separately and then attached together. The two components may be attached in any configuration. For instance, they may be attached via their terminal (i.e. amino or carboxy terminal) amino acids. Suitable configurations include, but are not limited to, the amino terminus of the enzyme being attached to the carboxy terminus of the subunit and vice versa. Alternatively, the two components may be attached via amino acids within their sequences. For instance, the enzyme may be attached to one or more amino acids in a loop region of the subunit. In a preferred embodiment, terminal amino acids of the enzyme are attached to one or more amino acids in the loop region of a subunit. Terminal amino acids and loop regions are discussed above.

[0093] In one preferred embodiment, the subunit is genetically fused to the enzyme. A subunit is genetically fused to an enzyme if the whole construct is expressed from a single polynucleotide sequence. The coding sequences of the subunit and enzyme may be combined in any way to form a single polynucleotide sequence encoding the construct.

[0094] The subunit and enzyme may be genetically fused in any configuration. The subunit and enzyme may be fused via their terminal amino acids. For instance, the amino terminus of the enzyme may be fused to the carboxy terminus of the subunit and vice versa. The amino acid sequence of the enzyme is preferably added in frame into the amino acid sequence of the subunit. In other words, the enzyme is preferably inserted within the sequence of the subunit. In such embodiments, the subunit and enzyme are typically attached at two points, i.e. via the amino and carboxy terminal amino acids of the enzyme. If the enzyme is inserted within the sequence of the subunit, it is preferred that the amino and carboxy terminal amino acids of the enzyme are in close proximity and are each attached to adjacent amino acids in the sequence of the subunit or variant thereof. In a preferred embodiment, the enzyme is inserted into a loop region of the subunit.

[0095] In another preferred embodiment, the subunit is chemically fused to the enzyme. A subunit is chemically fused to an enzyme if the two parts are chemically attached, for instance via a linker molecule.

[0096] The subunit may be transiently attached to the enzyme by a hex-his tag or Ni-NTA. The subunit and enzyme may also be modified such that they transiently attach to each other.

[0097] The construct retains the pore forming ability of the subunit. The pore forming ability of the subunit is typically provided by its .alpha.-helices and .beta.-strands. .beta.-barrel pores comprise a barrel or channel that is formed from .beta.-strands, whereas .alpha.-helix bundle pores comprise a barrel or channel that is formed from .alpha.-helices. The .alpha.-helices and .beta.-strands are typically connected by loop regions. In order to avoid affecting the pore forming ability of the subunit, the enzyme is preferably genetically fused to a loop region of the subunit or inserted into a loop region of the subunit. The loop regions of specific subunits are discussed in more detail below.

[0098] Similarly, the construct retains the nucleic acid handling ability of the enzyme, which is also typically provided by its secondary structural elements (.alpha.-helices and .beta.-strands) and tertiary structural elements. In order to avoid affecting the nucleic acid handling ability of the enzyme, the enzyme is preferably genetically fused to the subunit or inserted into the subunit via residues or regions that does not affect its secondary or tertiary structure.

[0099] The subunit may be attached directly to the enzyme. The subunit is preferably attached to the enzyme using one or more, such as two or three, linkers. The one or more linkers may be designed to constrain the mobility of the enzyme. The linkers may be attached to one or more reactive cysteine residues, reactive lysine residues or non-natural amino acids in the subunit and/or enzyme. Suitable linkers are well-known in the art. Suitable linkers include, but are not limited to, chemical crosslinkers and peptide linkers. Preferred linkers are amino acid sequences (i.e. peptide linkers). The length, flexibility and hydrophilicity of the peptide linker are typically designed such that it does not to disturb the functions of the subunit and enzyme. Preferred flexible peptide linkers are stretches of 2 to 20, such as 4, 6, 8, 10 or 16, serine and/or glycine amino acids. More preferred flexible linkers include (SG).sub.1, (SG).sub.2, (SG).sub.3, (SG).sub.4, (SG).sub.5 and (SG).sub.8 wherein S is serine and G is glycine. Preferred rigid linkers are stretches of 2 to 30, such as 4, 6, 8, 16 or 24, proline amino acids. More preferred rigid linkers include (P).sub.12 wherein P is proline.

[0100] Linkers may be attached to the subunit first and then the enzyme, the enzyme first and then the subunit or the enzyme and subunit at the same time. When the linker is attached to the subunit, it may be a monomeric subunit, part of an oligomer of two or more monomers or part of complete oligomeric pore. It is preferred that the linker is reacted before any purification step to remove any unbound linker.

[0101] A preferred method of attaching the subunit to the enzyme is via cysteine linkage. This can be mediated by a bi-functional chemical linker or by a polypeptide linker with a terminal presented cysteine residue. .alpha.-HL (SEQ ID NO: 2) lacks native cysteine residues so the introduction of a cysteine into the sequence of SEQ ID NO: 2 enables the controlled covalent attachment of the enzyme to the subunit. Cysteines can be introduced at various positions, such as position K8, T9 or N17 of SEQ ID NO: 2 or at the carboxy terminus of SEQ ID NO: 2. The length, reactivity, specificity, rigidity and solubility of any bi-functional linker may designed to ensure that the enzyme is positioned correctly in relation to the subunit and the function of both the subunit and enzyme is retained. Suitable linkers include bismaleimide crosslinkers, such as 1,4-bis(maleimido)butane (BMB) or bis(maleimido)hexane. One draw back of bi-functional linkers is the requirement of the enzyme to contain no further surface accessible cysteine residues, as binding of the bi-functional linker to these cannot be controlled and may affect substrate binding or activity. If the enzyme does contain several accessible cysteine residues, modification of the enzyme may be required to remove them while ensuring the modifications do not affect the folding or activity of the enzyme. In a preferred embodiment, a reactive cysteine is presented on a peptide linker that is genetically attached to the enzyme. This means that additional modifications will not necessarily be needed to remove other accessible cysteine residues from the enzyme. The reactivity of cysteine residues may be enhanced by modification of the adjacent residues, for example on a peptide linker. For instance, the basic groups of flanking arginine, histidine or lysine residues will change the pKa of the cysteines thiol group to that of the more reactive S.sup.- group. The reactivity of cysteine residues may be protected by thiol protective groups such as dTNB. These may be reacted with one or more cysteine residues of the enzyme or subunit, either as a monomer or part of an oligomer, before a linker is attached.

[0102] Cross-linkage of subunits or enzymes to themselves may be prevented by keeping the concentration of linker in a vast excess of the subunit and/or enzyme. Alternatively, a "lock and key" arrangement may be used in which two linkers are used. Only one end of each linker may react together to form a longer linker and the other ends of the linker each react with a different part of the construct (i.e. subunit or monomer).

[0103] The site of covalent attachment is selected such that, when the construct is used to form a pore, the enzyme handles a target nucleic acid sequence in such a way that a proportion of the nucleotides in the target sequence interacts with the pore. Nucleotides are then distinguished on the basis of the different ways in which they affect the current flowing through the pore during the interaction.

[0104] There are a number of ways that pores can be used to sequence nucleic acid molecules. One way involves the use of an exonuclease enzyme, such as a deoxyribonuclease. In this approach, the exonuclease enzyme is used to sequentially detach the nucleotides from a target nucleic strand. The nucleotides are then detected and discriminated by the pore in order of their release, thus reading the sequence of the original strand. For such an embodiment, the exonuclease enzyme is preferably attached to the subunit such that a proportion of the nucleotides released from the target nucleic acid is capable of entering and interacting with the barrel or channel of a pore comprising the construct. The exonuclease is preferably attached to the subunit at a site in close proximity to the part of the subunit that forms the opening of the barrel of channel of the pore. The exonuclease enzyme is more preferably attached to the subunit such that its nucleotide exit trajectory site is orientated towards the part of the subunit that forms part of the opening of the pore.

[0105] Another way of sequencing nucleic acids involves the use of an enzyme that pushes or pulls the target nucleic acid strand through the pore. In this approach, the ionic current fluctuates as a nucleotide in the target strand passes through the pore. The fluctuations in the current are indicative of the sequence of the strand. For such an embodiment, the enzyme is preferably attached to the subunit such that it is capable of pushing or pulling the target nucleic acid through the barrel or channel of a pore comprising the construct and does not interfere with the flow of ionic current through the pore. The enzyme is preferably attached to the subunit at a site in close proximity to the part of the subunit that forms part of the opening of the barrel of channel of the pore. The enzyme is more preferably attached to the subunit such that its active site is orientated towards the part of the subunit that forms part of the opening of the pore.

[0106] A third way of sequencing a nucleic acid strand is to detect the bi-products of a polymerase in close proximity to a pore detector. In this approach, nucleoside phosphates (nucleotides) are labelled so that a phosphate labelled species is released upon the addition of a polymerase to the nucleotide strand and the phosphate labelled species is detected by the pore. The phosphate species contains a specific label for each nucleotide. As nucleotides are sequentially added to the nucleic acid strand, the bi-products of the base addition are detected. The order that the phosphate labelled species are detected can be used to determine the sequence of the nucleic acid strand.

[0107] The enzyme is preferably attached to a part of the subunit that forms part of the cis side of a pore comprising the construct. In electrophysiology, the cis side is the grounded side. If a hemolysin pore is inserted correctly into an elcetrophysiology apparatus, the Cap region is on the cis side. It is well known that, under a positive potential, nucleotides will migrate from the cis to the trans side of pores used for stochastic sensing. Positioning the enzyme at the cis side of a pore allows it to handle the target nucleic acid such that a proportion of the nucleotides in the sequence enters the barrel or channel of the pore and interacts with it. Preferably, at least 20%, at least 40%, at least 50%, at least 80% or at least 90% of the nucleotides in the sequence enters the barrel or channel of the pore and interacts with it.

[0108] The site and method of covalent attachment is preferably selected such that mobility of the enzyme is constrained. This helps to ensure that the enzyme handles the target nucleic acid sequence in such a way that a proportion of the nucleotides in the target sequence interacts with the pore. For instance, constraining the ability of enzyme to move means that its active site can be permanently orientated towards the part of the subunit that forms part of the opening of the barrel of channel of the pore. The mobility of the enzyme may be constrained by increasing the number of points at which the enzyme is attached to the subunit and/or the use of specific linkers.

Subunit

[0109] The constructs of the invention comprise a subunit from a transmembrane protein pore. A transmembrane protein pore is a polypeptide or a collection of polypeptides that permits ions driven by an applied potential to flow from one side of a membrane. The pore preferably permits nucleotides to flow from one side of a membrane to the other along the applied potential. The pore preferably allows a nucleic acid, such as DNA or RNA, to be pushed or pulled through the pore.

[0110] The subunit is part of a pore. The pore may be a monomer or an oligomer. The subunit preferably forms part of a pore made up of several repeating subunits, such as 6, 7 or 8 subunits. The subunit more preferably forms part of a heptameric pore. The subunit typically forms part of a barrel or channel through which the ions may flow. The subunits of the pore typically surround a central axis and contribute strands to a transmembrane 13 barrel or channel or a transmembrane .alpha.-helix bundle or channel. When part of a construct of the invention, the subunit may be a monomer or part of an oligomeric pore.

[0111] The subunit typically forms part of a pore whose barrel or channel comprises amino acids that facilitate interaction with nucleotides or nucleic acids. These amino acids are preferably located near the constriction of the barrel or channel. The subunit typically comprises one or more positively charged amino acids, such as arginine, lysine or histidine. These amino acids typically facilitate the interaction between the pore and nucleotides or nucleic acids by interacting with the phosphate groups in the nucleotides or nucleic acids or by .pi.-cation interaction with the bases in the nucleotides or nucleic acids. The nucleotide detection can be facilitated with an adaptor.

[0112] Subunits for use in accordance with the invention can be derived from .beta.-barrel pores or .alpha.-helix bundle pores. .beta.-barrel pores comprise a barrel or channel that is formed from .beta.-strands. Suitable .beta.-barrel pores include, but are not limited to, .beta.-toxins, such as .alpha.-hemolysin and leukocidins, and outer membrane proteins/porins of bacteria, such as outer membrane porin F (OmpF), outer membrane porin G (OmpG), outer membrane phospholipase A and Neisseria autotransporter lipoprotein (NalP). .alpha.-helix bundle pores comprise a barrel or channel that is formed from .alpha.-helices. Suitable .alpha.-helix bundle pores include, but are not limited to, inner membrane proteins and a outer membrane proteins, such as WZA.

[0113] The subunit is preferably derived from .alpha.-hemolysin (.alpha.-HL). The wild-type .alpha.-HL pore is formed of seven identical monomers or subunits (i.e. it is heptameric). The sequence of one wild-type monomer or subunit of .alpha.-hemolysin is shown in SEQ ID NO: 2. The subunit in the constructs of the invention preferably comprises the sequence shown in SEQ ID NO: 2 or a variant thereof. Amino acids 1, 7 to 21, 31 to 34, 45 to 51, 63 to 66, 72, 92 to 97, 104 to 111, 124 to 136, 149 to 153, 160 to 164, 173 to 206, 210 to 213, 217, 218, 223 to 228, 236 to 242, 262 to 265, 272 to 274, 287 to 290 and 294 of SEQ ID NO: 2 form loop regions. The enzyme is preferably attached to one or more of amino acids 8, 9, 17, 18, 19, 44, 45, 50 and 51 of SEQ ID NO: 2. The enzyme is more preferably inserted between amino acids, 18 and 19, 44 and 45 or 50 and 51 of SEQ ID NO: 2.

[0114] A variant of SEQ ID NO: 2 is a subunit that has an amino acid sequence which varies from that of SEQ ID NO: 2 and which retains its pore forming ability. The ability of the variant to form pores can be assayed as described above. The variant may include modifications that facilitate covalent attachment to or interaction with the nucleic acid handling enzyme. The variant preferably comprises one or more reactive cysteine residues that facilitate attachment to the enzyme. For instance, the variant may include a cysteine at one or more of positions 8, 9, 17, 18, 19, 44, 45, 50 and 51 and/or on the amino or carboxy terminus of SEQ ID NO: 2. Preferred variants comprise a substitution of the residue at position 8, 9 or 17 of SEQ ID NO: 2 with cysteine (K8C, T9C or N17C).

[0115] The variant may be modified to facilitate genetic fusion of the enzyme. For instance, one or more residues adjacent to the insertion site may be modified, such as deleted, to facilitate insertion of the enzyme and/or linkers. If the enzyme is inserted into loop 2 of SEQ ID NO: 2, one or more of residues D45, K46, N47, H48, N49 and K50 of SEQ ID NO: 2 may be deleted. A preferred construct containing such a deletion comprises the sequence shown in SEQ ID NO: 26 or a variant thereof.

[0116] The variant may also include modifications that facilitate any interaction with nucleotides or facilitate orientation of a molecular adaptor as discussed below. The variant may also contain modifications that facilitate covalent attachment of a molecular adaptor.

[0117] The subunit may be any of the variants of SEQ ID NO: 2 described in a co-pending International application claiming priority from U.S. Application No. 61/078,687 and being filed simultaneously with this application [J A Kemp & Co Ref: N.104403A; Oxford Nanolabs Ref: ONL IP 004]. All the teachings of that application may be applied equally to the present invention. In particular, the variant preferably has a glutamine at position 139 of SEQ ID NO: 2. The variant preferably has an arginine at position 113 of SEQ ID NO: 2. The variant preferably has a cysteine at position 119, 121 or 135 of SEQ ID NO: 2. Any of the variants of SEQ ID NO: 2 shown in SEQ ID NOs: 4, 6, 8, 10, 12 and 14 of the co-pending application may be used to form a construct of the invention.

[0118] The subunit may be a naturally occurring variant which is expressed by an organism, for instance by a Staphylococcus bacterium. Variants also include non-naturally occurring variants produced by recombinant technology. Over the entire length of the amino acid sequence of SEQ ID NO: 2, a variant will preferably be at least 50% homologous to that sequence based on amino acid identity. More preferably, the subunit polypeptide may be at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90% and more preferably at least 95%, 97% or 99% homologous based on amino acid identity to the amino acid sequence of SEQ ID NO: 2 over the entire sequence. There may be at least 80%, for example at least 85%, 90% or 95%, amino acid identity over a stretch of 200 or more, for example 230, 250, 270 or 280 or more, contiguous amino acids ("hard homology").

[0119] Amino acid substitutions may be made to the amino acid sequence of SEQ ID NO: 2 in addition to those discussed above, for example up to 1, 2, 3, 4, 5, 10, 20 or 30 substitutions. Conservative substitutions may be made, for example, according to Table 1 below.

TABLE-US-00001 TABLE 1 Conservative substitutions Amino acids in the same block in the second column and preferably in the same line in the third column may be substituted for each other. NON-AROMATIC Non-polar G A P I L V Polar - uncharged C S T M N Q Polar - charged D E H K R AROMATIC H F W Y

[0120] One or more amino acid residues of the amino acid sequence of SEQ ID NO: 2 may additionally be deleted from the polypeptides described above. Up to 1, 2, 3, 4, 5, 10, 20 or 30 residues may be deleted, or more.

[0121] Variants may fragments of SEQ ID NO: 2. Such fragments retain pore forming activity. Fragments may be at least 50, 100, 200 or 250 amino acids in length. A fragment preferably comprises the pore forming domain of SEQ ID NO: 2. Fragments typically include residues 119, 121, 135. 113 and 139 of SEQ ID NO: 2.

[0122] One or more amino acids may be alternatively or additionally added to the polypeptides described above. An extension may be provided at the amino terminus or carboxy terminus of the amino acid sequence of SEQ ID NO: 2 or a variant or fragment thereof. The extension may be quite short, for example from 1 to 10 amino acids in length. Alternatively, the extension may be longer, for example up to 50 or 100 amino acids. A carrier protein may be fused to a subunit or variant.

[0123] As discussed above, a variant of SEQ ID NO: 2 is a subunit that has an amino acid sequence which varies from that of SEQ ID NO: 2 and which retains its ability to form a pore. A variant typically contains the regions of SEQ ID NO: 2 that are responsible for pore formation. The pore forming ability of o-HL, which contains a .beta.-barrel, is provided by .beta.-strands in each subunit. A variant of SEQ ID NO: 2 typically comprises the regions in SEQ ID NO: 2 that form .beta.-strands. The amino acids of SEQ ID NO: 2 that form .beta.-strands are discussed above. One or more modifications can be made to the regions of SEQ ID NO: 2 that form .beta.-strands as long as the resulting variant retains its ability to form a pore. Specific modifications that can be made to the .beta.-strand regions of SEQ ID NO: 2 are discussed above.

[0124] A variant of SEQ ID NO: 2 preferably includes one or more modifications, such as substitutions, additions or deletions, within its .alpha.-helices and/or loop regions. Amino acids that form .alpha.-helices and loops are discussed above.

[0125] Standard methods in the art may be used to determine homology. For example the UWGCG Package provides the BESTFIT program which can be used to calculate homology, for example used on its default settings (Devereux et al (1984) Nucleic Acids Research 12, p387-395). The PILEUP and BLAST algorithms can be used to calculate homology or line up sequences (such as identifying equivalent residues or corresponding sequences (typically on their default settings)), for example as described in Altschul S. F. (1993) J Mol Evol 36:290-300; Altschul, S. F et al (1990) J Mol Biol 215:403-10.

[0126] Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/). This algorithm involves first identifying high scoring sequence pair (HSPs) by identifying short words of length W in the query sequence that either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighbourhood word score threshold (Altschul et al, supra). These initial neighbourhood word hits act as seeds for initiating searches to find HSP's containing them. The word hits are extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Extensions for the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T and X determine the sensitivity and speed of the alignment. The BLAST program uses as defaults a word length (W) of 11, the BLOSUM62 scoring matrix (see Henikoff and Henikoff (1992) Proc. Natl. Acad. Sci. USA 89: 10915-10919) alignments (B) of 50, expectation (E) of 10, M=5, N=4, and a comparison of both strands.

[0127] The BLAST algorithm performs a statistical analysis of the similarity between two sequences; see e.g., Karlin and Altschul (1993) Proc. Natl. Acad. Sci. USA 90: 5873-5787. One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two amino acid sequences would occur by chance. For example, a sequence is considered similar to another sequence if the smallest sum probability in comparison of the first sequence to the second sequence is less than about 1, preferably less than about 0.1, more preferably less than about 0.01, and most preferably less than about 0.001.

[0128] The variant may be modified for example by the addition of histidine or aspartic acid residues to assist its identification or purification or by the addition of a signal sequence to promote their secretion from a cell where the polypeptide does not naturally contain such a sequence.

[0129] The subunit may be labelled with a revealing label. The revealing label may be any suitable label which allows the pore to be detected. Suitable labels include, but are not limited to, fluorescent molecules, radioisotopes, e.g. .sup.125I, .sup.35S, enzymes, antibodies, antigens, polynucleotides and ligands such as biotin.

[0130] The subunit may be isolated from a pore producing organism, such as Staphylococcus aureus, or made synthetically or by recombinant means. For example, the subunit may be synthesized by in vitro translation and transcription. The amino acid sequence of the subunit may be modified to include non-naturally occurring amino acids or to increase the stability of the subunit. When the subunit is produced by synthetic means, such amino acids may be introduced during production. The subunit may also be altered following either synthetic or recombinant production.

[0131] The subunit may also be produced using D-amino acids. For instance, the pores may comprise a mixture of L-amino acids and D-amino acids. This is conventional in the art for producing such proteins or peptides.

[0132] The subunit may also contain other non-specific chemical modifications as long as they do not interfere with its ability to form a pore. A number of non-specific side chain modifications are known in the art and may be made to the side chains of the pores. Such modifications include, for example, reductive alkylation of amino acids by reaction with an aldehyde followed by reduction with NaBH.sub.4, amidination with methylacetimidate or acylation with acetic anhydride. The modifications to the subunit can be made after expression of the subunit or construct or after the subunit has been used to form a pore.

[0133] The subunit can be produced using standard methods known in the art. Polynucleotide sequences encoding a subunit may be isolated and replicated using standard methods in the art. Such sequences are discussed in more detail below. Polynucleotide sequences encoding a subunit may be expressed in a bacterial host cell using standard techniques in the art. The subunit may be produced in a cell by in situ expression of the polypeptide from a recombinant expression vector. The expression vector optionally carries an inducible promoter to control the expression of the polypeptide.

[0134] A subunit may be produced in large scale following purification by any protein liquid chromatography system from pore producing organisms or after recombinant expression as described below. Typical protein liquid chromatography systems include FPLC, AKTA systems, the Bio-Cad system, the Bio-Rad BioLogic system and the Gilson HPLC system.

Nucleic Acid Handling Enzyme

[0135] The constructs of the invention comprise a nucleic acid handling enzyme. A nucleic acid handling enzyme is a polypeptide that is capable of interacting with and modifying at least one property of a nucleic acid. The enzyme may modify the nucleic acid by cleaving it to form individual nucleotides or shorter chains of nucleotides, such as di- or trinucleotides. The enzyme may modify the nucleic acid by orienting it or moving it to a specific position.

[0136] A nucleic acid is a macromolecule comprising two or more nucleotides. The nucleic acid handled by the enzyme may comprise any combination of any nucleotides. The nucleotides can be naturally occurring or artificial. A nucleotide typically contains a nucleobase, a sugar and at least one phosphate group. The nucleobase is typically heterocyclic. Nucleobases include, but are not limited to, purines and pyrimidines and more specifically adenine, guanine, thymine, uracil and cytosine. The sugar is typically a pentose sugar. Nucleotide sugars include, but are not limited to, ribose and deoxyribose. The nucleotide is typically a ribonucleotide or deoxyribonucleotide. The nucleotide typically contains a monophosphate, diphosphate or triphosphate. Phosphates may be attached on the 5' or 3' side of a nucleotide.

[0137] Nucleotides include, but are not limited to, adenosine monophosphate (AMP), adenosine diphosphate (ADP), adenosine triphosphate (ATP), guanosine monophosphate (GMP), guanosine diphosphate (GDP), guanosine triphosphate (GTP), thymidine monophosphate (TMP), thymidine diphosphate (TDP), thymidine triphosphate (TTP), uridine monophosphate (UMP), uridine diphosphate (UDP), uridine triphosphate (UTP), cytidine monophosphate (CMP), cytidine diphosphate (CDP), cytidine triphosphate (CTP), cyclic adenosine monophosphate (cAMP), cyclic guanosine monophosphate (cGMP), deoxyadenosine monophosphate (dAMP), deoxyadenosine diphosphate (dADP), deoxyadenosine triphosphate (dATP), deoxyguanosine monophosphate (dGMP), deoxyguanosine diphosphate (dGDP), deoxyguanosine triphosphate (dGTP), deoxythymidine monophosphate (dTMP), deoxythymidine diphosphate (dTDP), deoxythymidine triphosphate (dTTP), deoxyuridine monophosphate (dUMP), deoxyuridine diphosphate (dUDP), deoxyuridine triphosphate (dUTP), deoxycytidine monophosphate (dCMP), deoxycytidine diphosphate (dCDP) and deoxycytidine triphosphate (dCTP). The nucleotides are preferably selected from AMP, TMP, GMP, UMP, dAMP, dTMP, dGMP or dCMP.

[0138] The nucleic acid handled by the enzyme is preferably double stranded, such as DNA. The nucleic acid handled by the enzyme may be single stranded, such as cDNA or RNA. Enzymes that handle single stranded nucleic acids may be used to sequence double stranded DNA as long as the double stranded DNA is chemically or thermally dissociated into a single strand before it is handled by the enzyme.

[0139] It is preferred that the tertiary structure of the nucleic acid handling enzyme is known. Knowledge of the three dimensional structure of the enzyme allows modifications to be made to the enzyme to facilitate its function in the construct or pore of the invention.

[0140] The enzyme may be any size and have any structure. For instance, the enzyme may be an oligomer, such as a dimer or trimer. The enzyme is preferably a small, gloubular polypeptide formed from one monomer. Such enzymes are easy to handle and are less likely to interfere with the pore forming ability of the subunit, particularly if fused to or inserted into the sequence of the subunit.

[0141] The amino and carboxy terminii of the enzyme are preferably in close proximity. The amino and carboxy terminii of the enzyme are more preferably presented on same face of the enzyme. Such embodiments facilitate insertion of the enzyme into the sequence of the subunit. For instance, if the amino and carboxy terminii of the enzyme are in close proximity, each can be attached by genetic fusion to adjacent amino acids in the sequence of the subunit.

[0142] It is also preferred that the location and function of the active site of the enzyme is known. This prevents modifications being made to the active site that abolish the activity of the enzyme. It also allows the enzyme to be attached to the subunit so that the enzyme handles the target nucleic acid sequence in such a way that a proportion of the nucleotides in the target sequence interacts with the pore. It is beneficial to position the active site of the enzyme as close as possible to the part of the subunit that forms part of the opening of the barrel of channel of the pore, without the enzyme itself presenting a block to the flow of current. Knowledge of the way in which an enzyme may orient nucleic acids also allows an effective construct to be designed.

[0143] As discussed in more detail below, it may be necessary to purify the construct of the invention. It is preferred that the enzyme is capable of withstanding the conditions used to purify the construct.

[0144] The constructs of the invention are useful for forming pores. Such pores may be used to sequence nucleic acids. In order that most of the nucleotides in the target nucleic acid are correctly identified by stochastic sensing, the enzyme must handle the nucleic acid in a buffer background which is compatible with discrimination of the nucleotides. The enzyme preferably has at least residual activity in a salt concentration well above the normal physiological level, such as from 100 mM to 500 mM. The enzyme is more preferably modified to increase its activity at high salt concentrations. The enzyme may also be modified to improve its processivity, stability and shelf life.

[0145] Suitable modifications can be determined from the characterisation of nucleic acid handling enzymes from extremophiles such as halophilic, moderately halophilic bacteria, thermophilic and moderately thermophilic organisms, as well as directed evolution approaches to altering the salt tolerance, stability and temperature dependence of mesophilic or thermophilic exonucleases.

[0146] The enzyme also preferably retains at least partial activity at room temperature. This allows pores formed from the construct to sequence nucleic acids at room temperature.

[0147] The nucleic acid handling enzyme is preferably a nucleolytic enzyme. The nucleic acid handling enzyme is more preferably member of any of the Enzyme Classification (EC) groups 3.1.11, 3.1.13, 3.1.14, 3.1.15, 3.1.16, 3.1.21, 3.1.22, 3.1.25, 3.1.26, 3.1.27, 3.1.30 and 3.1.31. The nucleic acid handling enzyme is more preferably any one of the following enzymes: [0148] 3. 1.11.-Exodeoxyribonucleases producing 5'-phosphomonoesters. [0149] 3.1.11.1 Exodeoxyribonuclease I. [0150] 3.1.11.2 Exodeoxyribonuclease III. [0151] 3.1.11.3 Exodeoxyribonuclease (lambda-induced). [0152] 3.1.11.4 Exodeoxyribonuclease (phage SP3-induced). [0153] 3.1.11.5 Exodeoxyribonuclease V. [0154] 3.1.11.6 Exodeoxyribonuclease VII. [0155] 3. 1.13.-Exoribonucleases producing 5'-phosphomonoesters. [0156] 3.1.13.1 Exoribonuclease II. [0157] 3.1.13.2 Exoribonuclease H. [0158] 3.1.13.3 Oligonucleotidase. [0159] 3.1.13.4 Poly(A)-specific ribonuclease. [0160] 3.1.13.5 Ribonuclease D. [0161] 3. 1.14.-Exoribonucleases producing 3'-phosphomonoesters. [0162] 3.1.14.1 Yeast ribonuclease. [0163] 3. 1.15.-Exonucleases active with either ribo- or deoxyribonucleic acid producing 5' phosphomonoesters [0164] 3.1.15.1 Venom exonuclease. [0165] 3. 1.16.-Exonucleases active with either ribo- or deoxyribonucleic acid producing 3' phosphomonoesters [0166] 3.1.16.1 Spleen exonuclease. [0167] 3. 1.21.-Endodeoxyribonucleases producing 5'-phosphomonoesters. [0168] 3.1.21.1 Deoxyribonuclease I. [0169] 3.1.21.2 Deoxyribonuclease IV (phage-T(4)-induced). [0170] 3.1.21.3 Type I site-specific deoxyribonuclease. [0171] 3.1.21.4 Type II site-specific deoxyribonuclease. [0172] 3.1.21.5 Type III site-specific deoxyribonuclease. [0173] 3.1.21.6 CC-preferring endodeoxyribonuclease. [0174] 3.1.21.7 Deoxyribonuclease V. [0175] 3. 1.22.-Endodeoxyribonucleases producing other than 5'-phosphomonoesters. [0176] 3.1.22.1 Deoxyribonuclease II. [0177] 3.1.22.2 Aspergillus deoxyribonuclease K(1). [0178] 3.1.22.3 Transferred entry: 3.1.21.7. [0179] 3.1.22.4 Crossover junction endodeoxyribonuclease. [0180] 3.1.22.5 Deoxyribonuclease X. [0181] 3. 1.25.-Site-specific endodeoxyribonucleases specific for altered bases. [0182] 3.1.25.1 Deoxyribonuclease (pyrimidine dimer). [0183] 3.1.25.2 Transferred entry: 4.2.99.18. [0184] 3. 1.26.-Endoribonucleases producing 5'-phosphomonoesters. [0185] 3.1.26.1 Physarum polycephalum ribonuclease. [0186] 3.1.26.2 Ribonuclease alpha. [0187] 3.1.26.3 Ribonuclease III. [0188] 3.1.26.4 Ribonuclease H. [0189] 3.1.26.5 Ribonuclease P. [0190] 3.1.26.6 Ribonuclease IV. [0191] 3.1.26.7 Ribonuclease P4. [0192] 3.1.26.8 Ribonuclease M5. [0193] 3.1.26.9 Ribonuclease (poly-(U)-specific). [0194] 3.1.26.10 Ribonuclease IX. [0195] 3.1.26.11 Ribonuclease Z. [0196] 3. 1.27.-Endoribonucleases producing other than 5'-phosphomonoesters. [0197] 3.1.27.1 Ribonuclease T(2). [0198] 3.1.27.2 Bacillus subtilis ribonuclease. [0199] 3.1.27.3 Ribonuclease T(1). [0200] 3.1.27.4 Ribonuclease U(2). [0201] 3.1.27.5 Pancreatic ribonuclease. [0202] 3.1.27.6 Enterobacter ribonuclease. [0203] 3.1.27.7 Ribonuclease F. [0204] 3.1.27.8 Ribonuclease V. [0205] 3.1.27.9 tRNA-intron endonuclease. [0206] 3.1.27.10 rRNA endonuclease. [0207] 3. 1.30.-Endoribonucleases active with either ribo- or deoxyribonucleic producing 5' phosphomonoesters [0208] 3.1.30.1 Aspergillus nuclease S(1). [0209] 3.1.30.2 Serratia marcescens nuclease. [0210] 3. 1.31.-Endoribonucleases active with either ribo- or deoxyribonucleic producing 3' phosphomonoesters [0211] 3.1.31.1 Micrococcal nuclease.

[0212] The enzyme is most preferably an exonuclease, such as a deoxyribonuclease, which cleave nucleic acids to form individual nucleotides. The advantages of exodeoxyribonucleases are that they are active on both single stranded and double stranded DNA and hydrolyse bases either in either the 5'-3' or 3'-5' direction.

[0213] An individual nucleotide is a single nucleotide. An individual nucleotide is one which is not bound to another nucleotide or nucleic acid by a nucleotide bond. A nucleotide bond involves one of the phosphate groups of a nucleotide being bound to the sugar group of another nucleotide. An individual nucleotide is typically one which is not bound by a nucleotide bond to another nucleic acid sequence of at least 5, at least 10, at least 20, at least 50, at least 100, at least 200, at least 500, at least 1000 or at least 5000 nucleotides.

[0214] Preferred enzymes for use in the method include exonuclease III enzyme from E. coli (SEQ ID NO: 10), exonuclease I from E. coli (SEQ ID NO: 12), RecJ from T. thermophilus (SEQ ID NO: 14) and bacteriophage lambda exonuclease (SEQ ID NO: 16) and variants thereof. The exonuclease enzyme preferably comprises any of the sequences shown in SEQ ID NOs: 10, 12, 14 and 16 or a variant thereof. Three identical subunits of SEQ ID NO: 16 interact to form a trimer exonuclease. A variant of SEQ ID NO: 10, 12, 14 or 16 is an enzyme that has an amino acid sequence which varies from that of SEQ ID NO: 10, 12, 14 or 16 and which retains nucleic acid handling ability. The enzyme may include modifications that facilitate handling of the nucleic acid and/or facilitate its activity at high salt concentrations and/or room temperature. The enzyme may include modifications that facilitate covalent attachment to or its interaction with the subunit. As discussed above, accessible cysteines may be removed from the enzyme to avoid non-specific reactions with a linker. Alternatively, one or more reactive cysteines may be introduced into the enyme, for instance as part of a genetically-fused peptide linker, to facilitate attachment to the subunit.

[0215] Variants may differ from SEQ ID NO: 10, 12, 14 and 16 to the same extent as variants of SEQ ID NO: 2 differ from SEQ ID NO: 2 as discussed above.

[0216] A variant of SEQ ID NO: 10, 12, 14 or 16 retains its nucleic acid handling activity. A variant typically contains the regions of SEQ ID NO: 10, 12, 14 or 16 that are responsible for nucleic acid handling activity. The catalytic domains of SEQ ID NOs: 10, 12, 14 and 16 are discussed above. A variant of SEQ ID NO: 10, 12, 14 or 16 preferably comprises the relavant catalytic domain. A variant SEQ ID NO: 10, 12, 14 or 16 typically includes one or more modifications, such as substitutions, additions or deletions, outside the relevant catalytic domain.

[0217] Preferred enzymes that are capable of pushing or pulling the target nucleic acid sequence through the pore include polymerases, exonucleases, helicases and topoisomerases, such as gyrases. The polymerase is preferably a member of any of the Enzyme Classification (EC) groups 2.7.7.6, 2.7.7.7, 2.7.7.19, 2.7.7.48 and 2.7.7.49. The polymerase is preferably a DNA-dependent DNA polymerase, an RNA-dependent DNA polymerase, a DNA-dependent RNA polymerase or an RNA-dependent RNA polymerase. The helicase is preferably a member of any of the Enzyme Classification (EC) groups 3.6.1.- and 2.7.7.-. The helicase is preferably an ATP-dependent DNA helicase (EC group 3.6.1.8), an ATP-dependent RNA helicase (EC group 3.6.1.8) or an ATP-independent RNA helicase. The topoisomerase is preferably a member of any of the Enzyme Classification (EC) groups 5.99.1.2 and 5.99.1.3.

[0218] The enzyme may be labelled with a revealing label. The revealing label may be any of those described above.

[0219] The enzyme may be isolated from an enzyme-producing organism, such as E. coli, T. thermophilus or bacteriophage, or made synthetically or by recombinant means. For example, the enzyme may be synthesized by in vitro translation and transcription as described above and below. The enzyme may be produced in large scale following purification as described above.

Preferred Constructs

[0220] Preferred constructs of the invention comprise the sequence shown in any one of SEQ ID NOs: 18, 20, 22, 24, 26, 28 and 30 or a variant thereof. Variants of SEQ ID NO: 18, 20, 22, 24, 26, 28 or 30 must retain their pore forming ability and nucleic acid handling ability. Variants may differ from SEQ ID NOs: 18, 20, 22, 24, 26, 28 and 30 to the same extent and in the same way as discussed above for variants of SEQ ID NO: 2 and variants of SEQ ID NO: 10, 12, 14 or 16.

Polynucleotide Sequences

[0221] The present invention also provides polynucleotide sequences which encode a construct in which the enzyme is genetically fused to the subunit or is inserted into the sequence of the subunit. It is straightforward to generate such polynucleotide sequences using standard techniques. A polynucleotide sequence encoding the enzyme is either fused to or inserted into a polynucleotide sequence encoding the subunit. The fusion or insertion is typically in frame. If a polynucleotide sequence encoding the enzyme is inserted into a polynucleotide sequence encoding the subunit, the sequence encoding the enzyme is typically flanked at both ends by restriction endonuclease sites, such as those recognized by BspE1. It may also be flanked at both ends by polynucleotide sequences encoding linkers, such as 5 to 10 codons each encoding serine or glycine.

[0222] The polynucleotide sequence preferably encodes a construct comprising SEQ ID NO: 10, 12, 14 or 16 or a variant thereof genetically fused to or inserted into SEQ ID NO: 2 or a variant thereof. The variants of SEQ ID NO: 2, 10, 12, 14 or 16 may be any of those discussed above. SEQ ID NO: 10, 12, 14 or 16 or a variant thereof may be genetically fused to or inserted into SEQ ID NO: 2 or a variant thereof as described above.

[0223] The polynucleotide sequence preferably comprises SEQ ID NO: 9, 11, 13 or 15 or a variant thereof genetically fused to or inserted into SEQ ID NO: 1 or a variant thereof. SEQ ID NO: 9, 11, 13 or 15 or a variant thereof is preferably inserted into SEQ ID NO: 1 or a variant thereof between nucleotides 2765 and 2766, 2843 and 2844 or 2861 and 2862 of SEQ ID NO: 1. The polynucleotide sequence more preferably comprises the sequence shown in SEQ ID NO: 17, 19, 21, 23, 25, 27 or 29 or a variant thereof.

[0224] Variants of SEQ ID NOs: 1, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27 or 29 are sequences that are at least 50%, 60%, 70%, 80%, 90% or 95% homologous based on nucleotide identity to sequence of SEQ ID NO: 1, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27 or 29 over the entire sequence. There may be at least 80%, for example at least 85%, 90% or 95% nucleotide identity over a stretch of 600 or more, for example 700, 750, 850 or 900 or more, contiguous nucleotides ("hard homogly"). Homology may be calculated as described above. The polynucleotide sequence may comprise a sequence that differs from SEQ ID NO: 1, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27 or 29 on the basis of the degeneracy of the genetic code.

[0225] Polynucleotide sequences may be isolated and replicated using standard methods in the art. Chromosomal DNA may be extracted from a pore producing organism, such as Staphylococcus aureus, and/or an enzyme producing organism, such as E. coli, T. thermophilus or bacteriophage. The gene encoding the subunit and enzyme may be amplified using PCR involving specific primers. The amplified sequences may then be incorporated into a recombinant replicable vector such as a cloning vector. The vector may be used to replicate the polynucleotide in a compatible host cell. Thus polynucleotide sequences encoding a subunit and/or enzyme may be made by introducing a polynucleotide encoding a subunit and/or enzyme into a replicable vector, introducing the vector into a compatible host cell, and growing the host cell under conditions which bring about replication of the vector. The vector may be recovered from the host cell. Suitable host cells for cloning of polynucleotides are known in the art and described in more detail below.

[0226] The polynucleotide sequence may be cloned into suitable expression vector. In an expression vector, the polynucleotide sequence encoding a construct is typically operably linked to a control sequence which is capable of providing for the expression of the coding sequence by the host cell. Such expression vectors can be used to express a construct.

[0227] The term "operably linked" refers to a juxtaposition wherein the components described are in a relationship permitting them to function in their intended manner. A control sequence "operably linked" to a coding sequence is ligated in such a way that expression of the coding sequence is achieved under conditions compatible with the control sequences. Multiple copies of the same or different polynucleotide may be introduced into the vector.

[0228] The expression vector may then be introduced into a suitable host cell. Thus, a construct can be produced by inserting a polynucleotide sequence encoding a construct into an expression vector, introducing the vector into a compatible bacterial host cell, and growing the host cell under conditions which bring about expression of the polynucleotide sequence. The recombinantly-expressed construct may self-assemble into a pore in the host cell membrane. Alternatively, the recombinant construct produced in this manner may be isolated from the host cell and inserted into another membrane. When producing an oligomeric pore comprising a construct of the invention and at least one different subunit, the construct and different subunits may be expressed separately in different host cells as described above, removed from the host cells and assembled into a pore in a separate membrane, such as a rabbit cell membrane.

[0229] The vectors may be for example, plasmid, virus or phage vectors provided with an origin of replication, optionally a promoter for the expression of the said polynucleotide sequence and optionally a regulator of the promoter. The vectors may contain one or more selectable marker genes, for example an ampicillin resistance gene. Promoters and other expression regulation signals may be selected to be compatible with the host cell for which the expression vector is designed. A T7, trc, lac, ara or .lamda..sub.L, promoter is typically used.

[0230] The host cell typically expresses the construct at a high level. Host cells transformed with a polynucleotide sequence encoding a construct will be chosen to be compatible with the expression vector used to transform the cell. The host cell is typically bacterial and preferably E. coli. Any cell with a .lamda. DE3 lysogen, for example C41 (DE3), BL21 (DE3), JM109 (DE3), B834 (DE3), TUNER, Origami and Origami B, can express a vector comprising the T7 promoter.

Modified Pores

[0231] The present invention also provides modified pores for use in sequencing nucleic acids. The pores comprise at least one construct of the invention. The pores may comprise more than one, such as 2, 3 or 4, constructs of the invention.

[0232] A pore of the invention may be isolated, substantially isolated, purified or substantially purified. A pore of the invention is isolated or purified if it is completely free of any other components, such as lipids or other pores. A pore is substantially isolated if it is mixed with carriers or diluents which will not interfere with its intended use. For instance, a pore is substantially isolated or substantially purified if it present in a form that comprises less than 10%, less than 5%, less than 2% or less than 1% of other components, such as lipids or other pores. Alternatively, a pore of the invention may be present in a lipid bilayer or in a surfactant micelle.

[0233] The enzyme attached to the construct handles a target nucleic acid sequence in such a way that a proportion of the nucleotide in the target sequence interacts with the pore, preferably the barrel or channel of the pore. Nucleotides are then distinguished on the basis of the different ways in which they affect the current flowing through the pore during the interaction.

[0234] The fixed nature of the enzyme means that a target nucleic acid sequence is handled by the pore in a specific manner. For instance, each nucleotide may be digested from one of the target sequence in a processive manner or the target sequence may be pushed or pulled through the pore. This ensures that a proportion of the nucleotides in the target nucleic acid sequence interacts with the pore and is identified. The lack of any interruption in the signal is important when sequencing nucleic acids. In addition, the fixed nature of the enzyme and the pore means they can be stored together, thereby allowing the production of a ready-to-use sensor.

[0235] In a preferred embodiment, an exonuclease enzyme, such as a deoxyribonuclease, is attached to the pore such that a proportion of the nucleotides is released from the target nucleic acid and interacts with the barrel or channel of the pore. In another preferred embodiment, an enzyme that is capable of pushing or pulling the target nucleic acid sequence through the pore is attached to the pore such that the target nucleic acid sequence is pushed or pulled through the barrel or channel of the pore and a proportion of the nucleotides in the target sequence interacts with the barrel or channel. In this embodiment, the nucleotides may interact with the pore in blocks or groups of more than one, such as 2, 3 or 4. Suitable enzymes include, but are not limited to, polymerases, exonucleases, helicases and topoisomerases, such as gyrases. In each embodiment, the enzyme is preferably attached to the pore at a site in close proximity to the opening of the barrel of channel of the pore. The enzyme is more preferably attached to the pore such that its active site is orientated towards the opening of the barrel of channel of the pore. This means that a proportion of the nucleotides of the target nucleic acid sequence is fed in the barrel or channel. The enzyme is preferably attached to the cis side of the pore.

[0236] The modified pore may be based on any of the transmembrane protein pores discussed above, including the .beta.-barrel pores and .alpha.-helix bundle pores.

[0237] For constructs comprising the sequence shown in SEQ ID NO: 2 or a variant thereof, the pore typically comprises an appropriate number of additional subunits comprising the sequence shown in SEQ ID NO: 2 or a variant thereof. A preferred pore of the invention comprises one construct comprising the sequence shown in SEQ ID NO: 2 or a variant thereof and six subunits comprising the sequence shown in SEQ ID NO: 2 or a variant thereof. The pore may comprise one or more subunits comprising the sequence shown in SEQ ID NO: 4 or a variant thereof. SEQ ID NO: 4 shows the sequence of SEQ ID NO: 2 except that it has an arginine at position 113 (M113R) and a glutamine at position 139 (N139Q). A variant of SEQ ID NO: 4 may differ from SEQ ID NO: 4 in the same way and to the same extent as discussed for SEQ ID NO: 2 above. A preferred pore of the invention comprises one construct comprising the sequence shown in SEQ ID NO: 2 or a variant thereof and six subunits comprising the sequence shown in SEQ ID NO: 4 or a variant thereof.

[0238] The pores may comprise a molecular adaptor that facilitates the interaction between the pore and the nucleotides or the target nucleic acid sequence. The presence of the adaptor improves the host-guest chemistry of the pore and nucleotides released from or present in the target nucleic acid sequence. The principles of host-guest chemistry are well-known in the art. The adaptor has an effect on the physical or chemical properties of the pore that improves its interaction with nucleotides. The adaptor typically alters the charge of the barrel or channel of the pore or specifically interacts with or binds to nucleotides thereby facilitating their interaction with the pore.

[0239] The adaptor mediates the interaction between nucleotides released from or present in the target nucleic acid sequence and the pore. The nucleotides preferably reversibly bind to the pore via or in conjunction with the adaptor. The nucleotides most preferably reversibly bind to the pore via or in conjunction with the adaptor as they pass through the pore across the membrane. The nucleotides can also reversibly bind to the barrel or channel of the pore via or in conjunction with the adaptor as they pass through the pore across the membrane. The adaptor preferably constricts the barrel or channel so that it may interact with the nucleotides.

[0240] The adaptor is typically cyclic. The adaptor preferably has the same symmetry as the pore. An adaptor having seven-fold symmetry is typically used if the pore is heptameric (e.g. has seven subunits around a central axis that contribute 14 strands to a transmembrane .beta. barrel). Likewise, an adaptor having six-fold symmetry is typically used if the pore is hexameric (e.g. has six subunits around a central axis that contribute 12 strands to a transmembrane .beta. barrel, or is a 12-stranded .beta. barrel). Any adaptor that that facilitates the interaction between the pore and the nucleotide can be used. Suitable adaptors include, but are not limited to, cyclodextrins, cyclic peptides and cucurbiturils. The adaptor is preferably a cyclodextrin or a derivative thereof. The adaptor is more preferably heptakis-6-amino-.beta.-cyclodextrin (am.sub.7-.beta.CD), 6-monodeoxy-6-monoamino-.beta.-cyclodextrin (am.sub.1-.beta.CD) or heptakis-(6-deoxy-6-guanidino)-cyclodextrin (gu.sub.7-.beta.CD). Table 2 below shows preferred combinations of pores and adaptors.

TABLE-US-00002 TABLE 2 Suitable combinations of pores and adaptors Number of strands in the transmembrane Pore .beta.-barrel Adaptor Leukocidin 1.6 .gamma.-cyclodextrin (.gamma.-CD) OmpF 16 .gamma.-cyclodextrin (.gamma.-CD) .alpha.-hemolysin 14 .beta.-cyclodextrin (.beta.-CD) (or a variant 6-monodeoxy-6- thereof monoamino-.beta.-cyclodextrin discussed above) (am.sub.1.beta.-CD) heptakis-6-amino-.beta.- cyclodextrin (am.sub.7-.beta.-CD) heptakis-(6-deoxy-6- guanidino)-cyclodextrin (gu.sub.7-.beta.-CD) OmpG 14 .beta.-cyclodextrin (.beta.-CD) 6-monodeoxy-6- monoamino-(.beta.-cyclodextrin (am.sub.1.beta.-CD) heptakis-6-amino-.beta.- cyclodextrin (am.sub.7-.beta.-CD) heptakis-(6-deoxy-6- guanidino)-cyclodextrin (gu.sub.7-.beta.-CD) NalP 12 .alpha.-cyclodextrin (.alpha.-CD) OMPLA 12 .alpha.-cyclodextrin (.alpha.-CD)

[0241] The adaptor is preferably covalently attached to the pore. The adaptor can be covalently attached to the pore using any method known in the art. The adaptor may be attached directly to the pore. The adaptor is preferably attached to the pore using a bifunctional crosslinker. Suitable crosslinkers are well-known in the art. Preferred crosslinkers include 2,5-dioxopyrrolidin-1-yl 3-(pyridin-2-yldisulfanyl)propanoate, 2,5-dioxopyrrolidin-1-yl 4-(pyridin-2-yldisulfanyl)butanoate and 2,5-dioxopyrrolidin-1-yl 8-(pyridin-2-yldisulfanyl)octananoate. The most preferred crosslinker is succinimidyl 3-(2-pyridyldithio)propionate (SPDP). Typically, the adaptor is covalently attached to the bifunctional crosslinker before the adaptor/crosslinker complex is covalently attached to the pore but it is also possible to covalently attach the bifunctional crosslinker to the pore before the bifunctional crosslinker/pore complex is attached to the adaptor.

[0242] The site of covalent attachment is selected such that the adaptor facilitates interaction of nucleotides released from or present in the target nucleic acid sequence with the pore and thereby allows detection of nucleotides. This can be done as explained in the co-pending International application claiming priority from U.S. Application No. 61/078,687 and being filed simultaneously with this application [J A Kemp & Co Ref: N.104403A; Oxford Nanolabs Ref: ONL IP 004].

[0243] For pores based on .alpha.-HL, the correct orientation of the adaptor within the barrel or channel of the pore and the covalent attachment of adaptor to the pore can be facilitated as described in the co-pending International application claiming priority from U.S. Application No. 61/078,687 and being filed simultaneously with this application [J A Kemp & Co Ref: N.104403A; Oxford Nanolabs Ref: ONL IP 004]. Any of the specific modifications to SEQ ID NO: 2 disclosed in the co-pending application are equally applicable to the pores of this invention. In particular, every subunit of the pore, including the construct(s), preferably has a glutamine at position 139 of SEQ ID NO: 2. One or more of the subunits of the pore, including the construct(s), may have an arginine at position 113 of SEQ ID NO: 2. One or more of the subunits of the pore, including the construct(s), may have a cysteine at position 119, 121 or 135 of SEQ ID NO: 2. Any of the variants of SEQ ID NO: 2 shown in SEQ ID NOs: 4, 6, 8, 10, 12 and 14 of the co-pending application may be used to form a modified pore of the invention.

[0244] Preferred modified pores of the invention comprise:

[0245] (a) a construct comprising the sequence shown in SEQ ID NO: 18, 20, 22, 24, 26, 28 or 30 or a variant thereof and six subunits of .alpha.-HL M113R/N139Q shown in SEQ ID NO: 4;

[0246] (b) a construct of the invention comprising the sequence shown in SEQ ID NO: 2 or a variant thereof, five subunits of .alpha.-HL M113R/N139Q shown in SEQ ID NO: 4 or a variant thereof and one subunit of .alpha.-HL M113R/N139Q/G119C-D8 shown in SEQ ID NO: 10 of the co-pending application;

[0247] (c) a construct of the invention comprising the sequence shown in SEQ ID NO: 2 or a variant thereof, five subunits of .alpha.-HL M113R/N139Q shown in SEQ ID NO: 4 or a variant thereof and one subunit of .alpha.-HL M113R/N139Q/N121C-D8 shown in SEQ ID NO: 12 of the co-pending application; or

[0248] (d) a construct of the invention comprising the sequence shown in SEQ ID NO: 2 or a variant thereof, five subunits of .alpha.-HL M113R/N139Q shown in SEQ ID NO: 4 or a variant thereof and one subunit of .alpha.-HL M113R/N139Q/L135C-D8 shown in SEQ ID NO: 14 of the co-pending application.

Methods of Producing Constructs of the Invention

[0249] The invention also provides methods of producing a construct of the invention. The methods comprise covalently attaching a nucleic acid handling enzyme to a transmembrane protein pore subunit. Any of the subunits and enzymes discussed above can be used in the methods. The site of and method of covalent attachment are selected as discussed above.

[0250] The methods also comprise determining whether or not the construct is capable of forming a pore and handling nucleic acids. Assays for doing this are described above. If a pore can be formed and nucleic acids can be handled, the subunit and enzyme have been attached correctly and a construct of the invention has been produced. If a pore cannot be formed or nucleic acids cannot be handled, a construct of the invention has not been produced.

Methods of Producing Modified Pores

[0251] The present invention also provides methods of producing modified pores of the invention. The modified pore may be formed by allowing at least one construct of the invention to form a pore with other suitable subunits or by covalently attaching an enzyme to a subunit in an oligomeric pore. Any of the constructs, subunits, enzymes or pores discussed above can be used in the methods. The site of and method of covalent attachment are selected as discussed above.

[0252] The methods also comprise determining whether or not the pore is capable of handling nucleic acids and detecting nucleotides. The pore may be assessed for its ability to detect individual nucleotides or short chains of nucleotides, such as di- or trinucleotides. Assays for doing this are described above and below. If the pore is capable of handling nucleic acids and detecting nucleotides, the subunit and enzyme have been attached correctly and a pore of the invention has been produced. If a pore cannot be handle nucleic acids and detect nucleotides, a pore of the invention has not been produced.

[0253] In a preferred embodiment, a heteroheptamer of seven subunits comprising the sequence shown in SEQ ID NO: 2 or a variant thereof and containing one cysteine in an appropriate place is reacted with a bifunctional cross-linker. The pore may be reacted with the linker before or after it has been purified, typically by SDS PAGE. The pore/linker construct is then reacted with an enzyme containing at least one reactive cysteine, for instance on a genetically-fused peptide linker. After the coupling reaction, the modified pore of the invention is removed from any unreacted enzyme or pore/linker construct.

Method of Purifying Pores

[0254] The present invention also provides methods of purifying modified pores of the invention. The methods allow the purification of pores comprising at least one construct of the invention. The methods do not involve the use of anionic surfactants, such as sodium dodecyl sulphate (SDS), and therefore avoid any detrimental effects on the enzyme part of the construct. The methods are particularly good for purifying pores comprising a construct of the invention in which the subunit and enzyme have been genetically fused.

[0255] The methods involve providing at least one construct of the invention and any remaining subunits required to form a pore of the invention. Any of the constructs and subunits discussed above can be used. The construct(s) and remaining subunits are inserted into synthetic lipid vesicles and allowed to oligomerise. Methods for inserting the construct(s) and remaining subunits into synthetic vesicles are well known in the art.

[0256] The synthetic vesicles should have similar properties to rabbit cell membranes, but should lack the rabbit cell membrane proteins. The vesicles may comprise any components and are typically made of a blend of lipids. Suitable lipids are well-known in the art. The synthetic vesicles preferably comprise 30% cholesterol, 30% phosphatidylcholine (PC), 20% phosphatidylethanolamine (PE), 10% sphingomyelin (SM) and 10% phosphatidylserine (PS).

[0257] The vesicles are then contacting with a non-ionic surfactant or a blend of non-ionic surfactants. The non-ionic surfactant is preferably an Octyl Glucoside (OG) or DoDecyl Maltoside (DDM) detergent. The oligomerised pores are then purified, for example by using affinity purification based on his-tag or Ni-NTA.

Methods of Sequencing Nucleic Acids

[0258] The present invention also provides methods of sequencing a target nucleic acid sequence. In one embodiment, the method comprises (a) contacting the target sequence with a pore of the invention, which comprises an exonuclease, such that the exonuclease digests an individual nucleotide from one end of the target sequence; (b) contacting the nucleotide with the pore so that the nucleotide interacts with the adaptor; (c) measuring the current passing through the pore during the interaction and thereby determining the identity of the nucleotide; and (d) repeating steps (a) to (c) at the same end of the target sequence and thereby determining the sequence of the target sequence. Hence, the method involves stochastic sensing of a proportion of the nucleotides in a target nucleic acid sequence in a successive manner in order to sequence the target sequence. Individual nucleotides are described above.

[0259] In another embodiment, the method comprises (a) contacting the target sequence with a pore of the invention so that the target sequence is pushed or pulled through the pore and a proportion of the nucleotides in the target sequence interacts with the pore and (b) measuring the current passing through the pore during each interaction and thereby determining the sequence of the target sequence. Hence, the method involves stochastic sensing of a proportion of the nucleotides in a target nucleic acid sequence as the nucleotides pass through the barrel or channel in a successive manner in order to sequence the target sequence.

[0260] Pores comprising a construct of the invention are particularly suited to these methods. In order to effectively sequence the nucleic acid, it is important to ensure that a proportion of the nucleotides in the nucleic acid is identified in a successive manner. The fixed nature of the enzyme means that a proportion of the nucleotides in the target sequence affects the current flowing through the pore.

[0261] The whole or only part of the target nucleic acid sequence may be sequenced using this method. The nucleic acid sequence can be any length. For example, the nucleic acid sequence can be at least 10, at least 50, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400 or at least 500 nucleotides in length. The nucleic acid sequence can be naturally occurring or artificial. For instance, the method may be used to verify the sequence of a manufactured oligonucleotide. The methods are typically carried out in vitro.

[0262] The methods may be carried out using any suitable membrane/pore system in which a pore comprising a construct of the invention is inserted into a membrane. The methods are typically carried out using (i) an artificial membrane comprising a pore comprising a construct of the invention, (ii) an isolated, naturally occurring membrane comprising a pore comprising a construct of the invention, or (iii) a cell expressing a pore comprising a construct of the invention. The methods are preferably carried out using an artificial membrane. The membrane may comprise other transmembrane and/or intramembrane proteins as well as other molecules in addition to the pore of the invention.

[0263] The membrane forms a barrier to the flow of ions, nucleotides and nucleic acids. The membrane is preferably a lipid bilayer. Lipid bilayers suitable for use in accordance with the invention can be made using methods known in the art. For example, lipid bilayer membranes can be formed using the method of Montal and Mueller (1972). Lipid bilayers can also be formed using the method described in International Application No. PCT/GB08/000,563.

[0264] The methods of the invention may be carried out using lipid bilayers formed from any membrane lipid including, but not limited to, phospholipids, glycolipids, cholesterol and mixtures thereof. Any of the lipids described in International Application No. PCT/GB08/000,563 may be used.

[0265] Methods are known in the art for inserting pores into membranes, such as lipid bilayers. Some of those methods are discussed above.

Interaction Between the Pore and Nucleotides

[0266] The nucleotide or nucleic acid may be contacted with the pore on either side of the membrane. The nucleotide or nucleic acid may be introduced to the pore on either side of the membrane. The nucleotide or nucleic acid is typically contacted with the side of the membrane on which the enzyme is attached to the pore. This allows the enzyme to handle the nucleic acid during the method.

[0267] A proportion of the nucleotides of the target nucleic acid sequence interacts with the pore and/or adaptor as it passes across the membrane through the barrel or channel of the pore. Alternatively, if the target sequence is digested by an exonuclease, the nucleotide may interact with the pore via or in conjunction with the adaptor, dissociate from the pore and remain on the same side of the membrane. The methods may involve the use of pores in which the orientation of the adaptor is fixed. In such embodiments, the nucleotide is preferably contacted with the end of the pore towards which the adaptor is oriented. Most preferably, the nucleotide is contacted with the end of the pore towards which the portion of the adaptor that interacts with the nucleotide is orientated.

[0268] The nucleotides may interact with the pore in any manner and at any site. As discussed above, the nucleotides preferably reversibly bind to the pore via or in conjunction with the adaptor. The nucleotides most preferably reversibly bind to the pore via or in conjunction with the adaptor as they pass through the pore across the membrane. The nucleotides can also reversibly bind to the barrel or channel of the pore via or in conjunction with the adaptor as they pass through the pore across the membrane.

[0269] During the interaction between a nucleotides and the pore, the nucleotide affects the current flowing through the pore in a manner specific for that nucleotide. For example, a particular nucleotide will reduce the current flowing through the pore for a particular mean time period and to a particular extent. In other words, the current flowing through the pore is distinctive for a particular nucleotide. Control experiments may be carried out to determine the effect a particular nucleotide has on the current flowing through the pore. Results from carrying out the method of the invention on a test sample can then be compared with those derived from such a control experiment in order to identify a particular nucleotide.

Apparatus

[0270] The methods may be carried out using any apparatus that is suitable for investigating a membrane/pore system in which a pore comprising a construct of the invention is inserted into a membrane. The methods may be carried out using any apparatus that is suitable for stochastic sensing. For example, the apparatus comprises a chamber comprising an aqueous solution and a barrier that separates the chamber into two sections. The barrier has an aperture in which the membrane containing the pore is formed. The nucleotide or nucleic acid may be contacted with the pore by introducing the nucleic acid into the chamber. The nucleic acid may be introduced into either of the two sections of the chamber, but is preferably introduced into the section of the chamber containing the enzyme.

[0271] The methods may be carried out using the apparatus described in International Application No. PCT/GB08/000562.

[0272] The methods involve measuring the current passing through the pore during interaction with the nucleotides. Therefore the apparatus also comprises an electrical circuit capable of applying a potential and measuring an electrical signal across the membrane and pore. The methods may be carried out using a patch clamp or a voltage clamp. The methods preferably involves the use of a voltage clamp.

Conditions

[0273] The methods of the invention involve the measuring of a current passing through the pore during interaction with nucleotides in a target nucleic acid sequence. Suitable conditions for measuring ionic currents through transmembrane protein pores are known in the art and disclosed in the Examples. The method is carried out with a voltage applied across the membrane and pore. The voltage used is typically from -400 mV to +400 mV. The voltage used is preferably in a range having a lower limit selected from -400 mV, -300 mV, -200 mV, -150 mV, -100 mV, -50 mV, -20 mV and 0 mV and an upper limit independently selected from +10 mV, +20 mV, +50 mV, +100 mV, +150 mV, +200 mV, +300 mV and +400 mV. The voltage used is more preferably in the range 120 mV to 170 mV. It is possible to increase discrimination between different nucleotides by a pore of the invention by using an increased applied potential.

[0274] The methods are carried out in the presence of any alkali metal chloride salt. In the exemplary apparatus discussed above, the salt is present in the aqueous solution in the chamber. Potassium chloride (KCl), sodium chloride (NaCl) or caesium chloride (CsCl) is typically used. KCl is preferred. The salt concentration is typically from 0.1 to 2.5M, from 0.3 to 1.9M, from 0.5 to 1.8M, from 0.7 to 1.7M, from 0.9 to 1.6M or from 1M to 1.4M. High salt concentrations provide a high signal to noise ratio and allow for currents indicative of the presence of a nucleotide to be identified against the background of normal current fluctuations. However, lower salt concentrations are preferably used so that the enzyme is capable of functioning. The salt concentration is preferably from 150 to 500 mM. Good nucleotide discrimination at these low salt concentrations can be achieved by carrying out the method at temperatures above room temperature, such as from 30.degree. C. to 40.degree. C.

[0275] The methods are typically carried out in the presence of a buffer. In the exemplary apparatus discussed above, the buffer is present in the aqueous solution in the chamber. Any buffer may be used in the methods. One suitable buffer is Tris-HCl buffer. The methods are typically carried out at a pH of from 4.0 to 10.0, from 4.5 to 9.5, from 5.0 to 9.0, from 5.5 to 8.8, from 6.0 to 8.7 or from 7.0 to 8.8 or 7.5 to 8.5. The pH used is preferably about 7.5.

[0276] The methods are typically carried out at from 0.degree. C. to 100.degree. C., from 15.degree. C. to 95.degree. C., from 16.degree. C. to 90.degree. C., from 17.degree. C. to 85.degree. C., from 18.degree. C. to 80.degree. C., 19.degree. C. to 70.degree. C., or from 20.degree. C. to 60.degree. C. The methods may be carried out at room temperature. The methods are preferably carried out at a temperature that supports enzyme function, such as about 37.degree. C. Good nucleotide discrimination can be achieved at low salt concentrations if the temperature is increased.

[0277] In addition to increasing the solution temperature, there are a number of other strategies that can be employed to increase the conductance of the solution, while maintaining conditions that are suitable for enzyme activity. One such strategy is to use the lipid bilayer to divide two different concentrations of salt solution, a low salt concentration of salt on the enzyme side and a higher concentration on the opposite side. One example of this approach is to use 200 mM of KCl on the cis side of the membrane and 500 mM KCl in the trans chamber. At these conditions, the conductance through the pore is expected to be roughly equivalent to 400 mM KCl under normal conditions, and the enzyme only experiences 200 mM if placed on the cis side. Another possible benefit of using asymmetric salt conditions is the osmotic gradient induced across the pore. This net flow of water could be used to pull nucleotides into the pore for detection. A similar effect can be achieved using a neutral osmolyte, such as sucrose, glycerol or PEG. Another possibility is to use a solution with relatively low levels of KCl and rely on an additional charge carrying species that is less disruptive to enzyme activity.

Exonuclease-Based Methods

[0278] In one embodiment, the method of sequencing a target nucleic acid sequence involves contacting the target sequence with a pore having an exonuclease enzyme, such as deoxyribonuclease, attached thereto. The constructs needed to make such pores are discussed above. Any of the exonuclease enzymes discussed above may be used in the method. The exonuclease releases individual nucleotides from one end of the target sequence. Exonucleases are enzymes that typically latch onto one end of a nucleic acid sequence and digest the sequence one nucleotide at a time from that end. The exonuclease can digest the nucleic acid in the 5' to 3' direction or 3' to 5' direction. The end of the nucleic acid to which the exonuclease binds is typically determined through the choice of enzyme used and/or using methods known in the art. Hydroxyl groups or cap structures at either end of the nucleic acid sequence may typically be used to prevent or facilitate the binding of the exonuclease to a particular end of the nucleic acid sequence.

[0279] The method involves contacting the nucleic acid sequence with the exonuclease so that the nucleotides are digested from the end of the nucleic acid at a rate that allows identification of a proportion of nucleotides as discussed above. Methods for doing this are well known in the art. For example, Edman degradation is used to successively digest single amino acids from the end of polypeptide such that they may be identified using High Performance Liquid Chromatography (HPLC). A homologous method may be used in the present invention.

[0280] The rate at which the exonuclease functions is typically slower than the optimal rate of a wild-type exonuclease. A suitable rate of activity of the exonuclease in the method of sequencing involves digestion of from 0.5 to 1000 nucleotides per second, from 0.6 to 500 nucleotides per second, 0.7 to 200 nucleotides per second, from 0.8 to 100 nucleotides per second, from 0.9 to 50 nucleotides per second or 1 to 20 or 10 nucleotides per second. The rate is preferably 1, 10, 100, 500 or 1000 nucleotides per second. A suitable rate of exonuclease activity can be achieved in various ways. For example, variant exonucleases with a reduced optimal rate of activity may be used in accordance with the invention.

Pushing or Pulling DNA Through the Pore

[0281] Strand sequencing involves the controlled and stepwise translocation of nucleic acid polymers through a pore. The majority of DNA handling enzymes are suitable for use in this application provided they hydrolyse, polymerise or process single stranded DNA or RNA. Preferred enzymes are polymerases, exonucleases, helicases and topoisomerases, such as gyrases. The enzyme moiety is not required to be in as close a proximity to the pore lumen as for individual nucleotide sequencing as there is no potential for disorder in the series in which nucleotides reach the sensing moiety of the pore.

[0282] The two strategies for single strand DNA sequencing are the translocation of the DNA through the nanopore, both cis to trans and trans to cis, either with or against an applied potential. The most advantageous mechanism for strand sequencing is the controlled translocation of single strand DNA through the nanopore with an applied potential. Exonucleases that act progressively or processively on double stranded DNA can be used on the cis side of the pore to feed the remaining single strand through under an applied potential or the trans side under a reverse potential. Likewise, a helicase that unwinds the double stranded DNA can also be used in a similar manner. There are also possibilities for sequencing applications that require strand translocation against an applied potential, but the DNA must be first "caught" by the enzyme under a reverse or no potential. With the potential then switched back following binding the strand will pass cis to trans through the pore and be held in an extended conformation by the current flow. The single strand DNA exonucleases or single strand DNA dependent polymerases can act as molecular motors to pull the recently translocated single strand back through the pore in a controlled stepwise manner, trans to cis, against the applied potential.

Kits

[0283] The present invention also provides kits for producing a modified pore for use in sequencing nucleic acids. In one embodiment, the kits comprise at least one construct of the invention and any remaining subunits need to form a pore. The kits may comprise enough constructs of the invention to form a complete pore (i.e. a homo-oligomer). The kits may comprise any of the constructs and subunits discussed above. A preferred kit comprises (i) a construct comprising a subunit comprising the sequence shown in SEQ ID NO: 2 or a variant thereof and (ii) six subunits comprising the sequence shown in SEQ ID NO: 2 or a variant thereof. A more preferred kit comprises (i) a construct comprising the sequence shown in SEQ ID NO: 18, 20, 22, 24, 26, 28 or 30 or a variant thereof and (ii) six subunits comprising the sequence shown in SEQ ID NO: 2 or a variant thereof.

[0284] In another embodiment, the kits comprise at least one polynucleotide sequence of the invention and polynucleotide sequences encoding any remaining subunits needed to form a pore. The kit may comprise enough polynucleotides of the invention to encode a complete pore (i.e. a homo-oligomer). The kits may comprise any of the polynucleotides described above. A preferred kit comprises (i) a polynucleotide sequence encoding a construct, which comprises a subunit comprising the sequence shown in SEQ ID NO: 2 or a variant thereof and (ii) six polynucleotide sequences each encoding a subunit comprising the sequence shown in SEQ ID NO: 2 or a variant thereof. A more preferred kit comprises (i) a polynucleotide sequence encoding a construct comprising the sequence shown in SEQ ID NO: 18, 20, 22, 24, 26, 28 or 30 or a variant thereof and (ii) six polynucleotide sequences each encoding a subunit comprising the sequence shown in SEQ ID NO: 2 or a variant thereof.

[0285] The kits of the invention may additionally comprise one or more other reagents or instruments which enable any of the embodiments mentioned above to be carried out. Such reagents or instruments include one or more of the following: suitable buffer(s) (aqueous solutions), means to obtain a sample from a subject (such as a vessel or an instrument comprising a needle), means to amplify and/or express polynucleotide sequences, a membrane as defined above or voltage or patch clamp apparatus. Reagents may be present in the kit in a dry state such that a fluid sample resuspends the reagents. The kit may also, optionally, comprise instructions to enable the kit to be used in the method of the invention or details regarding which patients the method may be used for. The kit may, optionally, comprise nucleotides.

[0286] The following Example illustrates the invention:

Example

1 Materials and Methods

1.1 Bacterial Strains and Growth Conditions

[0287] The bacterial strains used in this work were E. coli strains XL-10 Gold and BL21 DE3 pLysS (Stratagene). E. coli strains were grown at 37.degree. C. either in Luria-Bertani Broth (LB), Terrific Broth at 225 rpm, Luria-Bertani agar (LA) or tryptone-yeast extract agar (TY) (Bertani, G. (1951). Studies on lysogenesis. I. The mode of phage liberation by lysogenic Escherichia coli. Journal of Bacteriology. 62, 293-300; Beringer, J. (1974). R factor transfer in Rhizobium leguminosarum. Journal of General Microbiology. 84, 188-98; and Tartoff, K. and Hobbs, C. (1987). Improved media for growing plasmid and cosmid clones. Bethesda Research Labs Focus. 9, 12). Antibiotics were used at the following concentrations: Ampicillin 100 .mu.g ml.sup.-1; chloramphenicol 30 .mu.g ml.sup.-1.

1.2 Genetic Manipulations

[0288] All general DNA cloning was performed as adapted methods of that previously described (Sambrook, J. and Russell, D. (2001). Molecular Cloning: A Laboratory Manual, 3rd Edition. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.). DNA polymerases, restriction endonucleases, exonuclease, ligases and phosphatases were all obtained from New England Biolabs. Exonuclease genes were manufactured by GenScript Corporation and received as fragments cloned into pT7-SC1, by BspEI or NdeI/HindIII. All mutations and fusion constructs were assembled in the expression vector pT7-SC1 (Cheley, S., Malghani, M., Song, L., Hobaugh, M., Gouaux, E., Yang, J. and Bayley, H. (1997). Spontaneous oligomerization of a staphylococcal alpha-hemolysin conformationally constrained by removal of residues that form the transmembrane beta-barrel. Protein Engineering. 10, 1433-43) and verified by sequencing using either the T7 forward or reverse primers, EcoExoIII_seq and EcoExoI_seq.

[0289] Site directed mutagenesis of the .alpha.HL gene was performed by in vivo homologous recombination of PCR products (Jones, D. (1995) PCR mutagenesis and recombination in vivo. In PCR primer: a laboratory manual. In: Dveksler, C. (ed). Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.). Amplification of two halves of the target plasmid with complimentary primer pairs generates two PCR products with complimentary sequences at both the 5' and 3' ends. Transformation of both products into chemically competent E. coli allows in vivo homologous recombination. For all mutagenesis SC46 was used as the antisense primer for amplification of product 1 and SC47 as the sense primer for amplification of product 2. These complementary primer binding sites are within the .beta.-lactamase gene of pT7-SC1. Colonies recovered on LA 100 ng .mu.l.sup.-1 ampicillin therefore indicated successful homologous recombination.

[0290] PCR was conducted in 50 .mu.l reactions using 1 unit Phusion.TM. DNA polymerase, 0.2 mM dNTPs, 1 .mu.M primers and 4 ng BamHI/HindIII or NdeI/EcoNI digested plasmid DNA. Reactions were cycled as follows: 1 cycle of 98.degree. C. for 2 min; 30 cycles of 98.degree. C. for 15 s, 57.degree. C. for 30 s and 72.degree. C. for 45 s; and a final extension of 72.degree. C. for 5 min. 2.5 .mu.l of each pair of PCR products were mixed and used to transform chemically competent E. coli (XL-10 Gold).

1.3 Rapid In Vitro Transcription Translation

[0291] [.sup.35S]L-methionine labelled proteins were generated by coupled in vitro transcription and translation (IVTT) using an E. coli T7-S30 extract system for circular DNA (Promega). The complete amino acid mixture (1 mM) minus cysteine and the complete amino acid mixture (1 mM) minus methionine, supplied in the kit, were mixed in equal volumes to obtain the working amino acid solution required to generate high concentrations of the protein. Reactions were scaled up or down based on the following, for a 50 .mu.l reaction volume: 20 .mu.l S30 Premix solution; 5 .mu.l amino acid mix; 1 .mu.l [.sup.35S]L-methionine (MP Biomedicals, 1175 Ci mmol.sup.-1, 10 mCi ml.sup.-1), 1 .mu.l rifampicin (0.8 mg ml.sup.-1), 8 .mu.l plasmid DNA (400 ng .mu.l.sup.-1) and 15 .mu.l T7 S30 extract. Synthesis was carried out for 1.5 hours at 37.degree. C. to produce 50 .mu.l of radiolabelled IVTT protein. Different proteins were also co-expressed in one reaction as for coupled transcription, translation and oligomerisation. The reaction components remained the same except the DNA concentration was divided accordingly for each plasmid encoding each protein. Protein samples were centrifuged at 14,000 rpm for 10 minutes to separate insoluble debris of IVTT reactions.

1.4 In Vivo Protein Expression

[0292] Wild-type .alpha.-hemolysin and fusion constructs were cloned into the expression vector pT7-SC1, under the control of the inducible T7 promoter, and expressed in E. coli (BL21 DE3 pLysS, Stratagene) as soluble proteins. Cultures were grown to a high OD.sub.600 (approximately 1.5-2) at 37.degree. C. and 240 rpm in Terrific broth medium (100 .mu.g .mu.l.sup.-1 ampicillin and 30 .mu.g .mu.l.sup.-1 chloramphenicol). The temperature was reduced to 18.degree. C. and cultures left for 30 minutes to equilibrate. Over expression of the target protein was induced by addition of IPTG to the medium (0.2 mM). After 18 hours cells were pelleted at 10,000 rpm for 30 minutes at 4.degree. C. Cells were resuspended and lysed by the addition of BugBuster (Novagen) supplemented with the addition of benzonase, EDTA-free proteinase inhibitors (Roche) and to 50 mM MgCl.sub.2. Cell debris was pelleted by centrifugation at 10,000 rpm for 30 minutes at 4.degree. C. and polyethyleneimine (PEI) added to the supernatant. The recovered supernatant was incubated for 30 mins at 4.degree. C. after which precipitate was removed by centrifugation at 10,000 rpm for 30 minutes at 4.degree. C. Clarified lysate was filtered and adjusted to pH 8.0, 500 mM NaCl, 10 mM Imidazole.

[0293] His-tagged proteins were purified as standard practice by Ni-NTA affinity chromatography and gel filtration. Non-tagged .alpha.-hemolysin subunits were purified as standard practice by cation exchange followed by gel filtration.

1.4.1 Affinity Purification (His-tag)

[0294] Clarified lysate was filtered and adjusted to pH 8.0, 500 mM NaCl, 10 mM Imidazole before loading onto a His-Trap crude column (GE Healthcare) and eluted with 300 mM Imidazole. Fractions containing the protein of interest were combined and applied to a gel filtration column equilibrated with 10 mM TRIS pH 8.0, 100 mM NaCl, 1 mM DTT. Eluted protein was evaluated by SDS-PAGE.

1.4.2 Ion Exchange

[0295] Clarified lysate was filtered and adjusted to 10 mM MES pH 6.0 before loading onto a cation exchange column (GE Healthcare) and eluting with 0-500 mM NaCl. Fractions containing the protein of interest were combined and applied to a gel filtration column. Eluted protein was evaluated by SDS-PAGE.

[0296] To maintain the reactivity of engineered cysteine residues in .alpha.-Hemolysin derivatives, required as sites for chemical modification, proteins were purified using the same buffers but supplemented to 1 mM DTT. Exonucleases or exonuclease fusion proteins were purified using the same buffers supplemented to 1 mM MgCl.sub.2.

1.5 Oligomerisation on Red Blood Cell Membranes

[0297] .alpha.-Hemolysin monomers were mixed in various molar ratios and allowed to oligomerise on rabbit erythrocyte membranes (2.5 mg protein ml.sup.-1) for 1 hour at either room temperature, 30.degree. C., 37.degree. C. or 42.degree. C. After the incubation, reaction mixture was centrifuged at 14,000 rpm for 10 minutes and supernatant discarded. Membrane pellet was washed by resuspension in 200 .mu.l MBSA (10 mM MOPS, 150 mM NaCl, pH 7.4 containing 1 mg ml.sup.-1 bovine serum albumin) and centrifuging again at 14,000 rpm for 10 minutes. After discarding the supernatant, membrane pellet was dissolved in 75 .mu.l of 1.times. Laemmli sample buffer, with the addition of .beta.-mercaptoethanol. The entire sample was loaded into a single well of a 5% SDS-polyacrylamide gel and electrophoresed for .about.18 hours at 50 V, with 0.01 mM sodium thioglycolate included in the running buffer. Gel was vacuum-dried onto a Whatman 3 mm filter paper at 50.degree. C. for about three hours and exposed to an X-ray film overnight (Kodak). The oligomer band was excised from the gel, using the autoradiogram as template, and the gel slice rehydrated in 300 .mu.l TE buffer (10 mM Tris, 1 mM EDTA, pH 8.0) containing 2 mM DTT. After removing the Whatman filter paper slice, gel piece was crushed using a sterile pestle. Oligomer protein was separated from gel debris by centrifuging through 0.2 UM cellulose acetate microfilterage tubes (Rainin) at 14,000 rpm for 30 min. Filtrate was stored in aliquots at -80.degree. C.

1.6 Oligomerisation on Synthetic Lipid Vesicles

[0298] Synthetic lipid vesicles composed of: 30% cholesterol; 30% phosphatidylcholine (PC); 20% phosphatidylethanolamine (PE); 10% sphingomyelin (SM); 10% phosphatidylserine (PS); were prepared by bath sonication for 15 minutes at room temperature. Organic solvent is evaporated by a gentle stream of nitrogen until a dry film is produced. Deionised water added to give a required concentration of 2.5 mg ml.sup.-1 and mixture bath sonicated again for 15 minutes. Wild-type .alpha.-hemolysin and fusion monomers were mixed in various molar ratios and allowed to oligomerise on synthetic lipid vesicles (2.5 mg ml.sup.-1 for every 1 mg .alpha.-hemolysin monomer) for 1 hour at either room temperature, 30.degree. C., 37.degree. C. or 42.degree. C. and 350 rpm. To pellet lipid associated proteins samples were centrifuged at 14,000 rpm for 10 minutes. Pellet was washed once in MBSA (10 mM MOPS, 150 mM NaCl, pH 7.4 containing 1 mg ml.sup.-1 bovine serum albumin) and lipids were dissolved by addition of 0.1-1% n-Dodecyl-D-maltopyranoside (DDM), for 1 hour at either 4.degree. C. or room temperature. To purify the fusion homo and heteroheptamers away from wild-type homoheptamer 300 .mu.l of Ni-NTA agarose (Qiagen) was added and left overnight at 4.degree. C. and 350 rpm. Affinity bound heptamer was pelted with Ni-NTA agarose by centrifugation at 14,000 rpm for 10 minutes. The Ni-NTA agarose beads were washed twice in 500 .mu.l wash buffer (10 mM Tris, 10 mM Imidazole, 500 mM NaCl, pH 8.0) for 10 minutes and recovered by centrifugation. Purified heteroheptamer was eluted in 500 .mu.l elution buffer (10 mM Tris, 250 mM Imidazole, pH 8.0) for 1 hour at 4.degree. C. The Ni-NTA agarose was removed by centrifugation and the supernatant containing the eluted purified fusion heptamers removed. Eluted heptamers were de-salted by passage through a buffer exchange column (NAP-5, GE Healthcare), equilibrated with 10 mM Tris pH 8.0.

1.7 Exonuclease Fluorescence Assay

[0299] Recombinant E. coli Exonuclease III was purchased from New England Biolabs (100 units .mu.l.sup.-1). Double stranded DNA template labelled with a 5' fluorophore (5HEX) on the sense strand and a 3' black hole quencher (BHQ-2a-Q) on the antisense strand was obtained from Operon.

[0300] The oligo sequences are given below along with the respective fluorophore and quencher pair:

TABLE-US-00003 (SEQ ID NO: 31) 5'[5HEX]GCAACAGAGCTGATGGATCAAATGCATTAGGTAAACATGTT ACGTCGTAA 3' (SEQ ID NO: 32) 5'CGATCTTACGACGTAACATGTTTACCTAATGCATTTGATCCATCAGC TCTGTTGC[BHQ2a]3'

The substrate dsDNA has a 5 bp overhang at the 5' end of the antisense strand, enabling initiation of exonuclease III on the 3' end of the sense strand.

[0301] Fluorescence measurements were taken using a Cary Eclipse (Varian) with an excitation and emission wavelength of 535 and 554 nm respectively and an excitation and emission slit of 5 nm. Measurements were taken every 4 seconds for 60 minutes. 40 .mu.l reactions were performed at 37.degree. C. and consisted of: 200 nm substrate dsDNA; 25 mM Tris pH 7.5; 1 mM MgCl.sub.2; 100 mM KCl; 0.001 units Exo III; unless otherwise stated.

1.8 Planar Bilayer Recordings

[0302] All bilayers were formed by apposition of two monolayers of 1,2-diphytanoyl-sn-glycero-3-phosphocholine (Avanti Polar Lipids) across a 60-150 .mu.m diameter aperture in Teflon film (25 .mu.m thickness from Goodfellow, Malvern, Pa.), which divided a chamber into two buffer compartments (cis and trans) each with a volume of 1 ml. Bilayers were formed across the aperture by consecutively raising the buffer level in each compartment until a high resistance seal was observed (.gtoreq.10 G.OMEGA.). Unless otherwise stated, fusion heptamers and DNA or dNMPs were added to the cis compartment, which was connected to ground. The adapter molecule am7.beta.CD or am6-amPDP1-.beta.CD was added to the trans compartment if required, which was connected to the head-stage of the amplifier. Unless stated otherwise, experiments were carried out in 25 mM Tris.HCl, 400 mM KCl pH 8.0, at 22.degree. C.

1.9 Exonucleases

[0303] Exonucleases, such as deoxyribonucleases, are a subgroup of the EC 3.1 enzymes. They catalyse the hydrolysis of the phosphodiester bond between adjacent bases in a DNA strand to release individual nucleoside 5' mono-phosphates (FIG. 1). Attractive activities catalyse the cleavage of this bond (through nucleophilic attack of an activated water molecule upon the phosphorus) as shown.

[0304] There are a limited number of distinct enzymatic activities that degrade nucleic acids into their component parts, although numerous homologues will exist in different organisms (for example, Exonuclease III). From a detailed literature search, the two most processive exonuclease enzymes are Exonuclease I, encoded by the sbcB gene of E. coli, and .lamda.-exonuclease, encoded by the exo gene of bacteriophage .lamda. (Thomas, K. and Olivera, B. (1978) Processivity of DNA exonucleases. Journal of Biological Chemistry. 253, 424-429; and Zagursky, R. and Hays, J. (1983). Expression of the phage lambda recombination genes exo and bet under lacPO control on a multi-copy plasmid. Gene. 23, 277-292). In addition, activity of Exonuclease I has been demonstrated in high salt concentrations (Hornblower, B., Coombs, A., Whitaker, R., Kolomeisky, A., Picone, S., Meller, A. Akeson, M. (2007). Single-molecule analysis of DNA-protein complexes using nanopores. Nature Methods. 4, 315-317). As .lamda. exonuclease is a trimer the attachment of a functional exonuclease is more challenging so the monomeric enzyme Exonuclease III was also included, as despite its shorter processivity rate it also degrades one strand of dsDNA to yield nucleoside 5' monophosphates. Whilst Exo I degrades ssDNA in a 3'-5' direction RecJ acts 5'-3' and so was also included in this work (Lovett, S, and Kolodner, R. (1989). Identification and purification of a single-stranded-DNA-specific exonuclease encoded by the real gene of Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America. 86, 2627-2631). Both ssDNA exonucleases have been demonstrated to interact and act cooperatively with single stranded binding protein (Genschel, J., Curth, U. and Urbanke, C. (2000) Interaction of E. coli single-stranded DNA binding protein (SSB) with exonuclease I. The carboxy terminus of SSB is the recognition site for the nuclease. Biological Chemistry. 381, 183-192; and Han, E., Cooper, D., Persky, N., Sutera, V., Whitaker, R., Montello, M. and Lovett, S. (2006). RecJ exonuclease: substrates, products and interaction with SSB. Nucleic Acids Research. 34, 1084-1091). The use of these proteins may be required to prevent secondary structure formation of the ssDNA substrate that may enzyme initiation or processivity in high salt concentrations.

[0305] Four exonucleases are used in this Example:

1. Exo III from E. coli, Monomeric, dsDNA, 3'-5' (SEQ ID NOs: 9 and 10) 2. Exo I from E. coli, Monomeric, ssDNA, 3'-5' (SEQ ID NOs: 11 and 12) 3. RecJ from T. thermophilus, Monomeric, ssDNA, 5'-3' (SEQ ID NOs: 13 and 14) 4. .lamda. Exo from .lamda. bacteriophage, Trimeric, dsDNA, 5'-3' (the sequence of one monomer is shown in SEQ ID NOs: 15 and 16)

[0306] High resolution crystal structures are available for all these enzymes (Mol, C., Kuo, C., Thayer, M., Cunningham, R. and Tainer, J. (1995) Structure and function of the multifunctional DNA-repair enzyme exonuclease III. Nature. 374, 381-386; Kovall, R. and Matthews, B. (1997). Toroidal structure of lambda-exonuclease. Science. 277, 1824-1827; and Busam, R. (2008). Structure of Escherichia coli exonuclease I in complex with thymidine 5'-monophosphate. Acta Crystallographica. 64, 206-210) and are shown in FIG. 2. The TthRecJ is the enzymes core domain as identified by Yamagata et al. (Yamagata, A., Masui, R., Kakuta, Y., Kuramitsu, S, and Fukuyama, K. (2001).

1.10 Genetic Attachment

[0307] Taking the characteristics of the exonuclease as detailed above, the work described here was guided by the generation of a hypothetical model in which just one of the seven subunits of the .alpha.HL heptamer is modified to carry the exonuclease activity. FIG. 3 is a representation of the fusion construct assembled into a heteroheptamer with the exonuclease attached to a loop on the cis side of the protein. This model satisfies other additional desirable characteristics. An exonuclease fused on the cis side of the .alpha.HL heptamer under positive potential should release monophosphate nucleosides or ssDNA that will migrate from the cis to the trans side of the pore. This direction of migration is standard in much of the published literature of nanopore sensing. The genetic attachment of an exonuclease within a loop region also invariably means that the N and C terminal linkers can be designed to limit and constrain the mobility of the exonuclease in relation to the lumen of the pore.

[0308] In order to create a genetic fusion of the .alpha.-HL and the exonuclease proteins, genetic manipulation of the pre-existing expression plasmid pT7-SC1 carrying the wild-type .alpha.-HL gene was made (SEQ ID NO: 3). This plasmid carries the gene encoding the wild-type .alpha.-HL (SEQ ID NO: 1) without the benefit of any mutations that have been demonstrated to enhance the capacity of the pore to detect and discriminate monophosphate nucleosides. Unique BspEI restriction endonuclease sites were engineered into the .alpha.-HL gene at three specific locations, to enable insertion of the exonuclease gene, detailed below. Three plasmids are thus generated, with each one carrying just a single BspEI site for exonuclease gene infusion.

[0309] The first insertion site, L1, is located between residues T18 and T19 of the first loop region (N6-V20) of the .alpha.-hemolysin protein (SEQ ID NO: 6). The second insertion site, L2, is located between residues D44 and D45 of the start of the second loop region (D44-K50) of the .alpha.-hemolysin protein (SEQ ID NO: 7). The third insertion site, L2b, is located between residues K50 and K51 of the end of the second loop region (D44-K50) of the .alpha.-hemolysin protein (SEQ ID NO: 8).

[0310] Exonuclease genes were codon optimised for expression in E. coli and synthesised by GenScript Corporation (SEQ ID NOs: 10, 12, 15 and 16). Genes were flanked by regions encoding 10 residues of repeating serine-glycine. Such a protein sequence is believed to be substantially devoid of a defined secondary or tertiary structure. The terminal ends of the linkers were also defined by recognition sequences for the restriction endonuclease BspEI, as this sequence also encodes a serine and glycine that form part of the linker. The recognition site of this enzyme (TCCGGA) was similarly engineered into the three specific locations within the .alpha.HL gene to provide a means of inserting the exonuclease genes in frame at these defined locations.

[0311] The recombinant gene encodes a fusion protein consisting of: a portion of .alpha.HL; a 10 serine-glycine linker region; an exonuclease; a 10 serine-glycine linker region; and the remaining portion of .alpha.HL. Once made, the chimeric gene construct was sequenced and verified to be as shown in FIG. 4.

[0312] Both the N and C-terminii of .alpha.-hemolysin are suitable for genetic fusion to an enzyme. It has been shown that the 17 N-terminal residues, which constitute the amino latch, are dispensable for heptamer formation. Whilst it is not possible to delete more than 3 residues from the C-terminus, without effecting oligomerisation, it is already readily presented as a possible attachment point at the back of the cap domain (Walker, B. and Bayley, H. (1995). Key residues for membrane binding, oligomerization and pore-forming activity of Staphylococcal .alpha.-hemolysin identified by cysteine scanning mutagenesis and targeted chemical modification. The Journal of Biological Chemistry. 270, 23065-23071).

[0313] The attachment of enzymes at the N and C-terminus of .alpha.-hemolysin was carried out in a similar manner to that described above. The enzyme and .alpha.-hemolysin domains were again mediated by serine-glycine rich linkers to ensure the physical separation necessary for correct folding and spatial separation of each protein domain. The exact details of attachment are however detailed in a later section.

[0314] The hemolysin monomers were initially used as a wildtype monomer (wt), however we have shown that a HL-M113R/N139Q monomer shows improved base discrimination and the baseline was changed to this background. Further work showed that the base best resolution was achieved when an adapter molecule was attached to the L135C position, this was added to the hemolysin-exonuclease fusion in later constructs.

[0315] In the construct nomenclature, the monomer HL-M113R/N139Q is abbreviated to HL-RQ and the HL-M113R/N139Q/L135C monomer is abbreviated to HL-RQC. Therefore the fusion construct HL-(M113R/N139Q).sub.6(M113R/N139Q/L135C-EcoExoIII-L1-H6).sub.1 is shortened to HL-(RQ).sub.6(RQC-EcoExoIII-L1-H6).sub.1.

2 Results

2.1 Oligomerisation of Loop 1 Fusion Proteins

[0316] Water soluble .alpha.-hemolysin monomers can bind to and self-assemble on a lipid membrane to form a transmembrane pore of defined structure, via an intermediate heptameric prepore (Walker, B. and Bayley, H. (1995). Key residues for membrane binding, oligomerization and pore-forming activity of Staphylococcal .alpha.-hemolysin identified by cysteine scanning mutagenesis and targeted chemical modification. The Journal of Biological Chemistry. 270, 23065-23071). Fully assembled pores can then be isolated and recovered through SDS PAGE, for biophysical characterisation. Radiolabelled .alpha.-hemolysin monomers produced through in vitro transcription translation (IVTT) and oligomerised on purified rabbit red blood cell membranes, enable heptamers to be recovered from the gel using the autoradiograph as template. Modified monomers can also be incorporated into the heptamer in any number and at any of the subunit positions (1-7). The modified subunit also typically carries a poly-aspartate tail to allow the differential migration of homo or heteroheptamers on SDS PAGE for ease of purification for each variant (Braha, O., Walker, B., Cheley, S., Kasianowicz, J., Song, L., Gouaux, J. and Bayley, H. (1997). Designed protein pores as components for biosensors. Chemistry and Biology. 4, 497-505). Due to the size of the exonuclease proteins it was not expected that a poly-aspartate tail would be required on the fusion monomers, as the exonuclease alone should cause a significant shift in electrophoretic mobility to enable identification of individual heteroheptamers away from wild-type homoheptamer.

[0317] To determine if a mixture of HL-RQ and fusion monomers were able to form heteroheptamers [.sup.35S]L-methionine labelled HL-RQ and fusion proteins (HL-wt-EcoExoIII-L1-H6 (SEQ ID NO: 18), HL-RQC-EcoExoIII-L1-H6 (SEQ ID NO: 20), HL-RQC-EcoExoI-L1-H6 (SEQ ID NO: 22) and HL-RQC-TthRecJ-L1-H6 (SEQ ID NO: 24) were expressed by IVTT and oligomerised on purified rabbit red blood cell membranes. The autoradiograph of the gel identified several putative heptamer bands of differing size for all enzyme fusions (FIG. 5).

[0318] To characterise these heptamer bands and to identify the ratio of subunits within each, proteins were excised from the gel. Heating heptamer at 95.degree. C. for 10 minutes breaks the protein into its constitutive monomers, which can then be visualised on SDS PAGE for densitometry to determine the heptamer subunit composition. The different characteristic heptamer bands can then be identified as homo or heteroheptamers that consist of different ratios of wild-type and fusion .alpha.-HL monomers. This characterisation was performed for putative heptamer bands generated using both the HL-wt-EcoExoIII-L1-H6 and HL-RQC-EcoExoI-L1-H6 fusion proteins.

[0319] An importance for a sequencing application is that there preferentially be only one exonuclease moiety, ensuring bases are released only from a single DNA stand being processed at any one time. Electrophoretic migration of a 6:1 HL-monomer:HL-Exonuclease species away from other oligomers is therefore desired for ease of purification. Surprisingly, the HL-(RQ).sub.6(wt-EcoExoIII-L1-H6).sub.1 heptamer migrates to a position slightly lower down the gel than HL-(RQ).sub.7, despite the presence of a .about.36 kDa exonuclease being present on one of the subunits. This band also has a "doublet" appearance, possibly caused by incorrect incorporation of the fusion subunits amino latch due to the downstream insertion of the exonuclease in loop 1 or translation initiating at two points (the start of the fusion protein at hemolysin M1 and also at the first methionine of ExoIII) giving a mixed pool of fusion proteins. The EcoExoIII fusion protein gives formation of all theoretical heteroheptamer varieties and the wild-type and fusion protein homoheptamers. As a significantly smaller protein, .about.36 kDa, and with its N and C terminus co-localised it is perhaps unsurprising that EcoExoIII performs better than EcoExoI or TthRecJ as an exonuclease suitable for inserting into loop regions to give good heteroheptamer formation. Both the EcoExoI and TthRecJ fusion proteins give still show formation of heteroheptamers, although with a limited number of fusion monomer subunits, but in contrast the 6:1 heteroheptamer of EcoExoIII these 6:1 heteroheptamers migrate to a position identical to HL-(RQ).sub.7.

[0320] It is an important consideration that by varying the ratio of wild-type to fusion monomer different bands corresponding to the different homo and heteroheptamers were observed. This allows the control of homo or heteroheptamer formation based on the molar ratio of different monomer subunits, which is important for the preferential generation of HL-(RQ).sub.6 (RQ-Exonuclease-H6).sub.1 (FIG. 6).

[0321] The conditions for the HL-(RQ).sub.6(wt-EcoExoIII-L1-H6).sub.1 heteroheptamer formation were optimised by varying the ratios of monomer proteins. A preferred ratio of 100:1 gives predominately formation of one type of heteroheptamer, HL-(RQ).sub.6(wt-EcoExoIII-L1-H6).sub.1, as well as wild-type homoheptamer, HL-(RQ).sub.7. Affinity purification by the hexa-His tag of the fusion subunit then allows separation of heteroheptamer from HL-RQ homoheptamer.

[0322] The HL-(wt-EcoExoIII-L1-H6).sub.7 homoheptamer and the HL-(RQ).sub.6(wt-EcoExoIII-L1-H6).sub.1 heteroheptamer bands were excised from the gel and the protein pores recovered by re-hydration and maceration of the gel slice. These isolated heptamers were both able to insert into planar lipid bilayers to give single channel recordings. The single channel trace for the HL-(wt-EcoExoIII-L1-H6).sub.7 homoheptamer, however, exhibited numerous blocking events at .gtoreq.80 mV. This could be attributed to the presence of seven denatured exonuclease peptide chains surrounding the cap domain, as these events were significantly less pronounced with the HL-(RQ).sub.6(wt-EcoExoIII-L1-H6).sub.1 heteroheptamer. The HL-(RQ).sub.6(wt-EcoExoIII-L1-H6).sub.1 heteroheptamer gave an open pore current of .about.160 pA and a heteroheptamer containing the mutations necessary for base discrimination HL-(RQ).sub.6(RQC-EcoExoIII-L1-H6).sub.1 showed covalent attachment of the .beta.-cyclodexterin adapter molecule, which is characterised by an persistent current block to .about.90 pA.

[0323] The construction of a fusion protein involves the linking of two proteins or domains of proteins by a peptide linker. Linker sequence with regard to length, flexibility and hydrophilicity is important so as not to disturb the functions of the domains. The linker regions of loop 1 fusion constructs were initially designed to be of sufficient length to allow the correct folding of both the exonuclease and .alpha.-hemolysin domains of the fusion protein. However, of importance to the release of monophosphate nucleosides in a proximity to the pore lumen is the length and conformation of the linker regions. At some point, however, the linkers will become too short to connect the subunits in their native conformation without strain, which may be particularly detrimental to exonuclease activity and probably oligomerisation. The length of the linkers was therefore reduced to (SG).sub.4, (SG).sub.2 and (SG).sub.1 to determine the effect on oligomerisation efficiency. For oligomerisation the shortened (SG).sub.4 and (SG).sub.2 linkers had no adverse effect on the efficiency of heteroheptamer formation. The effect of these shortened linkers on the enzyme activity was not determined but the (SG).sub.4 fusion protein showed increased expression of soluble protein, which is an indicator of correctly folded proteins.

[0324] The conformational flexibility of these linkers will also have an effect on the exonuclease position in relation to the pore lumen at any given time. While conformational flexibility may be required at the N and C-terminus linker juncture too much flexibility in the rest of the linker may be detrimental to the co-localisation of the exonuclease active site to the pore lumen. The absence of a .beta.-carbon in glycine permits the polypeptide backbone to access dihedral angles that other amino acids cannot. Proline, as a cyclic imino acid, has no amide hydrogen to donate in hydrogen bonding so cannot fit into either .alpha.-helix or .beta.-strand secondary structure. Poly-proline regions are therefore stiff with the absence of secondary structure. By in vivo homologous recombination of PCR products the 10 serine-glycine linker was replaced with 5 proline residues. The use of a rigid polyproline "molecular rulers" was the determined for loop 1 EcoExoIII constructs as the linker between the c-terminus of the exonuclease and the N-terminus of .alpha.-hemolysin (FIG. 7).

[0325] Heteroheptamer formation was not abolished demonstrating the potential use of polyproline as a linker between the C-terminus of EcoExoIII and .alpha.-hemolysin T19 for the fusion protein. Although both fusion proteins showed a lower yield of heteroheptamers where the fusion protein is predominant the formation in particular of HL-(RQ).sub.6(RQC-EcoExoIII-L1-H6).sub.1 was unaffected.

[0326] The use of different length flexible linkers and alternative rigid linkers for optimising the position and conformational freedom of the exonuclease in relation to the pore lumen, as well as a method for optimising the formation of preferentially 6:1 heteroheptamers, has been demonstrated.

2.2 Mutagenesis and Oligomerisation of Loop 2 Fusion Proteins

[0327] The high yield of heteroheptamers generated by IVTT proteins for the EcoExoIII in loop 1 gave confidence for insertion of EcoExoIII into other loop regions, in particular both positions within loop 2 (FIG. 8). As this loop region connects two integral beta stands then it is likely that any enzymes that do not have a co-localised N and C-terminus will be too disruptive to the .alpha.-hemolysin domain, abolishing the ability of this protomer to oligomerize. Only very long linker regions may enable genetic attachment of EcoExoI or TthRecJ at these positions, due to their N and C-terminus localising to domains at distal ends of the respective enzymes.

[0328] The oligomerisation of the HL-RQC-EcoExoIII-L2a-H6 and HL-RQC-EcoExoIII-L2b-H6 fusion proteins was poor and only heptamers with an electrophoretic mobility similar to HL-(RQ).sub.7 and HL-(RQ).sub.6(RQC-EcoExoIII-L1-H6).sub.1 were observed. As oligomerisation of HL-RQC-EcoExoIII-L2a-H6 was slightly improved over the HL-RQC-EcoExoIII-L2b-H6 fusion protein, modification was carried out to improve the formation of heteroheptamer. Deletions of residues around the insertion site were made in an attempt to accommodate the terminal linker residues. In addition certain residues in loop 2 may be important for heptamer self-assembly. Sequence alignment of the .alpha.-hemolysin monomer with other .beta.-pore forming toxin monomers, LukS and LukF, indicates loop 2 is a highly conserved region and in particular residue D45, which is the residue immediately after the exonuclease linker juncture.

[0329] The crystal structure of the .alpha.-hemolysin heptamer also indicates that H48 is important to binding the amino latch of the adjoining subunit, at position T22 and D24 (Song, L., Hohaugh, M., Shustak, C., Cheley, S., Bayley, H. and Gouaux, E. (1996). Structure of Staphylococcal .alpha.-hemolysin, a heptameric transmembrane pore. Science. 274, 1859-1865). Attempts to modify the insertion point to accommodate and characterise these potentially important interactions were therefore made.

[0330] Around the loop 2a EcoExoIII insertion site (D44-D45) residues D45, K46 and N47 were sequentially deleted by in vivo homologous recombination of PCR products. To determine the importance of H48 the site of insertion was also changed to lie between N47-N49, deleting H48 entirely. As previously stated linker flexibility can have an important effect of interaction of domains within a fusion protein. Therefore the flexible 10 serine glycine linkers were replaced with rigid 8 proline linkers in an attempt to confer greater domain separation. Each loop 2 fusion construct was expressed via IVTT and mixed in a 2.5:1 ratio with wild-type in the presence of purified rabbit red blood cell membranes. Any improvement in oligomerisation was determined by densitometry of the autoradiograph (FIG. 9).

[0331] Oligomerisation of the L2 fusion protein was abolished when the flexibility of the linker was changed to a more rigid polyproline linker. In addition deletion of H48 and positioning of the exonuclease insertion between N47 and N49 abolished heteroheptamer formation. It appeared that only deletion of residues from around the D44-D45 insertion site improved oligomerisation of the fusion protein. To determine if this could further be improved residue D45 was added back to the loop 2 deletion fusion proteins in a position adjacent to D44, before the EcoExoIII insertion site (FIG. 10).

[0332] Heteroheptamer formation was not affected by the position of residue D45 and indeed adding back this residue to all fusion proteins was detrimental to oligomerisation, possibly as it reduced the number of residues deleted to accommodate the exonuclease by one as a consequence. Accommodating the exonuclease is therefore the key to improving the oligomerisation of the loop 2 fusion protein (as in SEQ ID NO: 26). The insertion site was varied further in an attempt to determine how close to the .beta..sub.2 strand the insertion site could be. The position within the loop region could be important for the relative positioning of the EcoExoIII active site in relation to the pore lumen and it is predicted the closer to .beta..sub.2 the better the presentation of cleaved monophosphate nucleosides. In each fusion construct the insertion site was not only varied but the following three residues of .alpha.-hemolysin at the C-terminus of EcoExoIII were deleted in order to accommodate the exonuclease. Oligomerisation of the alternative loop 2 fusion proteins HL-(RQ).sub.6(RQC-EcoExoIII-L2-D45-N47.DELTA.-H6).sub.1, HL-(RQ).sub.6(RQC-EcoExoIII-L2-F42-D46.DELTA.-H6).sub.1 and HL-(RQ).sub.6(RQC-EcoExoIII-L2-I43-D46.DELTA.-H6).sub.1 determined that the insertion point can lie anywhere within the loop region but as soon as it breaks a region of secondary structure all oligomerisation is abolished (FIG. 10).

[0333] Whilst the linkers in the loop 2 fusion protein require some degree of flexibility, as determined by the fact that rigid polyproline linkers could not substitute, the length can be reduced. The linker regions were shortened as for the loop 1 EcoExoIII fusion protein to (SG).sub.4, (SG).sub.3, (SG).sub.2 and (SG).sub.1 to determine the effect on oligomerisation efficiency. For oligomerisation the shortened (SG).sub.4, (SG).sub.3 and (SG).sub.2 linkers had no adverse effect on the efficiency of heteroheptamer formation. The effect of these shortened linkers on the enzyme activity was not, however, determined.

2.3 Genetic Attachment at the N and C-Terminus of .alpha.-Hemolysin

[0334] Genetic attachment of two proteins, typically an enzyme to an antibody, has previously focused on the fusion of one protein's C-terminus to another protein's N-terminus, mediated by a peptide linker. As previously mentioned strategies for the attachment of a DNA handling enzyme to the C or N-terminus of .alpha.-hemolysin was considered, in particular the attachment of EcoExoI and the Klenow fragment. Attachment of EcoExoI at the C-terminus was mediated by five different linkers in order to determine the optimum fusion protein for oligomerisation. As the C-terminus is at the back of the .alpha.-hemolysin cap domain a turn of approximately 180.degree. was desired. In order to initiate this turn either a Gly-Asp or Trp-Pro-Val motif was added at the start of the linker peptide. Two linker peptides were also used, either a flexible 16 serine-glycine or a 12 polyproline. As early results from the EcoExoI loop 1 fusion protein indicated that the 6:1 heteroheptamer had the same electrophoretic mobility as wild-type homoheptamer then a mixture of radiolabelled and non-radio labelled IVTT monomers were used for oligomerisation. Monomers were mixed in a 1:1 ratio and oligomerised on purified rabbit red blood cell membranes (FIG. 11).

[0335] Although the predominant fusion protein produced is the 6:1 heteroheptamer this migrates to the same position as the HL-(RQ).sub.7 homoheptamer. Therefore the proteins corresponding to HL-(RQ).sub.5(RQC-EcoExoI-Cter-{SG}8-H6).sub.2, HL-(RQ).sub.5(RQC-EcoExoI-Cter-DG{SG}8-H6).sub.2 as well as the HL-(RQ).sub.5(RQC-EcoExoI-L1-H6).sub.2 heteroheptamer from an earlier experiment were purified from SDS and the ability to insert into planar lipid bilayers determined. All heteroheptamers were capable of inserting into the lipid bilayer to give single channel recordings.

[0336] The success for fusion of the EcoExoI at the C-terminus of .alpha.-hemolysin mediated by an (SG).sub.8 and DG(SG).sub.8 peptide linker provides the method for the later attachment of other DNA handling enzymes via genetic fusion, such as the Klenow fragment (SEQ ID NOs: 28 and 30). The advantages of the Klenow fragment are the fact it provides a molecular motor for strand sequencing and also shows some resistance to SDS PAGE (Akeson, Personal Communication).

2.4 Non-SDS PAGE Purification of Heptamers

[0337] Sodium dodecyl sulphate (SDS) is an anionic surfactant that is highly denaturing to proteins, due to its ability to disrupt non-covalent bonds and bind to the peptide chain. As existing heptamer purification techniques rely on the use of SDS PAGE then the effect of this detergent on EcoExoIII was determined by a fluorescence based activity assay (FIG. 12, left panel).

[0338] Even a low concentration of SDS abolished EcoExoIII activity for the native enzyme, making the classical SDS PAGE purification of heptamers denaturing with regard to the exonuclease moiety of a fusion protein heteroheptamer. An alternative purification method was developed therefore using the alternative detergent, n-dodecyl-D-maltopyranoside (DDM). The effect of this surfactant on the EcoExoIII was determined and found to be non-denaturing to the native enzyme (FIG. 12, right panel). Following oligomerisation on rabbit red blood cell membranes instead of purifying heptamers via SDS PAGE the lipid membranes were dissolved by addition of 0.1% DDM for 15 minutes. Heteroheptamers were then purified away from the wild-type homoheptamer by affinity purification to the hexa-His tag on the C-terminus of the fusion protein. A buffer exchange further removed any surfactant and heptamers were then used for single channel recordings. This method does not distinguish entirely between heteroheptamers so the formation of 5:2 was limited by optimising the ratios of monomers mixed.

[0339] Purification via DDM extraction produced heptamers that showed an increased number of blocking events and surfactant behaviour on the lipid bilayer in single channel recordings. Whilst the cause of this instability remains undetermined, it is likely to be a result of other membrane proteins released from the rabbit red blood cell membranes, either affecting the lipid bilayer directly or else increasing the protein associated surfactant carryover. Oligomerisation of .alpha.-hemolysin monomers is classically facilitated either on purified rabbit red blood cell membranes or deoxycholate micelles. The yield of heptamer from deoxycholate is too poor in this instance to be of use and as previously mentioned the use of purified rabbit red blood cell membranes led to lipid bilayer instability. As an alternative, synthetic lipid vesicles were developed based on the lipid composition of rabbit red blood cell membranes, which lack other the membrane proteins of rabbit red blood cell membranes. These are composed of 30% cholesterol, 30% phosphatidylcholine (PC), 20% phosphatidylethanolamine (PE), 10% sphingomyelin (SM) and 10% phosphatidylserine (PS). The synthetic lipid vesicles developed here give approximately the same efficiency of heptamerisation as observed for rabbit red blood cell membranes. Heptamers purified from these synthetic lipid vesicles by DDM extraction also showed a dramatic decrease in the occurrences of lipid bilayer instability.

[0340] Oligomerisation and DDM purification of heptamers was also determined for E. coli expressed proteins. Expression of wild-type and fusion monomers in E. coli gives a concentration sufficient for large scale production of enzyme pores, typically 3 mg ml.sup.-1 and 1 mg ml.sup.-1 respectively. Monomers were oligomerised on synthetic lipid vesicles at a ratio of 100:1 (wild-type:fusion) and purified as detailed previously (FIG. 13).

[0341] High level E. coli expression of monomers that can be oligomerised on synthetic lipid vesicles was achieved. Purification of the 6:1 heteroheptamer was also achieved in conditions that are non-denaturing to enzymes, ensuring activity of the pores exonuclease moiety.

2.5 Enzymatic Activity of Fusion Protein Heptamers

[0342] As the terminal ends of the enzyme are conformationally constrained within loop regions of the .alpha.-hemolysin monomer then the dynamic movements of the exonuclease domains necessary for activity could be impacted. The native enzyme (Exonuclease III, NEB)) was able to cleave nucleotides from the dsDNA substrate to a point where the sense strand was no longer of sufficient length to hybridise to the antisense strand (.about.8 bp). On dissociation of the DNA strands the fluorophore, at the 5' end of the sense strand, was sufficiently spatially separated from its quencher pair, at the 3' end of the antisense strand, giving a fluorescence increase relative to the enzyme activity. The activity of the native enzyme was also determined in a range of salt concentrations (0-1M KCl). Activity of the native enzyme was demonstrated in concentrations .ltoreq.300 mM KCl, which is within the experimental conditions required for single channel recordings and base discrimination. To determine if exonuclease activity of the EcoExoIII moiety on the fusion proteins was maintained after genetic attachment and oligomerisation, its activity was determined in this same fluorescence based DNA degradation assay (FIG. 14).

[0343] The EcoExoIII fusion proteins demonstrated retained exonuclease activity but as yet this is a qualitative rather than quantitative indication as amount of fusion protein was not determined. Therefore the effect of genetic fusion of the EcoExoIII to an .alpha.-hemolysin monomer on the rate of exonuclease activity cannot be determined as yet.

[0344] The exonuclease activity of the fusion protein was checked at all stages of purification and found to retain activity. Following oligomerisation and DDM purification the activity of fully formed pores was also checked and found to show some exonuclease activity. This demonstrates the ability to genetically couple an enzyme to a protein pore and still retain activity of the enzyme after expression and oligomerisation to a fully assembled pore.

2.6 Pore Forming Activity of Fusion Protein Heptamers.

[0345] As previously mentioned in the text the ability of a variety of different enzyme pore constructs to insert into lipid bilayers for single channel recordings has been shown. We have demonstrated that changes to the .beta.-barrel of the .alpha.-hemolysin protein can enable covalent linkage and stabilisation of an adapter molecule for continuous base detection. For this the pore preferentially requires 6 subunits with mutations M113R/N139Q and 1 subunit with mutations M113R/N139Q/L135C. To determine if the exonuclease domain of the fusion protein within loop regions affected the ability of the pore to discriminate bases the M113R/N139Q/L135C mutations were made in the fusion constructs. As base discrimination preferentially requires a heteroheptamer with only one subunit carrying the L135C mutation and the enzyme pore preferentially one subunit being a fusion protein, the L135C mutation was made in the fusion protein. The wild-type M113R and N139Q construct from previous work was used for the other subunits. E. coli expressed HL-RQ and HL-RQC-EcoExoIII-L2-D46-N47.DELTA.-H6 were oligomerised on synthetic lipid vesicles (at a ratio of 100:1) and purified by DDM extraction. The exonuclease activity of the fully formed pore was determined and indicated correct folding of the exonuclease moiety. The protein was also used for electrophysiology to determine firstly pore functionality and secondly if base discrimination was possible (FIG. 19.).

[0346] The 6:1 heteroheptamer can be inserted into a lipid bilayer and a stable transmembrane current established. This current can be modulated by the introduction of .beta.-cyclodexterin, and is further reduced by the addition of monophosphate nucleosides. The presence of the exonuclease domain appears to have no detrimental effect on current flow or the base discrimination by the pore. Although the work shown is for a heteroheptamer incorporating a fusion protein with the insertion of EcoExoIII at the loop 2 position, similar data was acquired for the loop 1 heteroheptamers.

TABLE-US-00004 Sequence listing SEQ ID NO: 1 1 ATGGCAGATT CTGATATTAA TATTAAAACC GGTACTACAG ATATTGGAAG CAATACTACA GTAAAAACAG 71 GTGATTTAGT CACTTATGAT AAAGAAAATG GCATGCACAA AAAAGTATTT TATAGTTTTA TCGATGATAA 141 AAATCACAAT AAAAAACTGC TAGTTATTAG AACAAAAGGT ACCATTGCTG GTCAATATAG AGTTTATAGC 211 GAAGAAGGTG CTAACAAAAG TGGTTTAGCC TGGCCTTCAG CCTTTAAGGT ACAGTTGCAA CTACCTGATA 281 ATGAAGTAGC TCAAATATCT GATTACTATC CAAGAAATTC GATTGATACA AAAGAGTATA TGAGTACTTT 351 AACTTATGGA TTCAACGGTA ATGTTACTGG TGATGATACA GGAAAAATTG GCGGCCTTAT TGGTGCAAAT 421 GTTTCGATTG GTCATACACT GAAATATGTT CAACCTGATT TCAAAACAAT TTTAGAGAGC CCAACTGATA 491 AAAAAGTAGG CTGGAAAGTG ATATTTAACA ATATGGTGAA TCAAAATTGG GGACCATACG ATCGAGATTC 561 TTGGAACCCG GTATATGGCA ATCAACTTTT CATGAAAACT AGAAATGGTT CTATGAAAGC AGCAGATAAC 631 TTCCTTGATC CTAACAAAGC AAGTTCTCTA TTATCTTCAG GGTTTTCACC AGACTTCGCT ACAGTTATTA 701 CTATGGATAG AAAAGCATCC AAACAACAAA CAAATATAGA TGTAATATAC GAACGAGTTC GTGATGATTA 771 CCAATTGCAT TGGACTTCAA CAAATTGGAA AGGTACCAAT ACTAAAGATA AATGGACAGA TCGTTCTTCA 841 GAAAGATATA AAATCGATTG GGAAAAAGAA GAAATGACAA AT SEQ ID NO: 2 1 ADSDINIKTG TTDIGSNTTV KTGDLVTYDK ENGMHKKVFY SFIDDKNHNK KLLVIRTKGT IAGQYRVYSE 71 EGANKSGLAW PSAFKVQLQL PDNEVAQISD YYPRNSIDTK EYMSTLTYGF NGNVTGDDTG KIGGLIGANV 141 SIGHTLKYVQ PDFKTILESP TDKKVGWKVI FNNMVNQNWG PYDRDSWNPV YGNQLFMKTR NGSMKAADNF 211 LDPNKASSLL SSGFSPDFAT VITMDRKASK QQTNIDVIYE RVRDDYQLHW TSTNWKGTNT KDKWTDRSSE 281 RYKIDWEKEE MTN SEQ ID NO: 3 1 ATGGCAGATT CTGATATTAA TATTAAAACC GGTACTACAG ATATTGGAAG CAATACTACA GTAAAAACAG 71 GTGATTTAGT CACTTATGAT AAAGAAAATG GCATGCACAA AAAAGTATTT TATAGTTTTA TCGATGATAA 141 AAATCACAAT AAAAAACTGC TAGTTATTAG AACAAAAGGT ACCATTGCTG GTCAATATAG AGTTTATAGC 211 GAAGAAGGTG CTAACAAAAG TGGTTTAGCC TGGCCTTCAG CCTTTAAGGT ACAGTTGCAA CTACCTGATA 281 ATGAAGTAGC TCAAATATCT GATTACTATC CAAGAAATTC GATTGATACA AAAGAGTATA GGAGTACTTT 351 AACTTATGGA TTCAACGGTA ATGTTACTGG TGATGATACA GGAAAAATTG GCGGCCTTAT TGGTGCACAA 421 GTTTCGATTG GTCATACACT GAAATATGTT CAACCTGATT TCAAAACAAT TTTAGAGAGC CCAACTGATA 491 AAAAAGTAGG CTGGAAAGTG ATATTTAACA ATATGGTGAA TCAAAATTGG GGACCATACG ATCGAGATTC 561 TTGGAACCCG GTATATGGCA ATCAACTTTT CATGAAAACT AGAAATGGTT CTATGAAAGC AGCAGATAAC 631 TTCCTTGATC CTAACAAAGC AAGTTCTCTA TTATCTTCAG GGTTTTCACC AGACTTCGCT ACAGTTATTA 701 CTATGGATAG AAAAGCATCC AAACAACAAA CAAATATAGA TGTAATATAC GAACGAGTTC GTGATGATTA 771 CCAATTGCAT TGGACTTCAA CAAATTGGAA AGGTACCAAT ACTAAAGATA AATGGACAGA TCGTTCTTCA 841 GAAAGATATA AAATCGATTG GGAAAAAGAA GAAATGACAA AT SEQ ID NO: 4 1 ADSDINIKTG TTDIGSNTTV KTGDLVTYDK ENGMHKKVFY SFIDDKNHNK KLLVIRTKGT IAGQYRVYSE 71 EGANKSGLAW PSAFKVQLQL PDNEVAQISD YYPRNSIDTK EYRSTLTYGF NGNVTGDDTG KIGGLIGAQV 141 SIGHTLKYVQ PDFKTILESP TDKKVGWKVI FNNMVNQNWG PYDRDSWNPV YGNQLFMKTR NGSMKAADNF 211 LDPNKASSLL SSGFSPDFAT VITMDRKASK QQTNIDVIYE RVRDDYQLHW TSTNWKGTNT KDKWTDRSSE 281 RYKIDWEKEE MTN SEQ ID NO: 5 1 TTCTTGAAGA CGAAAGGGCC TCGTGATACG CCTATTTTTA TAGGTTAATG TCATGATAAT AATGGTTTCT 71 TAGACGTCAG GTGGCACTTT TCGGGGAAAT GTGCGCGGAA CCCCTATTTG TTTATTTTTC TAAATACATT 141 CAAATATGTA TCCGCTCATG AGACAATAAC CCTGATAAAT GCTTCAATAA TATTGAAAAA GGAAGAGTAT 211 GAGTATTCAA CATTTCCGTG TCGCCCTTAT TCCCTTTTTT GCGGCATTTT GCCTTCCTGT TTTTGCTCAC 281 CCAGAAACGC TGGTGAAAGT AAAAGATGCT GAAGATCAGT TGGGTGCACG AGTGGGTTAC ATCGAACTGG 351 ATCTCAACAG CGGTAAGATC CTTGAGAGTT TTCGCCCCGA AGAACGTTTT CCAATGATGA GCACTTTTAA 421 AGTTCTGCTA TGTGGCGCGG TATTATCCCG TGTTGACGCC GGGCAAGAGC AACTCGGTCG CCGCATACAC 491 TATTCTCAGA ATGACTTGGT TGAGTACTCA CCAGTCACAG AAAAGCATCT TACGGATGGC ATGACAGTAA 561 GAGAATTATG CAGTGCTGCC ATAACCATGA GTGATAACAC TGCGGCCAAC TTACTTCTGA CAACGATCGG 631 AGGACCGAAG GAGCTAACCG CTTTTTTGCA CAACATGGGG GATCATGTAA CTCGCCTTGA TCGTTGGGAA 701 CCGGAGCTGA ATGAAGCCAT ACCAAACGAC GAGCGTGACA CCACGATGCC TGCAGCAATG GCAACAACGT 771 TGCGCAAACT ATTAACTGGC GAACTACTTA CTCTAGCTTC CCGGCAACAA TTAATAGACT GGATGGAGGC 841 GGATAAAGTT GCAGGACCAC TTCTGCGCTC GGCCCTTCCG GCTGGCTGGT TTATTGCTGA TAAATCTGGA 911 GCCGGTGAGC GTGGGTCTCG CGGTATCATT GCAGCACTGG GGCCAGATGG TAAGCCCTCC CGTATCGTAG 981 TTATCTACAC GACGGGGAGT CAGGCAACTA TGGATGAACG AAATAGACAG ATCGCTGAGA TAGGTGCCTC 1051 ACTGATTAAG CATTGGTAAC TGTCAGACCA AGTTTACTCA TATATACTTT AGATTGATTT AAAACTTCAT 1121 TTTTAATTTA AAAGGATCTA GGTGAAGATC CTTTTTGATA ATCTCATGAC CAAAATCCCT TAACGTGAGT 1191 TTTCGTTCCA CTGAGCGTCA GACCCCGTAG AAAAGATCAA AGGATCTTCT TGAGATCCTT TTTTTCTGCG 1261 CGTAATCTGC TGCTTGCAAA CAAAAAAACC ACCGCTACCA GCGGTGGTTT GTTTGCCGGA TCAAGAGCTA 1331 CCAACTCTTT TTCCGAAGGT AACTGGCTTC AGCAGAGCGC AGATACCAAA TACTGTCCTT CTAGTGTAGC 1401 CGTAGTTAGG CCACCACTTC AAGAACTCTG TAGCACCGCC TACATACCTC GCTCTGCTAA TCCTGTTACC 1471 AGTGGCTGCT GCCAGTGGCG ATAAGTCGTG TCTTACCGGG TTGGACTCAA GACGATAGTT ACCGGATAAG 1541 GCGCAGCGGT CGGGCTGAAC GGGGGGTTCG TGCACACAGC CCAGCTTGGA GCGAACGACC TACACCGAAC 1611 TGAGATACCT ACAGCGTGAG CTATGAGAAA GCGCCACGCT TCCCGAAGGG AGAAAGGCGG ACAGGTATCC 1681 GGTAAGCGGC AGGGTCGGAA CAGGAGAGCG CACGAGGGAG CTTCCAGGGG GAAACGCCTG GTATCTTTAT 1751 AGTCCTGTCG GGTTTCGCCA CCTCTGACTT GAGCGTCGAT TTTTGTGATG CTCGTCAGGG GGGCGGAGCC 1821 TATGGAAAAA CGCCAGCAAC GCGTCCTTTT TACGGTTCCT GGCCTTTTGC TGGCCTTTTG CTCACATGTT 1891 CTTTCCTGCG TTATCCCCTG ATTCTGTGGA TAACCGTATT ACCGCCTTTG AGTGAGCTGA TACCGCTCGC 1961 CGCAGCCGAA CGACCGAGCG CAGCGAGTCA GTGAGCGAGG AAGCGGAAGA GCGCCTGATG CGGTATTTTC 2031 TCCTTACGCA TCTGTGCGGT ATTTCACACC GCATATATGG TGCACTCTCA GTACAATCTG CTCTGATGCC 2101 GCATAGTTAA GCCAGTATAC ACTCCGCTAT CGCTACGTGA CTGGGTCATG GCTGCGCCCC GACACCCGCC 2171 AACACCCGCT GACGCGCCCT GACGGGCTTG TCTGCTCCCG GCATCCGCTT ACAGACAAGC TGTGACCGTC 2241 TCCGGGAGCT GCATGTGTCA GAGGTTTTCA CCGTCATCAC CGAAACGCGC GAGGCAGCGC TCTCCCTTAT 2311 GCGACTCCTG CATTAGGAAG CAGCCCAGTA GTAGGTTGAG GCCGTTGAGC ACCGCCGCCG CAAGGAATGG 2381 TGCATGCAAG GAGATGGCGC CCAACAGTCC CCCGGCCACG GGGCCTGCCA CCATACCCAC GCCGAAACAA 2451 GCGCTCATGA GCCCGAAGTG GCGAGCCCGA TCTTCCCCAT CGGTGATGTC GGCGATATAG GCGCCAGCAA 2521 CCGCACCTGT GGCGCCGGTG ATGCCGGCCA CGATGCGTCC GGCGTAGAGG ATCGAGATCT AGCCCGCCTA 2591 ATGAGCGGGC TTTTTTTTAG ATCTCGATCC CGCGAAATTA ATACGACTCA CTATAGGGAG ACCACAACGG 2661 TTTCCCTCTA GAAATAATTT TGTTTAACTT TAAGAAGGAG ATATACATAT GGCAGATTCT GATATTAATA 2731 TTAAAACCGG TACTACAGAT ATTGGAAGCA ATACTACAGT AAAAACAGGT GATTTAGTCA CTTATGATAA 2801 AGAAAATGGC ATGCACAAAA AAGTATTTTA TAGTTTTATC GATGATAAAA ATCACAATAA AAAACTGCTA 2871 GTTATTAGAA CAAAAGGTAC CATTGCTGGT CAATATAGAG TTTATAGCGA AGAAGGTGCT AACAAAAGTG 2941 GTTTAGCCTG GCCTTCAGCC TTTAAGGTAC AGTTGCAACT ACCTGATAAT GAAGTAGCTC AAATATCTGA 3011 TTACTATCCA AGAAATTCGA TTGATACAAA AGAGTATATG AGTACTTTAA CTTATGGATT CAACGGTAAT 3081 GTTACTGGTG ATGATACAGG AAAAATTGGC GGCCTTATTG GTGCAAATGT TTCGATTGGT CATACACTGA 3151 AATATGTTCA ACCTGATTTC AAAACAATTT TAGAGAGCCC AACTGATAAA AAAGTAGGCT GGAAAGTGAT 3221 ATTTAACAAT ATGGTGAATC AAAATTGGGG ACCATACGAT CGAGATTCTT GGAACCCGGT ATATGGCAAT

3291 CAACTTTTCA TGAAAACTAG AAATGGTTCT ATGAAAGCAG CAGATAACTT CCTTGATCCT AACAAAGCAA 3361 GTTCTCTATT ATCTTCAGGG TTTTCACCAG ACTTCGCTAC AGTTATTACT ATGGATAGAA AAGCATCCAA 3431 ACAACAAACA AATATAGATG TAATATACGA ACGAGTTCGT GATGATTACC AATTGCATTG GACTTCAACA 3501 AATTGGAAAG GTACCAATAC TAAAGATAAA TGGACAGATC GTTCTTCAGA AAGATATAAA ATCGATTGGG 3571 AAAAAGAAGA AATGACAAAT TAATGTAAAT TATTTGTACA TGTACAAATA AATATAATTT ATAACTTTAG 3641 CCGAAAGCTT GGATCCGGCT GCTAACAAAG CCCGAAAGGA AGCTGAGTTG GCTGCTGCCA CCGCTGAGCA 3711 ATAACTAGCA TAACCCCTTG GGGCCTCTAA ACGGGTCTTG AGGGGTTTTT TGCTGAAAGG AGGAACTATA 3781 TATAATTCGA GCTCGGTACC CACCCCGGTT GATAATCAGA AAAGCCCCAA AAACAGGAAG ATTGTATAAG 3851 CAAATATTTA AATTGTAAAC GTTAATATTT TGTTAAAATT CGCGTTAAAT TTTTGTTAAA TCAGCTCATT 3921 TTTTAACCAA TAGGCCGAAA TCGGCAAAAT CCCTTATAAA TCAAAAGAAT AGACCGAGAT AGGGTTGAGT 3991 GTTGTTCCAG TTTGGAACAA GAGTCCAGTA TTAAAGAACG TGGACTCCAA CGTCAAAGGG CGAAAAACCG 4061 TCTATCAGGG CGATGGCCCA CTACGTGAAC CATCACCCTA ATCAAGTTTT TTGGGGTCGA GGTGCCGTAA 4131 AGCACTAAAT CGGAACCCTA AAGGGATGCC CCGATTTAGA GCTTGACGGG GAAAGCCGGC GAACGTGGCG 4201 AGAAAGGAAG GGAAGAAAGC GAAAGGAGCG GGCGCTAGGG CGCTGGCAAG TGTAGCGGTC ACGCTGCGCG 4271 TAACCACCAC ACCCGCCGCG CTTAATGCGC CGCTACAGGG CGCGTGGGGA TCCTCTAGAG TCGACCTGCA 4341 GGCATGCAAG CTATCCCGCA AGAGGCCCGG CAGTACCGGC ATAACCAAGC CTATGCCTAC AGCATCCAGG 4411 GTGACGGTGC CGAGGATGAC GATGAGCGCA TTGTTAGATT TCATACACGG TGCCTGACTG CGTTAGCAAT 4481 TTAACTGTGA TAAACTACCG CATTAAAGCT AGCTTATCGA TGATAAGCTG TCAAACATGA GAA SEQ ID NO: 6 1 ATGGCAGATT CTGATATTAA TATTAAAACC GGTACTACAG ATATTGGAAG CAATACTTCC GGAACAGTAA 71 AAACAGGTGA TTTAGTCACT TATGATAAAG AAAATGGCAT GCACAAAAAA GTATTTTATA GTTTTATCGA 141 TGATAAAAAT CACAATAAAA AACTGCTAGT TATTAGAACA AAAGGTACCA TTGCTGGTCA ATATAGAGTT 211 TATAGCGAAG AAGGTGCTAA CAAAAGTGGT TTAGCCTGGC CTTCAGCCTT TAAGGTACAG TTGCAACTAC 281 CTGATAATGA AGTAGCTCAA ATATCTGATT ACTATCCAAG AAATTCGATT GATACAAAAG AGTATATGAG 351 TACTTTAACT TATGGATTCA ACGGTAATGT TACTGGTGAT GATACAGGAA AAATTGGCGG CCTTATTGGT 421 GCAAATGTTT CGATTGGTCA TACACTGAAA TATGTTCAAC CTGATTTCAA AACAATTTTA GAGAGCCCAA 491 CTGATAAAAA AGTAGGCTGG AAAGTGATAT TTAACAATAT GGTGAATCAA AATTGGGGAC CATACGATCG 561 AGATTCTTGG AACCCGGTAT ATGGCAATCA ACTTTTCATG AAAACTAGAA ATGGTTCTAT GAAAGCAGCA 631 GATAACTTCC TTGATCCTAA CAAAGCAAGT TCTCTATTAT CTTCAGGGTT TTCACCAGAC TTCGCTACAG 701 TTATTACTAT GGATAGAAAA GCATCCAAAC AACAAACAAA TATAGATGTA ATATACGAAC GAGTTCGTGA 771 TGATTACCAA TTGCATTGGA CTTCAACAAA TTGGAAAGGT ACCAATACTA AAGATAAATG GACAGATCGT 841 TCTTCAGAAA GATATAAAAT CGATTGGGAA AAAGAAGAAA TGACAAAT SEQ ID NO: 7 1 ATGGCAGATT CTGATATTAA TATTAAAACC GGTACTACAG ATATTGGAAG CAATACTACA GTAAAAACAG 71 GTGATTTAGT CACTTATGAT AAAGAAAATG GCATGCACAA AAAAGTATTT TATAGTTTTA TCGATTCCGG 141 AGATAAAAAT CACAATAAAA AACTGCTAGT TATTAGAACA AAAGGTACCA TTGCTGGTCA ATATAGAGTT 211 TATAGCGAAG AAGGTGCTAA CAAAAGTGGT TTAGCCTGGC CTTCAGCCTT TAAGGTACAG TTGCAACTAC 281 CTGATAATGA AGTAGCTCAA ATATCTGATT ACTATCCAAG AAATTCGATT GATACAAAAG AGTATATGAG 351 TACTTTAACT TATGGATTCA ACGGTAATGT TACTGGTGAT GATACAGGAA AAATTGGCGG CCTTATTGGT 421 GCAAATGTTT CGATTGGTCA TACACTGAAA TATGTTCAAC CTGATTTCAA AACAATTTTA GAGAGCCCAA 491 CTGATAAAAA AGTAGGCTGG AAAGTGATAT TTAACAATAT GGTGAATCAA AATTGGGGAC CATACGATCG 561 AGATTCTTGG AACCCGGTAT ATGGCAATCA ACTTTTCATG AAAACTAGAA ATGGTTCTAT GAAAGCAGCA 631 GATAACTTCC TTGATCCTAA CAAAGCAAGT TCTCTATTAT CTTCAGGGTT TTCACCAGAC TTCGCTACAG 701 TTATTACTAT GGATAGAAAA GCATCCAAAC AACAAACAAA TATAGATGTA ATATACGAAC GAGTTCGTGA 771 TGATTACCAA TTGCATTGGA CTTCAACAAA TTGGAAAGGT ACCAATACTA AAGATAAATG GACAGATCGT 841 TCTTCAGAAA GATATAAAAT CGATTGGGAA AAAGAAGAAA TGACAAAT SEQ ID NO: 8 1 ATGGCAGATT CTGATATTAA TATTAAAACC GGTACTACAG ATATTGGAAG CAATACTACA GTAAAAACAG 71 GTGATTTAGT CACTTATGAT AAAGAAAATG GCATGCACAA AAAAGTATTT TATAGTTTTA TCGATGATAA 141 AAATCACAAT AAATCCGGAA AACTGCTAGT TATTAGAACA AAAGGTACCA TTGCTGGTCA ATATAGAGTT 211 TATAGCGAAG AAGGTGCTAA CAAAAGTGGT TTAGCCTGGC CTTCAGGGTT TAAGGTACAG TTGCAACTAC 281 CTGATAATGA AGTAGCTCAA ATATCTGATT ACTATCCAAG AAATTCGATT GATACAAAAG AGTATATGAG 351 TACTTTAACT TATGGATTCA ACGGTAATGT TACTGGTGAT GATACAGGAA AAATTGGCGG CCTTATTGGT 421 GCAAATGTTT CGATTGGTCA TACACTGAAA TATGTTCAAC CTGATTTCAA AACAATTTTA GAGAGCCCAA 491 CTGATAAAAA AGTAGGCTGG AAAGTGATAT TTAACAATAT GGTGAATCAA AATTGGGGAC CATACGATCG 561 AGATTCTTGG AACCCGGTAT ATGGCAATCA ACTTTTCATG AAAACTAGAA ATGGTTCTAT GAAAGCAGCA 631 GATAACTTCC TTGATCCTAA CAAAGCAAGT TCTCTATTAT CTTCAGGGTT TTCACCAGAC TTCGCTACAG 701 TTATTACTAT GGATAGAAAA GCATCCAAAC AACAAACAAA TATAGATGTA ATATACGAAC GAGTTCGTGA 771 TGATTACCAA TTGCATTGGA CTTCAACAAA TTGGAAAGGT ACCAATACTA AAGATAAATG GACAGATCGT 841 TCTTCAGAAA GATATAAAAT CGATTGGGAA AAAGAAGAAA TGACAAAT SEQ ID NO: 9 1 ATGAAATTTG TCTCTTTTAA TATCAACGGC CTGCGCGCCA GACCTCACCA GCTTGAAGCC ATCGTCGAAA 71 AGCACCAACC GGATGTGATT GGCCTGCAGG AGACAAAAGT TCATGACGAT ATGTTTCCGC TCGAAGAGGT 141 GGCGAAGCTC GGCTACAACG TGTTTTATCA CGGGCAGAAA GGCCATTATG GCGTGGCGCT GCTGACCAAA 211 GAGACGCCGA TTGCCGTGCG TCGCGGCTTT CCCGGTGACG ACGAAGAGGC GCAGCGGCGG ATTATTATGG 281 CGGAAATCCC CTCACTGCTG GGTAATGTCA CCGTGATCAA CGGTTACTTC CCGCAGGGTG AAAGCCGCGA 351 CCATCCGATA AAATTGGCGG CAAAAGCGCA GTTTTATCAG AATCTGCAAA ACTACCTGGA AACCGAACTC 421 AAACGTGATA ATCCGGTACT GATTATGGGC GATATGAATA TCAGCCCTAC AGATCTGGAT ATCGGCATTG 491 GCGAAGAAAA CCGTAAGCGC TGGCTGCGTA CCGGTAAATG CTCTTTCCTG CCGGAAGAGC GCGAATGGAT 561 GGACAGGCTG ATGAGCTGGG GGTTGGTCGA TACCTTCCGC CATGCGAATC CGCAAACAGC AGATCGTTTC 631 TCATGGTTTG ATTACCGCTC AAAAGGTTTT GACGATAACC GTGGTCTGCG CATCGACCTG CTGCTCGCCA 701 GCCAACCGCT GGCAGAATGT TGCGTAGAAA CCGGCATCGA CTATGAAATC CGCAGCATGG AAAAACCGTC 771 CGATCACGCC CCCGTCTGGG CGACCTTCCG CCGC SEQ ID NO: 10 1 MKFVSFNING LRARPHQLEA IVEKHQPDVI GLQETKVHDD MFPLEEVAKL GYNVFYHGQK GHYGVALLTK 71 ETPIAVRRGF PGDDEEAQRR IIMAEIPSLL GNVTVINGYF PQGESRDHPI KFPAKAQFYQ NLQNYLETEL 141 KRDNPVLIMG DMNISPTDLD IGIGEENRKR WLRTGKCSFL PEEREWMDRL MSWGLVDTFR HANPQTADRF 211 SWFDYRSKGF DDNRGLRIDL LLASQPLAEC CVETGIDYEI RSMEKPSDHA PVWATFRR SEQ ID NO: 11 1 ATGATGAATG ACGGTAAGCA ACAATCTACC TTTTTGTTTC ACGATTACGA AACCTTTGGC ACGCACCCCG 71 CGTTAGATCG CCCTGCACAG TTCGCAGCCA TTCGCACCGA TAGCGAATTC AATGTCATCG GCGAACCCGA 141 AGTCTTTTAC TGCAAGCCCG CTGATGACTA TTTACCCCAG CCAGGAGCCG TATTAATTAC CGGTATTACC 211 CCGCAGGAAG CACGGGCGAA AGGAGAAAAC GAAGCCGCGT TTGCCGCCCG TATTCACTCG CTTTTTACCG 281 TACCGAAGAC CTGTATTCTG GGCTACAACA ATGTGCGTTT CGACGACGAA GTCACACGCA ACATTTTTTA 351 TCGTAATTTC TACGATCCTT ACGCCTGGAG CTGGCAGCAT GATAACTCGC GCTGGGATTT ACTGGATGTT 421 ATGCGTGCCT GTTATGCCCT GCGCCCGGAA GGAATAAACT GGCCTGAAAA TGATGACGGT CTACCGAGCT 491 TTCGCCTTGA GCATTTAACC AAAGCGAATG GTATTGAACA TAGCAACGCC CACGATGCGA TGGCTGATGT 561 GTACGCCACT ATTGCGATGG CAAAGCTGGT AAAAACGCGT CAGCCACGCC TGTTTGATTA TCTCTTTACC 631 CATCGTAATA AACACAAACT GATGGCGTTG ATTGATGTTC CGCAGATGAA ACCCCTGGTG CACGTTTCCG

701 GAATGTTTGG AGCATGGCGC GGCAATACCA GCTGGGTGGC ACCGCTGGCG TGGCATCCTG AAAATCGCAA 771 TGCCGTAATT ATGGTGGATT TGGCAGGAGA CATTTCGCCA TTACTGGAAC TGGATAGCGA CACATTGCGC 841 GAGCGTTTAT ATACCGCAAA AACCGATCTT GGCGATAACG CCGCCGTTCC GGTTAAGCTG GTGCATATCA 911 ATAAATGTCC GGTGCTGGCC CAGGCGAATA CGCTACGCCC GGAAGATGCC GACCGACTGG GAATTAATCG 981 TCAGCATTGC CTCGATAACC TGAAAATTCT GCGTGAAAAT CCGCAAGTGC GCGAAAAAGT GGTGGCGATA 1051 TTCGCGGAAG CCGAACCGTT TACGCCTTCA GATAACGTGG ATGCACAGCT TTATAACGGC TTTTTCAGTG 1121 ACGCAGATCG TGCAGCAATG AAAATTGTGC TGGAAACCGA GCCGCGTAAT TTACCGGCAC TGGATATCAC 1191 TTTTGTTGAT AAACGGATTG AAAAGCTGTT GTTCAATTAT CGGGCACGCA ACTTCCCGGG GACGCTGGAT 1261 TATGCCGAGC AGCAACGCTG GCTGGAGCAC CGTCGCCAGG TCTTCACGCC AGAGTTTTTG CAGGGTTATG 1331 CTGATGAATT GCAGATGCTG GTACAACAAT ATGCCGATGA CAAAGAGAAA GTGGCGCTGT TAAAAGCACT 1401 TTGGCAGTAC GCGGAAGAGA TTGTC SEQ ID NO: 12 1 MMNDGKQQST FLFHDYETFG THPALDRPAQ FAAIRTDSEF NVIGEPEVFY CKPADDYLPQ PGAVLITGIT 71 PQEARAKGEN EAAFAARIHS LFTVPKTCIL GYNNVRFDDE VTRNIFYRNF YDPYAWSWQH DNSRWDLLDV 141 MRACYALRPE GINWPENDDG LPSFRLEHLT KANGIEHSNA HDAMADVYAT IAMAKLVKTR QPRLFDYLFT 211 HRNKHKLMAL IDVPQMKPLV HVSGMFGAWR GNTSWVAPLA WHPENRNAVI MVDLAGDISP LLELDSDTLR 281 ERLYTAKTDL GDNAAVPVKL VHINKCPVLA QANTLRPEDA DRLGINRQHC LDNLKILREN PQVREKVVAI 351 FAEAEPFTPS DNVDAQLYNG FFSDADRAAM KIVLETEPRN LPALDITFVD KRIEKLLFNY RARNFPGTLD 421 YAEQQRWLEH RRQVFTPEFL QGYADELQML VQQYADDKEK VALLKALWQY AEEIV SEQ ID NO: 13 1 ATGTTTCGTC GTAAAGAAGA TCTGGATCCG CCGCTGGCAC TGCTGCCGCT GAAAGGCCTG CGCGAAGCCG 71 CCGCACTGCT GGAAGAAGCG CTGCGTCAAG GTAAACGCAT TCGTGTTCAC GGCGACTATG ATGCGGATGG 141 CCTGACCGGC ACCGCGATCC TGGTTCGTGG TCTGGCCGCC CTGGGTGCGG ATGTTCATCC GTTTATCCCG 211 CACCGCCTGG AAGAAGGCTA TGGTGTCCTG ATGGAACGCG TCCCGGAACA TCTGGAAGCC TCGGACCTGT 281 TTCTGACCGT TGACTGCGGC ATTACCAACC ATGCGGAACT GCGCGAACTG CTGGAAAATG GCGTGGAAGT 351 CATTGTTACC GATCATCATA CGCCGGGCAA AACGCCGCCG CCGGGTCTGG TCGTGCATCC GGCGCTGACG 421 CCGGATCTGA AAGAAAAACC GACCGGCGCA GGCGTGGCGT TTCTGCTGCT GTGGGCACTG CATGAACGCC 491 TGGGCCTGCC GCCGCCGCTG GAATACGCGG ACCTGGCAGC CGTTGGCACC ATTGCCGACG TTGCCCCGCT 561 GTGGGGTTGG AATCGTGCAC TGGTGAAAGA AGGTCTGGCA CGCATCCCGG CTTCATCTTG GGTGGGCCTG 631 CGTCTGCTGG CTGAAGCCGT GGGCTATACC GGCAAAGCGG TCGAAGTCGC TTTCCGCATC GCGCCGCGCA 701 TCAATGCGGC TTCCCGCCTG GGCGAAGCGG AAAAAGCCCT GCGCCTGCTG CTGACGGATG ATGCGGCAGA 771 AGCTCAGGCG CTGGTCGGCG AACTGCACCG TCTGAACGCC CGTCGTCAGA CCCTGGAAGA AGCGATGCTG 841 CGCAAACTGC TGCCGCAGGC CGACCCGGAA GCGAAAGCCA TCGTTCTGCT GGACCCGGAA GGCCATCCGG 911 GTGTTATGGG TATTGTGGCC TCTCGCATCC TGGAAGCGAC CCTGCGCCCG GTCTTTCTGG TGGCCCAGGG 981 CAAAGGCACC GTGCGTTCGC TGGCTCCGAT TTCCGCCGTC GAAGCACTGC GCAGCGCGGA AGATCTGCTG 1051 CTGCGTTATG GTGGTCATAA AGAAGCGGCG GGTTTCGCAA TGGATGAAGC GCTGTTTCCG GCGTTCAAAG 1121 CACGCGTTGA AGCGTATGCC GCACGTTTCC CGGATCCGGT TCGTGAAGTG GCACTGCTGG ATCTGCTGCC 1191 GGAACCGGGC CTGCTGCCGC AGGTGTTCCG TGAACTGGCA CTGCTGGAAC CGTATGGTGA AGGTAACCCG 1261 GAACCGCTGT TCCTG SEQ ID NO: 14 1 MFRRKEDLDP PLALLPLKGL REAAALLEEA LRQGKRIRVH GDYDADGLTG TAILVRGLAA LGADVHPFIP 71 HRLEEGYGVL MERVPEHLEA SDLFLTVDCG ITNHAELREL LENGVEVIVT DHHTPGKTPP PGLVVHPALT 141 PDLKEKPTGA GVAFLLLWAL HERLGLPPPL EYADLAAVGT IADVAPLWGW NRALVKEGLA RIPASSWVGL 211 RLLAEAVGYT GKAVEVAFRI APRINAASRL GEAEKALRLL LTDDAAEAQA LVGELHRLNA RRQTLEEAML 281 RKLLPQADPE AKAIVLLDPE GHPGVMGIVA SRILEATLRP VFLVAQGKGT VRSLAPISAV EALRSAEDLL 351 LRYGGHKEAA GFAMDEALFP AFKARVEAYA ARFPDPVREV ALLDLLPEPG LLPQVFRELA LLEPYGEGNP 421 EPLFL SEQ ID NO: 15 1 TCCGGAAGCG GCTCTGGTAG TGGTTCTGGC ATGACACCGG ACATTATCCT GCAGCGTACC GGGATCGATG 71 TGAGAGCTGT CGAACAGGGG GATGATGCGT GGCACAAATT ACGGCTCGGC GTCATCACCG CTTCAGAAGT 141 TCACAACGTG ATAGCAAAAC CCCGCTCCGG AAAGAAGTGG CCTGACATGA AAATGTCCTA CTTCCACACC 211 CTGCTTGCTG AGGTTTGCAC CGGTGTGGCT CCGGAAGTTA ACGCTAAAGC ACTGGCCTGG GGAAAACAGT 281 ACGAGAACGA CGCCAGAACC CTGTTTGAAT TCACTTCCGG CGTGAATGTT ACTGAATCCC CGATCATCTA 351 TCGCGACGAA AGTATGCGTA CCGCCTGCTC TCCCGATGGT TTATGCAGTG ACGGCAACGG CCTTGAACTG 421 AAATGCCCGT TTACCTCCCG GGATTTCATG AAGTTCCGGC TCGGTGGTTT CGAGGCCATA AAGTCAGCTT 491 ACATGGCCCA GGTGCAGTAC AGCATGTGGG TGACGCGAAA AAATGCCTGG TACTTTGCCA ACTATGACCC 561 GCGTATGAAG CGTGAAGGCC TGCATTATGT CGTGATTGAG CGGGATGAAA AGTACATGGC GAGTTTTGAC 631 GAGATCGTGC CGGAGTTCAT CGAAAAAATG GACGAGGCAC TGGCTGAAAT TGGTTTTGTA TTTGGGGAGC 701 AATGGCGATC TGGCTCTGGT TCCGGCAGCG GTTCCGGA SEQ ID NO: 16 1 MTPDIILQRT GIDVRAVEQG DDAWHKLRLG VITASEVHNV IAKPRSGKKW PDMKMSYFHT LLAEVCTGVA 71 PEVNAKALAW GKQYENDART LFEFTSGVNV TESPIIYRDE SMRTACSPDG LCSDGNGLEL KCPFTSRDFM 141 KFRLGGFEAI KSAYMAQVQY SMWVTRKNAW YFANYDPRMK REGLHYVVIE RDEKYMASFD EIVPEFIEKM 211 DEALAEIGFV FGEQWR SEQ ID NO: 17 1 ATGGCAGATT CTGATATTAA TATTAAAACC GGTACTACAG ATATTGGAAG CAATACTTCC GGAAGCGGCT 71 CTGGTAGTGG TTCTGGCATG AAATTTGTTA GCTTCAATAT CAACGGCCTG CGCGCGCGCC CGCATCAGCT 141 GGAAGCGATT GTGGAAAAAC ATCAGCCGGA TGTTATTGGT CTGCAGGAAA CCAAAGTTCA CGATGATATG 211 TTTCCGCTGG AAGAAGTGGC GAAACTGGGC TATAACGTGT TTTATCATGG CCAGAAAGGT CATTATGGCG 281 TGGCCCTGCT GACCAAAGAA ACCCCGATCG CGGTTCGTCG TGGTTTTCCG GGTGATGATG AAGAAGCGCA 351 GCGTCGTATT ATTATGGCGG AAATTCCGAG CCTGCTGGGC AATGTGACCG TTATTAACGG CTATTTTCCG 421 CAGGGCGAAA GCCGTGATCA TCCGATTAAA TTTCCGGCCA AAGCGCAGTT CTATCAGAAC CTGCAGAACT 491 ATCTGGAAAC CGAACTGAAA CGTGATAATC CGGTGCTGAT CATGGGCGAT ATGAACATTA GCCCGACCGA 561 TCTGGATATT GGCATTGGCG AAGAAAACCG TAAACGCTGG CTGCGTACCG GTAAATGCAG CTTTCTGCCG 631 GAAGAACGTG AATGGATGGA TCGCCTGATG AGCTGGGGCC TGGTGGATAC CTTTCGTCAT GCGAACCCGC 701 AGACCGCCGA TCGCTTTAGC TGGTTTGATT ATCGCAGCAA AGGTTTTGAT GATAACCGTG GCCTGCGCAT 771 TGATCTGCTG CTGGCGAGCC AGCCGCTGGC GGAATGCTGC GTTGAAACCG GTATTGATTA TGAAATTCGC 841 AGCATGGAAA AACCGAGCGA TCACGCCCCG GTGTGGGCGA CCTTTCGCCG CTCTGGCTCT GGTTCCGGCA 911 GCGGTTCCGG AACAGTAAAA ACAGGTGATT TAGTCACTTA TGATAAAGAA AATGGCATGC ACAAAAAAGT 981 ATTTTATAGT TTTATCGATG ATAAAAATCA CAATAAAAAA CTGCTAGTTA TTAGAACAAA AGGTACCATT 1051 GCTGGTCAAT ATAGAGTTTA TAGCGAAGAA GGTGCTAACA AAAGTGGTTT AGCCTGGCCT TCAGCCTTTA 1121 AGGTACAGTT GCAACTACCT GATAATGAAG TAGCTCAAAT ATCTGATTAC TATCCAAGAA ATTCGATTGA 1191 TACAAAAGAG TATATGAGTA CTTTAACTTA TGGATTCAAC GGTAATGTTA CTGGTGATGA TACAGGAAAA 1261 ATTGGCGGCC TTATTGGTGC AAATGTTTCG ATTGGTCATA CACTGAAATA TGTTCAACCT GATTTCAAAA 1331 CAATTTTAGA GAGCCCAACT GATAAAAAAG TAGGCTGGAA AGTGATATTT AACAATATGG TGAATCAAAA 1401 TTGGGGACCA TACGATCGAG ATTCTTGGAA CCCGGTATAT GGCAATCAAC TTTTCATGAA AACTAGAAAT 1471 GGTTCTATGA AAGCAGCAGA TAACTTCCTT GATCCTAACA AAGCAAGTTC TCTATTATCT TCAGGGIIII 1541 CACCAGACTT CGCTACAGTT ATTACTATGG ATAGAAAAGC ATCCAAACAA CAAACAAATA TAGATGTAAT 1611 ATACGAACGA GTTCGTGATG ATTACCAATT GCATTGGACT TCAACAAATT GGAAAGGTAC CAATACTAAA 1681 GATAAATGGA CAGATCGTTC TTCAGAAAGA TATAAAATCG ATTGGGAAAA AGAAGAAATG

ACAAATGGTG 1751 GTTCGGGCTC ATCTGGTGGC TCGAGTCACC ATCATCATCA CCAC SEQ ID NO: 18 1 ADSDINIKTG TTDIGSNTSG SGSGSGSGMK FVSFNINGLR ARPHQLEAIV EKHQPDVIGL QETKVHDDMF 71 PLEEVAKLGY NVFYHGQKGH YGVALLTKET PIAVRRGFPG DDEEAQRRII MAEIPSLLGN VTVINGYFPQ 141 GESRDHPIKF PAKAQFYQNL QNYLETELKR DNPVLIMGDM NISPTDLDIG IGEENRKRWL RTGKCSFLPE 211 EREWMDRLMS WGLVDTFRHA NPQTADRFSW FDYRSKGFDD NRGLRIDLLL ASQPLAECCV ETGIDYEIRS 281 MEKPSDHAPV WATFRRSGSG SGSGSGTVKT GDLVTYDKEN GMHKKVFYSF IDDKNHNKKL LVIRTKGTIA 351 GQYRVYSEEG ANKSGLAWPS AFKVQLQLPD NEVAQISDYY PRNSIDTKEY MSTLTYGFNG NVTGDDTGKI 421 GGLIGANVSI GHTLKYVQPD FKTILESPTD KKVGWKVIFN NMVNQNWGPY DRDSWNPVYG NQLFMKTRNG 491 SMKAADNFLD PNKASSLLSS GFSPDFATVI TMDRKASKQQ TNIDVIYERV RDDYQLHWTS TNWKGTNTKD 561 KWTDRSSERY KIDWEKEEMT NGGSGSSGGS SHHHHHH SEQ ID NO: 19 1 ATGGCAGATT CTGATATTAA TATTAAAACC GGTACTACAG ATATTGGAAG CAATACTTCC GGAAGCGGCT 71 CTGGTAGTGG TTCTGGCATG AAATTTGTTA GCTTCAATAT CAACGGCCTG CGCGCGCGCC CGCATCAGCT 141 GGAAGCGATT GTGGAAAAAC ATCAGCCGGA TGTTATTGGT CTGCAGGAAA CCAAAGTTCA CGATGATATG 211 TTTCCGCTGG AAGAAGTGGC GAAACTGGGC TATAACGTGT TTTATCATGG CCAGAAAGGT CATTATGGCG 281 TGGCCCTGCT GACCAAAGAA ACCCCGATCG CGGTTCGTCG TGGTTTTCCG GGTGATGATG AAGAAGCGCA 351 GCGTCGTATT ATTATGGCGG AAATTCCGAG CCTGCTGGGC AATGTGACCG TTATTAACGG CTATTTTCCG 421 CAGGGCGAAA GCCGTGATCA TCCGATTAAA TTTCCGGCCA AAGCGCAGTT CTATCAGAAC CTGCAGAACT 491 ATCTGGAAAC CGAACTGAAA CGTGATAATC CGGTGCTGAT CATGGGCGAT ATGAACATTA GCCCGACCGA 561 TCTGGATATT GGCATTGGCG AAGAAAACCG TAAACGCTGG CTGCGTACCG GTAAATGCAG CTTTCTGCCG 631 GAAGAACGTG AATGGATGGA TCGCCTGATG AGCTGGGGCC TGGTGGATAC CTTTCGTCAT GCGAACCCGC 701 AGACCGCCGA TCGCTTTAGC TGGTTTGATT ATCGCAGCAA AGGTTTTGAT GATAACCGTG GCCTGCGCAT 771 TGATCTGCTG CTGGCGAGCC AGCCGCTGGC GGAATGCTGC GTTGAAACCG GTATTGATTA TGAAATTCGC 841 AGCATGGAAA AACCGAGCGA TCACGCCCCG GTGTGGGCGA CCTTTCGCCG CTCTGGCTCT GGTTCCGGCA 911 GCGGTTCCGG AACAGTAAAA ACAGGTGATT TAGTCACTTA TGATAAAGAA AATGGCATGC ACAAAAAAGT 981 ATTTTATAGT TTTATCGATG ATAAAAATCA CAATAAAAAA CTGCTAGTTA TTAGAACAAA AGGTACCATT 1051 GCTGGTCAAT ATAGAGTTTA TAGCGAAGAA GGTGCTAACA AAAGTGGTTT AGCCTGGCCT TCAGCCTTTA 1121 AGGTACAGTT GCAACTACCT GATAATGAAG TAGCTCAAAT ATCTGATTAC TATCCAAGAA ATTCGATTGA 1191 TACAAAAGAG TATAGGAGTA CTTTAACTTA TGGATTCAAC GGTAATGTTA CTGGTGATGA TACAGGAAAA 1261 ATTGGCGGCT GTATTGGTGC ACAAGTTTCG ATTGGTCATA CACTGAAATA TGTTCAACCT GATTTCAAAA 1331 CAATTTTAGA GAGCCCAACT GATAAAAAAG TAGGCTGGAA AGTGATATTT AACAATATGG TGAATCAAAA 1401 TTGGGGACCA TACGATCGAG ATTCTTGGAA CCCGGTATAT GGCAATCAAC TTTTCATGAA AACTAGAAAT 1471 GGTTCTATGA AAGCAGCAGA TAACTTCCTT GATCCTAACA AAGCAAGTTC TCTATTATCT TCAGGGTTTT 1541 CACCAGACTT CGCTACAGTT ATTACTATGG ATAGAAAAGC ATCCAAACAA CAAACAAATA TAGATGTAAT 1611 ATACGAACGA GTTCGTGATG ATTACCAATT GCATTGGACT TCAACAAATT GGAAAGGTAC CAATACTAAA 1681 GATAAATGGA CAGATCGTTC TTCAGAAAGA TATAAAATCG ATTGGGAAAA AGAAGAAATG ACAAATGGTG 1751 GTTCGGGCTC ATCTGGTGGC TCGAGTCACC ATCATCATCA CCAC SEQ ID NO: 20 1 ADSDINIKTG TTDIGSNTSG SGSGSGSGMK FVSFNINGLR ARPHQLEAIV EKHQPDVIGL QETKVHDDMF 71 PLEEVAKLGY NVFYHGQKGH YGVALLTKET PIAVRRGFPG DDEEAQRRII MAEIPSLLGN VTVINGYFPQ 141 GESRDHPIKF PAKAQFYQNL QNYLETELKR DNPVLIMGDM NISPTDLDIG IGEENRKRWL RTGKCSFLPE 211 EREWMDRLMS WGLVDTFRHA NPQTADRFSW FDYRSKGFDD NRGLRIDLLL ASQPLAECCV ETGIDYEIRS 281 MEKPSDHAPV WATFRRSGSG SGSGSGTVKT GDLVTYDKEN GMHKKVFYSF IDDKNHNKKL LVIRTKGTIA 351 GQYRVYSEEG ANKSGLAWPS AFKVQLQLPD NEVAQISDYY PRNSIDTKEY RSTLTYGFNG NVTGDDTGKI 421 GGCIGAQVSI GHTLKYVQPD FKTILESPTD KKVGWKVIFN NMVNQNWGPY DRDSWNPVYG NQLFMKTRNG 491 SMKAADNFLD PNKASSLLSS GFSPDFATVI TMDRKASKQQ TNIDVIYERV RDDYQLHWTS TNWKGTNTKD 561 KWTDRSSERY KIDWEKEEMT NGGSGSSGGS SHHHHHH SEQ ID NO: 21 1 ATGGCAGATT CTGATATTAA TATTAAAACC GGTACTACAG ATATTGGAAG CAATACTTCC GGAAGCGGCT 71 CTGGTAGTGG TTCTGGCATG ATGAACGATG GCAAACAGCA GAGCACCTTC CTGTTTCATG ATTATGAAAC 141 CTTCGGTACC CATCCGGCCC TGGATCGTCC GGCGCAGTTT GCGGCCATTC GCACCGATAG CGAATTCAAT 211 GTGATTGGCG AACCGGAAGT GTTTTATTGC AAACCGGCCG ATGATTATCT GCCGCAGCCG GGTGCGGTGC 281 TGATTACCGG TATTACCCCG CAGGAAGCGC GCGCGAAAGG TGAAAACGAA GCGGCGTTTG CCGCGCGCAT 351 TCATAGCCTG TTTACCGTGC CGAAAACCTG CATTCTGGGC TATAACAATG TGCGCTTCGA TGATGAAGTT 421 ACCCGTAATA TCTTTTATCG TAACTTTTAT GATCCGTATG CGTGGAGCTG GCAGCATGAT AACAGCCGTT 491 GGGATCTGCT GGATGTGATG CGCGCGTGCT ATGCGCTGCG CCCGGAAGGC ATTAATTGGC CGGAAAACGA 561 TGATGGCCTG CCGAGCTTTC GTCTGGAACA TCTGACCAAA GCCAACGGCA TTGAACATAG CAATGCCCAT 631 GATGCGATGG CCGATGTTTA TGCGACCATT GCGATGGCGA AACTGGTTAA AACCCGTCAG CCGCGCCTGT 701 TTGATTATCT GTTTACCCAC CGTAACAAAC ACAAACTGAT GGCGCTGATT GATGTTCCGC AGATGAAACC 771 GCTGGTGCAT GTGAGCGGCA TGTTTGGCGC CTGGCGCGGC AACACCAGCT GGGTGGCCCC GCTGGCCTGG 841 CACCCGGAAA ATCGTAACGC CGTGATTATG GTTGATCTGG CCGGTGATAT TAGCCCGCTG CTGGAACTGG 911 ATAGCGATAC CCTGCGTGAA CGCCTGTATA CCGCCAAAAC CGATCTGGGC GATAATGCCG CCGTGCCGGT 981 GAAACTGGTT CACATTAACA AATGCCCGGT GCTGGCCCAG GCGAACACCC TGCGCCCGGA AGATGCGGAT 1051 CGTCTGGGTA TTAATCGCCA GCATTGTCTG GATAATCTGA AAATCCTGCG TGAAAACCCG CAGGTGCGTG 1121 AAAAAGTGGT GGCGATCTTC GCGGAAGCGG AACCGTTCAC CCCGAGCGAT AACGTGGATG CGCAGCTGTA 1191 TAACGGCTTC TTTAGCGATG CCGATCGCGC GGCGATGAAA ATCGTTCTGG AAACCGAACC GCGCAATCTG 1261 CCGGCGCTGG ATATTACCTT TGTTGATAAA CGTATTGAAA AACTGCTGTT TAATTATCGT GCGCGCAATT 1331 TTCCGGGTAC CCTGGATTAT GCCGAACAGC AGCGTTGGCT GGAACATCGT CGTCAGGTTT TCACCCCGGA 1401 ATTTCTGCAG GGTTATGCGG ATGAACTGCA GATGCTGGTT CAGCAGTATG CCGATGATAA AGAAAAAGTG 1471 GCGCTGCTGA AAGCGCTGTG GCAGTATGCG GAAGAAATCG TTTCTGGCTC TGGTTCCGGC AGCGGTTCCG 1541 GAACAGTAAA AACAGGTGAT TTAGTCACTT ATGATAAAGA AAATGGCATG CACAAAAAAG TATTTTATAG 1611 TTTTATCGAT GATAAAAATC ACAATAAAAA ACTGCTAGTT ATTAGAACAA AAGGTACCAT TGCTGGTCAA 1681 TATAGAGTTT ATAGCGAAGA AGGTGCTAAC AAAAGTGGTT TAGCCTGGCC TTCAGCCTTT AAGGTACAGT 1751 TGCAACTACC TGATAATGAA GTAGCTCAAA TATCTGATTA CTATCCAAGA AATTCGATTG ATACAAAAGA 1821 GTATAGGAGT ACTTTAACTT ATGGATTCAA CGGTAATGTT ACTGGTGATG ATACAGGAAA AATTGGCGGC 1891 TGTATTGGTG CACAAGTTTC GATTGGTCAT ACACTGAAAT ATGTTCAACC TGATTTCAAA ACAATTTTAG 1961 AGAGCCCAAC TGATAAAAAA GTAGGCTGGA AAGTGATATT TAACAATATG GTGAATCAAA ATTGGGGACC 2031 ATACGATCGA GATTCTTGGA ACCCGGTATA TGGCAATCAA CTTTTCATGA AAACTAGAAA TGGTTCTATG 2101 AAAGCAGCAG ATAACTTCCT TGATCCTAAC AAAGCAAGTT CTCTATTATC TTCAGGGTTT TCACCAGACT 2171 TCGCTACAGT TATTACTATG GATAGAAAAG CATCCAAACA ACAAACAAAT ATAGATGTAA TATACGAACG 2241 AGTTCGTGAT GATTACCAAT TGCATTGGAC TTCAACAAAT TGGAAAGGTA CCAATACTAA AGATAAATGG 2311 ACAGATCGTT CTTCAGAAAG ATATAAAATC GATTGGGAAA AAGAAGAAAT GACAAATGGT GGTTCGGGCT 2381 CATCTGGTGG CTCGAGTCAC CATCATCATC ACCAC SEQ ID NO: 22 1 ADSDINIKTG TTDIGSNTSG SGSGSGSGMM NDGKQQSTFL FHDYETFGTH PALDRPAQFA AIRTDSEFNV 71 IGEPEVFYCK PADDYLPQPG AVLITGITPQ EARAKGENEA AFAARIHSLF TVPKTCILGY NNVRFDDEVT 141 RNIFYRNFYD PYAWSWQHDN SRWDLLDVMR ACYALRPEGI NWPENDDGLP SFRLEHLTKA NGIEHSNAHD

211 AMADVYATIA MAKLVKTRQP RLFDYLFTHR NKHKLMALID VPQMKPLVHV SGMFGAWRGN TSWVAPLAWH 281 PENRNAVIMV DLAGDISPLL ELDSDTLRER LYTAKTDLGD NAAVPVKLVH INKCPVLAQA NTLRPEDADR 351 LGINRQHCLD NLKILRENPQ VREKVVAIFA EAEPFTPSDN VDAQLYNGFF SDADRAAMKI VLETEPRNLP 421 ALDITFVDKR IEKLLFNYRA RNFPGTLDYA EQQRWLEHRR QVFTPEFLQG YADELQMLVQ QYADDKEKVA 491 LLKALWQYAE EIVSGSGSGS GSGTVKTGDL VTYDKENGMH KKVFYSFIDD KNHNKKLLVI RTKGTIAGQY 561 RVYSEEGANK SGLAWPSAFK VQLQLPDNEV AQISDYYPRN SIDTKEYRST LTYGFNGNVT GDDTGKIGGC 631 IGAQVSIGHT LKYVQPDFKT ILESPTDKKV GWKVIFNNMV NQNWGPYDRD SWNPVYGNQL FMKTRNGSMK 701 AADNFLDPNK ASSLLSSGFS PDFATVITMD RKASKQQTNI DVIYERVRDD YQLHWTSTNW KGTNTKDKWT 771 DRSSERYKID WEKEEMTNGG SGSSGGSSHH HHHH SEQ ID NO: 23 1 ATGGCAGATT CTGATATTAA TATTAAAACC GGTACTACAG ATATTGGAAG CAATACTTCC GGAAGCGGCT 71 CTGGTAGTGG TTCTGGCATG TTTCGTCGTA AAGAAGATCT GGATCCGCCG CTGGCACTGC TGCCGCTGAA 141 AGGCCTGCGC GAAGCCGCCG CACTGCTGGA AGAAGCGCTG CGTCAAGGTA AACGCATTCG TGTTCACGGC 211 GACTATGATG CGGATGGCCT GACCGGCACC GCGATCCTGG TTCGTGGTCT GGCCGCCCTG GGTGCGGATG 281 TTCATCCGTT TATCCCGCAC CGCCTGGAAG AAGGCTATGG TGTCCTGATG GAACGCGTCC CGGAACATCT 351 GGAAGCCTCG GACCTGTTTC TGACCGTTGA CTGCGGCATT ACCAACCATG CGGAACTGCG CGAACTGCTG 421 GAAAATGGCG TGGAAGTCAT TGTTACCGAT CATCATACGC CGGGCAAAAC GCCGCCGCCG GGTCTGGTCG 491 TGCATCCGGC GCTGACGCCG GATCTGAAAG AAAAACCGAC CGGCGCAGGC GTGGCGTTTC TGCTGCTGTG 561 GGCACTGCAT GAACGCCTGG GCCTGCCGCC GCCGCTGGAA TACGCGGACC TGGCAGCCGT TGGCACCATT 631 GCCGACGTTG CCCCGCTGTG GGGTTGGAAT CGTGCACTGG TGAAAGAAGG TCTGGCACGC ATCCCGGCTT 701 CATCTTGGGT GGGCCTGCGT CTGCTGGCTG AAGCCGTGGG CTATACCGGC AAAGCGGTCG AAGTCGCTTT 771 CCGCATCGCG CCGCGCATCA ATGCGGCTTC CCGCCTGGGC GAAGCGGAAA AAGCCCTGCG CCTGCTGCTG 841 ACGGATGATG CGGCAGAAGC TCAGGCGCTG GTCGGCGAAC TGCACCGTCT GAACGCCCGT CGTCAGACCC 911 TGGAAGAAGC GATGCTGCGC AAACTGCTGC CGCAGGCCGA CCCGGAAGCG AAAGCCATCG TTCTGCTGGA 981 CCCGGAAGGC CATCCGGGTG TTATGGGTAT TGTGGCCTCT CGCATCCTGG AAGCGACCCT GCGCCCGGTC 1051 TTTCTGGTGG CCCAGGGCAA AGGCACCGTG CGTTCGCTGG CTCCGATTTC CGCCGTCGAA GCACTGCGCA 1121 GCGCGGAAGA TCTGCTGCTG CGTTATGGTG GTCATAAAGA AGCGGCGGGT TTCGCAATGG ATGAAGCGCT 1191 GTTTCCGGCG TTCAAAGCAC GCGTTGAAGC GTATGCCGCA CGTTTCCCGG ATCCGGTTCG TGAAGTGGCA 1261 CTGCTGGATC TGCTGCCGGA ACCGGGCCTG CTGCCGCAGG TGTTCCGTGA ACTGGCACTG CTGGAACCGT 1331 ATGGTGAAGG TAACCCGGAA CCGCTGTTCC TGTCTGGCTC TGGTTCCGGC AGCGGTTCCG GAACAGTAAA 1401 AACAGGTGAT TTAGTCACTT ATGATAAAGA AAATGGCATG CACAAAAAAG TATTTTATAG TTTTATCGAT 1471 GATAAAAATC ACAATAAAAA ACTGCTAGTT ATTAGAACAA AAGGTACCAT TGCTGGTCAA TATAGAGTTT 1541 ATAGCGAAGA AGGTGCTAAC AAAAGTGGTT TAGCCTGGCC TTCAGCCTTT AAGGTACAGT TGCAACTACC 1611 TGATAATGAA GTAGCTCAAA TATCTGATTA CTATCCAAGA AATTCGATTG ATACAAAAGA GTATAGGAGT 1681 ACTTTAACTT ATGGATTCAA CGGTAATGTT ACTGGTGATG ATACAGGAAA AATTGGCGGC TGTATTGGTG 1751 CACAAGTTTC GATTGGTCAT ACACTGAAAT ATGTTCAACC TGATTTCAAA ACAATTTTAG AGAGCCCAAC 1821 TGATAAAAAA GTAGGCTGGA AAGTGATATT TAACAATATG GTGAATCAAA ATTGGGGACC ATACGATCGA 1891 GATTCTTGGA ACCCGGTATA TGGCAATCAA CTTTTCATGA AAACTAGAAA TGGTTCTATG AAAGCAGCAG 1961 ATAACTTCCT TGATCCTAAC AAAGCAAGTT CTCTATTATC TTCAGGGTTT TCACCAGACT TCGCTACAGT 2031 TATTACTATG GATAGAAAAG CATCCAAACA ACAAACAAAT ATAGATGTAA TATACGAACG AGTTCGTGAT 2101 GATTACCAAT TGCATTGGAC TTCAACAAAT TGGAAAGGTA CCAATACTAA AGATAAATGG ACAGATCGTT 2171 CTTCAGAAAG ATATAAAATC GATTGGGAAA AAGAAGAAAT GACAAATGGT GGTTCGGGCT CATCTGGTGG 2241 CTCGAGTCAC CATCATCATC ACCAC SEQ ID NO: 24 1 ADSDINIKTG TTDIGSNTSG SGSGSGSGMF RRKEDLDPPL ALLPLKGLRE AAALLEEALR QGKRIRVHGD 71 YDADGLTGTA ILVRGLAALG ADVHPFIPHR LEEGYGVLME RVPEHLEASD LFLTVDCGIT NHAELRELLE 141 NGVEVIVTDH HTPGKTPPPG LVVHPALTPD LKEKPTGAGV AFLLLWALHE RLGLPPPLEY ADLAAVGTIA 211 DVAPLWGWNR ALVKEGLARI PASSWVGLRL LAEAVGYTGK AVEVAFRIAP RINAASRLGE AEKALRLLLT 281 DDAAEAQALV GELHRLNARR QTLEEAMLRK LLPQADPEAK AIVLLDPEGH PGVMGIVASR ILEATLRPVF 351 LVAQGKGTVR SLAPISAvEA LRSAEDLLLR YGGHKEAAGF AMDEALFPAF KARVEAYAAR FPDPVREVAL 421 LDLLPEPGLL PQVFRELALL EPYGEGNPEP LFLSGSGSGS GSGTVKTGDL VTYDKENGMH KKVFYSFIDD 491 KNHNKKLLVI RTKGTIAGQY RVYSEEGANK SGLAWPSAFK VQLQLPDNEV AQISDYYPRN SIDTKEYRST 561 LTYGFNGNVT GDDTGKIGGC IGAQVSIGHT LKYVQPDFKT ILESPTDKKV GWKVIFNNMV NQNWGPYDRD 631 SWNPVYGNQL FMKTRNGSMK AADNFLDPNK ASSLLSSGFS PDFATVITMD RKASKQQTNI DVIYERVRDD 701 YQLHWTSTNW KGTNTKDKWT DRSSERYKID WEKEEMTNGG SGSSGGSSHH HHRH SEQ ID NO: 25 1 ATGGCAGATT CTGATATTAA TATTAAAACC GGTACTACAG ATATTGGAAG CAATACTACA GTAAAAACAG 71 GTGATTTAGT CACTTATGAT AAAGAAAATG GCATGCACAA AAAAGTATTT TATAGTTTTA TCGATTCCGG 141 AAGCGGCTCT GGTAGTGGTT CTGGCATGAA ATTTGTTAGC TTCAATATCA ACGGCCTGCG CGCGCGCCCG 211 CATCAGCTGG AAGCGATTGT GGAAAAACAT CAGCCGGATG TTATTGGTCT GCAGGAAACC AAAGTTCACG 281 ATGATATGTT TCCGCTGGAA GAAGTGGCGA AACTGGGCTA TAACGTGTTT TATCATGGCC AGAAAGGTCA 351 TTATGGCGTG GCCCTGCTGA CCAAAGAAAC CCCGATCGCG GTTCGTCGTG GTTTTCCGGG TGATGATGAA 421 GAAGCGCAGC GTCGTATTAT TATGGCGGAA ATTCCGAGCC TGCTGGGCAA TGTGACCGTT ATTAACGGCT 491 ATTTTCCGCA GGGCGAAAGC CGTGATCATC CGATTAAATT TCCGGCCAAA GCGCAGTTCT ATCAGAACCT 561 GCAGAACTAT CTGGAAACCG AACTGAAACG TGATAATCCG GTGCTGATCA TGGGCGATAT GAACATTAGC 631 CCGACCGATC TGGATATTGG CATTGGCGAA GAAAACCGTA AACGCTGGCT GCGTACCGGT AAATGCAGCT 701 TTCTGCCGGA AGAACGTGAA TGGATGGATC GCCTGATGAG CTGGGGCCTG GTGGATACCT TTCGTCATGC 771 GAACCCGCAG ACCGCCGATC GCTTTAGCTG GTTTGATTAT CGCAGCAAAG GTTTTGATGA TAACCGTGGC 841 CTGCGCATTG ATCTGCTGCT GGCGAGCCAG CCGCTGGCGG AATGCTGCGT TGAAACCGGT ATTGATTATG 911 AAATTCGCAG CATGGAAAAA CCGAGCGATC ACGCCCCGGT GTGGGCGACC TTTCGCCGCT CTGGCTCTGG 981 TTCCGGCAGC GGTTCCGGAC ACAATAAAAA ACTGCTAGTT ATTAGAACAA AAGGTACCAT TGCTGGTCAA 1051 TATAGAGTTT ATAGCGAAGA AGGTGCTAAC AAAAGTGGTT TAGCCTGGCC TTCAGCCTTT AAGGTACAGT 1121 TGCAACTACC TGATAATGAA GTAGCTCAAA TATCTGATTA CTATCCAAGA AATTCGATTG ATACAAAAGA 1191 GTATAGGAGT ACTTTAACTT ATGGATTCAA CGGTAATGTT ACTGGTGATG ATACAGGAAA AATTGGCGGC 1261 TGTATTGGTG CACAAGTTTC GATTGGTCAT ACACTGAAAT ATGTTCAACC TGATTTCAAA ACAATTTTAG 1331 AGAGCCCAAC TGATAAAAAA GTAGGCTGGA AAGTGATATT TAACAATATG GTGAATCAAA ATTGGGGACC 1401 ATACGATCGA GATTCTTGGA ACCCGGTATA TGGCAATCAA CTTTTCATGA AAACTAGAAA TGGTTCTATG 1471 AAAGCAGCAG ATAACTTCCT TGATCCTAAC AAAGCAAGTT CTCTATTATC TTCAGGGTTT TCACCAGACT 1541 TCGCTACAGT TATTACTATG GATAGAAAAG CATCCAAACA ACAAACAAAT ATAGATGTAA TATACGAACG 1611 AGTTCGTGAT GATTACCAAT TGCATTGGAC TTCAACAAAT TGGAAAGGTA CCAATACTAA AGATAAATGG 1681 ACAGATCGTT CTTCAGAAAG ATATAAAATC GATTGGGAAA AAGAAGAAAT GACAAATGGT GGTTCGGGCT 1751 CATCTGGTGG CTCGAGTCAC CATCATCATC ACCAC SEQ ID NO: 26 1 ADSDINIKTG TTDIGSNTTV KTGDLVTYDK ENGMHKKVFY SFIDSGSGSG SGSGMKFVSF NINGLRARPH 71 QLEAIVEKHQ PDVIGLQETK VHDDMFPLEE VAKLGYNVFY HGQKGHYGVA LLTKETPIAV RRGFPGDDEE 141 AQRRIIMAEI PSLLGNVTVI NGYFPQGESR DHPIKFPAKA QFYQNLQNYL ETELKRDNPV LIMGDMNISP 211 TDLDIGIGEE NRKRWLRTGK CSFLPEEREW MDRLMSWGLV DTFRHANPQT ADRFSWFDYR SKGFDDNRGL 281 RIDLLLASQP LAECCVETGI DYEIRSMEKP SDHAPVWATF RRSGSGSGSG SGHNKKLLVI RTKGTIAGQY

351 RVYSEEGANK SGLAWPSAFK VQLQLPDNEV AQISDYYPRN SIDTKEYRST LTYGFNGNVT GDDTGKIGGC 421 IGAQVSIGHT LKYVQPDFKT ILESPTDKKV GWKVIFNNMV NQNWGPYDRD SWNPVYGNQL FMKTRNGSMK 491 AADNFLDPNK ASSLLSSGFS PDFATVITMD RKASKQQTNI DVIYERVRDD YQLHWTSTNW KGTNTKDKWT 561 DRSSERYKID WEKEEMTNGG SGSSGGSSHH HHHH SEQ ID NO: 27 1 ATGGCAGATT CTGATATTAA TATTAAAACC GGTACTACAG ATATTGGAAG CAATACTACA GTAAAAACAG 71 GTGATTTAGT CACTTATGAT AAAGAAAATG GCATGCACAA AAAAGTATTT TATAGTTTTA TCGATGATAA 141 AAATCACAAT AAAAAACTGC TAGTTATTAG AACAAAAGGT ACCATTGCTG GTCAATATAG AGTTTATAGC 211 GAAGAAGGTG CTAACAAAAG TGGTTTAGCC TGGCCTTCAG CCTTTAAGGT ACAGTTGCAA CTACCTGATA 281 ATGAAGTAGC TCAAATATCT GATTACTATC CAAGAAATTC GATTGATACA AAAGAGTATA GGAGTACTTT 351 AACTTATGGA TTCAACGGTA ATGTTACTGG TGATGATACA GGAAAAATTG GCGGCTGTAT TGGTGCACAA 421 GTTTCGATTG GTCATACACT GAAATATGTT CAACCTGATT TCAAAACAAT TTTAGAGAGC CCAACTGATA 491 AAAAAGTAGG CTGGAAAGTG ATATTTAACA ATATGGTGAA TCAAAATTGG GGACCATACG ATCGAGATTC 561 TTGGAACCCG GTATATGGCA ATCAACTTTT CATGAAAACT AGAAATGGTT CTATGAAAGC AGCAGATAAC 631 TTCCTTGATC CTAACAAAGC AAGTTCTCTA TTATCTTCAG GGTTTTCACC AGACTTCGCT ACAGTTATTA 701 CTATGGATAG AAAAGCATCC AAACAACAAA CAAATATAGA TGTAATATAC GAACGAGTTC GTGATGATTA 771 CCAATTGCAT TGGACTTCAA CAAATTGGAA AGGTACCAAT ACTAAAGATA AATGGACAGA TCGTTCTTCA 841 GAAAGATATA AAATCGATTG GGAAAAAGAA GAAATGACAA ATTCCGGTAG CGGCTCTGGT TCTGGCTCTG 911 GTTCCGGCAG CGGTTCCGGA CAGAGCACCT TCCTGTTTCA TGATTATGAA ACCTTCGGTA CCCATCCGGC 981 CCTGGATCGT CCGGCGCAGT TTGCGGCCAT TCGCACCGAT AGCGAATTCA ATGTGATTGG CGAACCGGAA 1051 GTGTTTTATT GCAAACCGGC CGATGATTAT CTGCCGCAGC CGGGTGCGGT GCTGATTACC GGTATTACCC 1121 CGCAGGAAGC GCGCGCGAAA GGTGAAAACG AAGCGGCGTT TGCCGCGCGC ATTCATAGCC TGTTTACCGT 1191 GCCGAAAACC TGCATTCTGG GCTATAACAA TGTGCGCTTC GATGATGAAG TTACCCGTAA TATCTTTTAT 1261 CGTAACTTTT ATGATCCGTA TGCGTGGAGC TGGCAGCATG ATAACAGCCG TTGGGATCTG CTGGATGTGA 1331 TGCGCGCGTG CTATGCGCTG CGCCCGGAAG GCATTAATTG GCCGGAAAAC GATGATGGCC TGCCGAGCTT 1401 TCGTCTGGAA CATCTGACCA AAGCCAACGG CATTGAACAT AGCAATGCCC ATGATGCGAT GGCCGATGTT 1471 TATGCGACCA TTGCGATGGC GAAACTGGTT AAAACCCGTC AGCCGCGCCT GTTTGATTAT CTGTTTACCC 1541 ACCGTAACAA ACACAAACTG ATGGCGCTGA TTGATGTTCC GCAGATGAAA CCGCTGGTGC ATGTGAGCGG 1611 CATGTTTGGC GCCTGGCGCG GCAACACCAG CTGGGTGGCC CCGCTGGCCT GGCACCCGGA AAATCGTAAC 1681 GCCGTGATTA TGGTTGATCT GGCCGGTGAT ATTAGCCCGC TGCTGGAACT GGATAGCGAT ACCCTGCGTG 1751 AACGCCTGTA TACCGCCAAA ACCGATCTGG GCGATAATGC CGCCGTGCCG GTGAAACTGG TTCACATTAA 1821 CAAATGCCCG GTGCTGGCCC AGGCGAACAC CCTGCGCCCG GAAGATGCGG ATCGTCTGGG TATTAATCGC 1891 CAGCATTGTC TGGATAATCT GAAAATCCTG CGTGAAAACC CGCAGGTGCG TGAAAAAGTG GTGGCGATCT 1961 TCGCGGAAGC GGAACCGTTC ACCCCGAGCG ATAACGTGGA TGCGCAGCTG TATAACGGCT TCTTTAGCGA 2031 TGCCGATCGC GCGGCGATGA AAATCGTTCT GGAAACCGAA CCGCGCAATC TGCCGGCGCT GGATATTACC 2101 TTTGTTGATA AACGTATTGA AAAACTGCTG TTTAATTATC GTGCGCGCAA TTTTCCGGGT ACCCTGGATT 2171 ATGCCGAACA GCAGCGTTGG CTGGAACATC GTCGTCAGGT TTTCACCCCG GAATTTCTGC AGGGTTATGC 2241 GGATGAACTG CAGATGCTGG TTCAGCAGTA TGCCGATGAT AAAGAAAAAG TGGCGCTGCT GAAAGCGCTG 2311 TGGCAGTATG CGGAAGAAAT CGTTTCTGGC TCTGGTCACC ATCATCATCA CCAC SEQ ID NO: 28 1 ADSDINIKTG TTDIGSNTTV KTGDLVTYDK ENGMHKKVFY SFIDDKNHNK KLLVIRTKGT IAGQYRVYSE 71 EGANKSGLAW PSAFKVQLQL PDNEVAQISD YYPRNSIDTK EYRSTLTYGF NGNVTGDDTG KIGGCIGAQV 141 SIGHTLKYVQ PDFKTILESP TDKKVGWKVI FNNMVNQNWG PYDRDSWNPV YGNQLFMKTR NGSMKAADNF 211 LDPNKASSLL SSGFSPDFAT VITMDRKASK QQTNIDVIYE RVRDDYQLHW TSTNWKGTNT KDKWTDRSSE 281 RYKIDWEKEE MTNSGSGSGS GSGSGSGSGQ STFLFHDYET FGTHPALDRP AQFAAIRTDS EFNVIGEPEV 351 FYCKPADDYL PQPGAVLITG ITPQEARAKG ENEAAFAARI HSLFTVPKTC ILGYNNVRFD DEVTRNIFYR 421 NFYDPYAWSW QHDNSRWDLL DVMRACYALR PEGINWPEND DGLPSFRLEH LTKANGIEHS NAHDAMADVY 491 ATIAMAKLVK TRQPRLFDYL FTHRNKHKLM ALIDVPQMKP LVHVSGMFGA WRGNTSWVAP LAWHPENRNA 561 VIMVDLAGDI SPLLELDSDT LRERLYTAKT DLGDNAAVPV KLVHINKCPV LAQANTLRPE DADRLGINRQ 631 HCLDNLKILR ENPQVREKVV AIFAEAEPFT PSDNVDAQLY NGFFSDADRA AMKIVLETEP RNLPALDITF 701 VDKRIEKLLF NYRARNFPGT LDYAEQQRWL EHRRQVFTPE FLQGYADELQ MLVQQYADDK EKVALLKALW 771 QYAEEIVSGS GHHHHHH SEQ ID NO: 29 1 ATGGCAGATT CTGATATTAA TATTAAAACC GGTACTACAG ATATTGGAAG CAATACTACA GTAAAAACAG 71 GTGATTTAGT CACTTATGAT AAAGAAAATG GCATGCACAA AAAAGTATTT TATAGTTTTA TCGATGATAA 141 AAATCACAAT AAAAAACTGC TAGTTATTAG AACAAAAGGT ACCATTGCTG GTCAATATAG AGTTTATAGC 211 GAAGAAGGTG CTAACAAAAG TGGTTTAGCC TGGCCTTCAG CCTTTAAGGT ACAGTTGCAA CTACCTGATA 281 ATGAAGTAGC TCAAATATCT GATTACTATC CAAGAAATTC GATTGATACA AAAGAGTATA GGAGTACTTT 351 AACTTATGGA TTCAACGGTA ATGTTACTGG TGATGATACA GGAAAAATTG GCGGCTGTAT TGGTGCACAA 421 GTTTCGATTG GTCATACACT GAAATATGTT CAACCTGATT TCAAAACAAT TTTAGAGAGC CCAACTGATA 491 AAAAAGTAGG CTGGAAAGTG ATATTTAACA ATATGGTGAA TCAAAATTGG GGACCATACG ATCGAGATTC 561 TTGGAACCCG GTATATGGCA ATCAACTTTT CATGAAAACT AGAAATGGTT CTATGAAAGC AGCAGATAAC 631 TTCCTTGATC CTAACAAAGC AAGTTCTCTA TTATCTTCAG GGTTTTCACC AGACTTCGCT ACAGTTATTA 701 CTATGGATAG AAAAGCATCC AAACAACAAA CAAATATAGA TGTAATATAC GAACGAGTTC GTGATGATTA 771 CCAATTGCAT TGGACTTCAA CAAATTGGAA AGGTACCAAT ACTAAAGATA AATGGACAGA TCGTTCTTCA 841 GAAAGATATA AAATCGATTG GGAAAAAGAA GAAATGACAA ATGATGGCTC CGGTAGCGGC TCTGGTTCTG 911 GCTCTGGTTC CGGCAGCGGT TCCGGACAGA GCACCTTCCT GTTTCATGAT TATGAAACCT TCGGTACCCA 981 TCCGGCCCTG GATCGTCCGG CGCAGTTTGC GGCCATTCGC ACCGATAGCG AATTCAATGT GATTGGCGAA 1051 CCGGAAGTGT TTTATTGCAA ACCGGCCGAT GATTATCTGC CGCAGCCGGG TGCGGTGCTG ATTACCGGTA 1121 TTACCCCGCA GGAAGCGCGC GCGAAAGGTG AAAACGAAGC GGCGTTTGCC GCGCGCATTC ATAGCCTGTT 1191 TACCGTGCCG AAAACCTGCA TTCTGGGCTA TAACAATGTG CGCTTCGATG ATGAAGTTAC CCGTAATATC 1261 TTTTATCGTA ACTTTTATGA TCCGTATGCG TGGAGCTGGC AGCATGATAA CAGCCGTTGG GATCTGCTGG 1331 ATGTGATGCG CGCGTGCTAT GCGCTGCGCC CGGAAGGCAT TAATTGGCCG GAAAACGATG ATGGCCTGCC 1401 GAGCTTTCGT CTGGAACATC TGACCAAAGC CAACGGCATT GAACATAGCA ATGCCCATGA TGCGATGGCC 1471 GATGTTTATG CGACCATTGC GATGGCGAAA CTGGTTAAAA CCCGTCAGCC GCGCCTGTTT GATTATCTGT 1541 TTACCCACCG TAACAAACAC AAACTGATGG CGCTGATTGA TGTTCCGCAG ATGAAACCGC TGGTGCATGT 1611 GAGCGGCATG TTTGGCGCCT GGCGCGGCAA CACCAGCTGG GTGGCCCCGC TGGCCTGGCA CCCGGAAAAT 1681 CGTAACGCCG TGATTATGGT TGATCTGGCC GGTGATATTA GCCCGCTGCT GGAACTGGAT AGCGATACCC 1751 TGCGTGAACG CCTGTATACC GCCAAAACCG ATCTGGGCGA TAATGCCGCC GTGCCGGTGA AACTGGTTCA 1821 CATTAACAAA TGCCCGGTGC TGGCCCAGGC GAACACCCTG CGCCCGGAAG ATGCGGATCG TCTGGGTATT 1891 AATCGCCAGC ATTGTCTGGA TAATCTGAAA ATCCTGCGTG AAAACCCGCA GGTGCGTGAA AAAGTGGTGG 1961 CGATCTTCGC GGAAGCGGAA CCGTTCACCC CGAGCGATAA CGTGGATGCG CAGCTGTATA ACGGCTTCTT 2031 TAGCGATGCC GATCGCGCGG CGATGAAAAT CGTTCTGGAA ACCGAACCGC GCAATCTGCC GGCGCTGGAT 2101 ATTACCTTTG TTGATAAACG TATTGAAAAA CTGCTGTTTA ATTATCGTGC GCGCAATTTT CCGGGTACCC 2171 TGGATTATGC CGAACAGCAG CGTTGGCTGG AACATCGTCG TCAGGTTTTC ACCCCGGAAT TTCTGCAGGG 2241 TTATGCGGAT GAACTGCAGA TGCTGGTTCA GCAGTATGCC GATGATAAAG AAAAAGTGGC GCTGCTGAAA 2311 GCGCTGTGGC AGTATGCGGA AGAAATCGTT TCTGGCTCTG GTCACCATCA TCATCACCAC

SEQ ID NO: 30 1 ADSDINIKTG TTDIGSNTTV KTGDLVTYDK ENGMHKKVFY SFIDDKNHNK KLLVIRTKGT IAGQYRVYSE 71 EGANKSGLAW PSAFKVQLQL PDNEVAQISD YYPRNSIDTK EYRSTLTYGF NGNVTGDDTG KIGGCIGAQV 141 SIGHTLKYVQ PDFKTILESP TDKKVGWKVI FNNMVNQNWG PYDRDSWNPV YGNQLFMKTR NGSMKAADNF 211 LDPNKASSLL SSGFSPDFAT VITMDRKASK QQTNIDVIYE RVRDDYQLHW TSTNWKGTNT KDKWTDRSSE 281 RYKIDWEKEE MTNDGSGSGS GSGSGSGSGS GQSTFLFHDY ETFGTHPALD RPAQFAAIRT DSEFNVIGEP 351 EVFYCKPADD YLPQPGAVLI TGITPQEARA KGENEAAFAA RIHSLFTVPK TCILGYNNVR FDDEVTRNIF 421 YRNFYDPYAW SWQHDNSRWD LLDVMRACYA LRPEGINWPE NDDGLPSFRL EHLTKANGIE HSNAHDAMAD 491 VYATIAMAKL VKTRQPRLFD YLFTHRNKHK LMALIDVPQM KPLVHVSGMF GAWRGNTSWV APLAWHPENR 561 NAVIMVDLAG DISPLLELDS DTLRERLYTA KTDLGDNAAV PVKLVHINKC PVLAQANTLR PEDADRLGIN 631 RQHCLDNLKI LRENPQVREK VVAIFAEAEP FTPSDNVDAQ LYNGFFSDAD RAAMKIVLET EPRNLPALDI 701 TFVDKRIEKL LFNYRARNFP GTLDYAEQQR WLEHRRQVFT PEFLQGYADE LQMLVQQYAD DKEKVALLKA 771 LWQYAEEIVS GSGHHHHHH

Sequence CWU 1

1

321882DNAStaphylococcus aureusCDS(4)..(882) 1atg gca gat tct gat att aat att aaa acc ggt act aca gat att gga 48 Ala Asp Ser Asp Ile Asn Ile Lys Thr Gly Thr Thr Asp Ile Gly 1 5 10 15agc aat act aca gta aaa aca ggt gat tta gtc act tat gat aaa gaa 96Ser Asn Thr Thr Val Lys Thr Gly Asp Leu Val Thr Tyr Asp Lys Glu 20 25 30aat ggc atg cac aaa aaa gta ttt tat agt ttt atc gat gat aaa aat 144Asn Gly Met His Lys Lys Val Phe Tyr Ser Phe Ile Asp Asp Lys Asn 35 40 45cac aat aaa aaa ctg cta gtt att aga aca aaa ggt acc att gct ggt 192His Asn Lys Lys Leu Leu Val Ile Arg Thr Lys Gly Thr Ile Ala Gly 50 55 60caa tat aga gtt tat agc gaa gaa ggt gct aac aaa agt ggt tta gcc 240Gln Tyr Arg Val Tyr Ser Glu Glu Gly Ala Asn Lys Ser Gly Leu Ala 65 70 75tgg cct tca gcc ttt aag gta cag ttg caa cta cct gat aat gaa gta 288Trp Pro Ser Ala Phe Lys Val Gln Leu Gln Leu Pro Asp Asn Glu Val80 85 90 95gct caa ata tct gat tac tat cca aga aat tcg att gat aca aaa gag 336Ala Gln Ile Ser Asp Tyr Tyr Pro Arg Asn Ser Ile Asp Thr Lys Glu 100 105 110tat atg agt act tta act tat gga ttc aac ggt aat gtt act ggt gat 384Tyr Met Ser Thr Leu Thr Tyr Gly Phe Asn Gly Asn Val Thr Gly Asp 115 120 125gat aca gga aaa att ggc ggc ctt att ggt gca aat gtt tcg att ggt 432Asp Thr Gly Lys Ile Gly Gly Leu Ile Gly Ala Asn Val Ser Ile Gly 130 135 140cat aca ctg aaa tat gtt caa cct gat ttc aaa aca att tta gag agc 480His Thr Leu Lys Tyr Val Gln Pro Asp Phe Lys Thr Ile Leu Glu Ser 145 150 155cca act gat aaa aaa gta ggc tgg aaa gtg ata ttt aac aat atg gtg 528Pro Thr Asp Lys Lys Val Gly Trp Lys Val Ile Phe Asn Asn Met Val160 165 170 175aat caa aat tgg gga cca tac gat cga gat tct tgg aac ccg gta tat 576Asn Gln Asn Trp Gly Pro Tyr Asp Arg Asp Ser Trp Asn Pro Val Tyr 180 185 190ggc aat caa ctt ttc atg aaa act aga aat ggt tct atg aaa gca gca 624Gly Asn Gln Leu Phe Met Lys Thr Arg Asn Gly Ser Met Lys Ala Ala 195 200 205gat aac ttc ctt gat cct aac aaa gca agt tct cta tta tct tca ggg 672Asp Asn Phe Leu Asp Pro Asn Lys Ala Ser Ser Leu Leu Ser Ser Gly 210 215 220ttt tca cca gac ttc gct aca gtt att act atg gat aga aaa gca tcc 720Phe Ser Pro Asp Phe Ala Thr Val Ile Thr Met Asp Arg Lys Ala Ser 225 230 235aaa caa caa aca aat ata gat gta ata tac gaa cga gtt cgt gat gat 768Lys Gln Gln Thr Asn Ile Asp Val Ile Tyr Glu Arg Val Arg Asp Asp240 245 250 255tac caa ttg cat tgg act tca aca aat tgg aaa ggt acc aat act aaa 816Tyr Gln Leu His Trp Thr Ser Thr Asn Trp Lys Gly Thr Asn Thr Lys 260 265 270gat aaa tgg aca gat cgt tct tca gaa aga tat aaa atc gat tgg gaa 864Asp Lys Trp Thr Asp Arg Ser Ser Glu Arg Tyr Lys Ile Asp Trp Glu 275 280 285aaa gaa gaa atg aca aat 882Lys Glu Glu Met Thr Asn 2902293PRTStaphylococcus aureus 2Ala Asp Ser Asp Ile Asn Ile Lys Thr Gly Thr Thr Asp Ile Gly Ser1 5 10 15Asn Thr Thr Val Lys Thr Gly Asp Leu Val Thr Tyr Asp Lys Glu Asn 20 25 30Gly Met His Lys Lys Val Phe Tyr Ser Phe Ile Asp Asp Lys Asn His 35 40 45Asn Lys Lys Leu Leu Val Ile Arg Thr Lys Gly Thr Ile Ala Gly Gln 50 55 60Tyr Arg Val Tyr Ser Glu Glu Gly Ala Asn Lys Ser Gly Leu Ala Trp65 70 75 80Pro Ser Ala Phe Lys Val Gln Leu Gln Leu Pro Asp Asn Glu Val Ala 85 90 95Gln Ile Ser Asp Tyr Tyr Pro Arg Asn Ser Ile Asp Thr Lys Glu Tyr 100 105 110Met Ser Thr Leu Thr Tyr Gly Phe Asn Gly Asn Val Thr Gly Asp Asp 115 120 125Thr Gly Lys Ile Gly Gly Leu Ile Gly Ala Asn Val Ser Ile Gly His 130 135 140Thr Leu Lys Tyr Val Gln Pro Asp Phe Lys Thr Ile Leu Glu Ser Pro145 150 155 160Thr Asp Lys Lys Val Gly Trp Lys Val Ile Phe Asn Asn Met Val Asn 165 170 175Gln Asn Trp Gly Pro Tyr Asp Arg Asp Ser Trp Asn Pro Val Tyr Gly 180 185 190Asn Gln Leu Phe Met Lys Thr Arg Asn Gly Ser Met Lys Ala Ala Asp 195 200 205Asn Phe Leu Asp Pro Asn Lys Ala Ser Ser Leu Leu Ser Ser Gly Phe 210 215 220Ser Pro Asp Phe Ala Thr Val Ile Thr Met Asp Arg Lys Ala Ser Lys225 230 235 240Gln Gln Thr Asn Ile Asp Val Ile Tyr Glu Arg Val Arg Asp Asp Tyr 245 250 255Gln Leu His Trp Thr Ser Thr Asn Trp Lys Gly Thr Asn Thr Lys Asp 260 265 270Lys Trp Thr Asp Arg Ser Ser Glu Arg Tyr Lys Ile Asp Trp Glu Lys 275 280 285Glu Glu Met Thr Asn 2903882DNAArtificial sequencealpha-HL M113R/N139Q 3atg gca gat tct gat att aat att aaa acc ggt act aca gat att gga 48 Ala Asp Ser Asp Ile Asn Ile Lys Thr Gly Thr Thr Asp Ile Gly 1 5 10 15agc aat act aca gta aaa aca ggt gat tta gtc act tat gat aaa gaa 96Ser Asn Thr Thr Val Lys Thr Gly Asp Leu Val Thr Tyr Asp Lys Glu 20 25 30aat ggc atg cac aaa aaa gta ttt tat agt ttt atc gat gat aaa aat 144Asn Gly Met His Lys Lys Val Phe Tyr Ser Phe Ile Asp Asp Lys Asn 35 40 45cac aat aaa aaa ctg cta gtt att aga aca aaa ggt acc att gct ggt 192His Asn Lys Lys Leu Leu Val Ile Arg Thr Lys Gly Thr Ile Ala Gly 50 55 60caa tat aga gtt tat agc gaa gaa ggt gct aac aaa agt ggt tta gcc 240Gln Tyr Arg Val Tyr Ser Glu Glu Gly Ala Asn Lys Ser Gly Leu Ala 65 70 75tgg cct tca gcc ttt aag gta cag ttg caa cta cct gat aat gaa gta 288Trp Pro Ser Ala Phe Lys Val Gln Leu Gln Leu Pro Asp Asn Glu Val80 85 90 95gct caa ata tct gat tac tat cca aga aat tcg att gat aca aaa gag 336Ala Gln Ile Ser Asp Tyr Tyr Pro Arg Asn Ser Ile Asp Thr Lys Glu 100 105 110tat agg agt act tta act tat gga ttc aac ggt aat gtt act ggt gat 384Tyr Arg Ser Thr Leu Thr Tyr Gly Phe Asn Gly Asn Val Thr Gly Asp 115 120 125gat aca gga aaa att ggc ggc ctt att ggt gca caa gtt tcg att ggt 432Asp Thr Gly Lys Ile Gly Gly Leu Ile Gly Ala Gln Val Ser Ile Gly 130 135 140cat aca ctg aaa tat gtt caa cct gat ttc aaa aca att tta gag agc 480His Thr Leu Lys Tyr Val Gln Pro Asp Phe Lys Thr Ile Leu Glu Ser 145 150 155cca act gat aaa aaa gta ggc tgg aaa gtg ata ttt aac aat atg gtg 528Pro Thr Asp Lys Lys Val Gly Trp Lys Val Ile Phe Asn Asn Met Val160 165 170 175aat caa aat tgg gga cca tac gat cga gat tct tgg aac ccg gta tat 576Asn Gln Asn Trp Gly Pro Tyr Asp Arg Asp Ser Trp Asn Pro Val Tyr 180 185 190ggc aat caa ctt ttc atg aaa act aga aat ggt tct atg aaa gca gca 624Gly Asn Gln Leu Phe Met Lys Thr Arg Asn Gly Ser Met Lys Ala Ala 195 200 205gat aac ttc ctt gat cct aac aaa gca agt tct cta tta tct tca ggg 672Asp Asn Phe Leu Asp Pro Asn Lys Ala Ser Ser Leu Leu Ser Ser Gly 210 215 220ttt tca cca gac ttc gct aca gtt att act atg gat aga aaa gca tcc 720Phe Ser Pro Asp Phe Ala Thr Val Ile Thr Met Asp Arg Lys Ala Ser 225 230 235aaa caa caa aca aat ata gat gta ata tac gaa cga gtt cgt gat gat 768Lys Gln Gln Thr Asn Ile Asp Val Ile Tyr Glu Arg Val Arg Asp Asp240 245 250 255tac caa ttg cat tgg act tca aca aat tgg aaa ggt acc aat act aaa 816Tyr Gln Leu His Trp Thr Ser Thr Asn Trp Lys Gly Thr Asn Thr Lys 260 265 270gat aaa tgg aca gat cgt tct tca gaa aga tat aaa atc gat tgg gaa 864Asp Lys Trp Thr Asp Arg Ser Ser Glu Arg Tyr Lys Ile Asp Trp Glu 275 280 285aaa gaa gaa atg aca aat 882Lys Glu Glu Met Thr Asn 2904293PRTArtificial sequencealpha-HL M113R/N139Q 4Ala Asp Ser Asp Ile Asn Ile Lys Thr Gly Thr Thr Asp Ile Gly Ser1 5 10 15Asn Thr Thr Val Lys Thr Gly Asp Leu Val Thr Tyr Asp Lys Glu Asn 20 25 30Gly Met His Lys Lys Val Phe Tyr Ser Phe Ile Asp Asp Lys Asn His 35 40 45Asn Lys Lys Leu Leu Val Ile Arg Thr Lys Gly Thr Ile Ala Gly Gln 50 55 60Tyr Arg Val Tyr Ser Glu Glu Gly Ala Asn Lys Ser Gly Leu Ala Trp65 70 75 80Pro Ser Ala Phe Lys Val Gln Leu Gln Leu Pro Asp Asn Glu Val Ala 85 90 95Gln Ile Ser Asp Tyr Tyr Pro Arg Asn Ser Ile Asp Thr Lys Glu Tyr 100 105 110Arg Ser Thr Leu Thr Tyr Gly Phe Asn Gly Asn Val Thr Gly Asp Asp 115 120 125Thr Gly Lys Ile Gly Gly Leu Ile Gly Ala Gln Val Ser Ile Gly His 130 135 140Thr Leu Lys Tyr Val Gln Pro Asp Phe Lys Thr Ile Leu Glu Ser Pro145 150 155 160Thr Asp Lys Lys Val Gly Trp Lys Val Ile Phe Asn Asn Met Val Asn 165 170 175Gln Asn Trp Gly Pro Tyr Asp Arg Asp Ser Trp Asn Pro Val Tyr Gly 180 185 190Asn Gln Leu Phe Met Lys Thr Arg Asn Gly Ser Met Lys Ala Ala Asp 195 200 205Asn Phe Leu Asp Pro Asn Lys Ala Ser Ser Leu Leu Ser Ser Gly Phe 210 215 220Ser Pro Asp Phe Ala Thr Val Ile Thr Met Asp Arg Lys Ala Ser Lys225 230 235 240Gln Gln Thr Asn Ile Asp Val Ile Tyr Glu Arg Val Arg Asp Asp Tyr 245 250 255Gln Leu His Trp Thr Ser Thr Asn Trp Lys Gly Thr Asn Thr Lys Asp 260 265 270Lys Trp Thr Asp Arg Ser Ser Glu Arg Tyr Lys Ile Asp Trp Glu Lys 275 280 285Glu Glu Met Thr Asn 29054543DNAArtificial sequencepT7-SC1_BspEI-KO 5ttcttgaaga cgaaagggcc tcgtgatacg cctattttta taggttaatg tcatgataat 60aatggtttct tagacgtcag gtggcacttt tcggggaaat gtgcgcggaa cccctatttg 120tttatttttc taaatacatt caaatatgta tccgctcatg agacaataac cctgataaat 180gcttcaataa tattgaaaaa ggaagagtat gagtattcaa catttccgtg tcgcccttat 240tccctttttt gcggcatttt gccttcctgt ttttgctcac ccagaaacgc tggtgaaagt 300aaaagatgct gaagatcagt tgggtgcacg agtgggttac atcgaactgg atctcaacag 360cggtaagatc cttgagagtt ttcgccccga agaacgtttt ccaatgatga gcacttttaa 420agttctgcta tgtggcgcgg tattatcccg tgttgacgcc gggcaagagc aactcggtcg 480ccgcatacac tattctcaga atgacttggt tgagtactca ccagtcacag aaaagcatct 540tacggatggc atgacagtaa gagaattatg cagtgctgcc ataaccatga gtgataacac 600tgcggccaac ttacttctga caacgatcgg aggaccgaag gagctaaccg cttttttgca 660caacatgggg gatcatgtaa ctcgccttga tcgttgggaa ccggagctga atgaagccat 720accaaacgac gagcgtgaca ccacgatgcc tgcagcaatg gcaacaacgt tgcgcaaact 780attaactggc gaactactta ctctagcttc ccggcaacaa ttaatagact ggatggaggc 840ggataaagtt gcaggaccac ttctgcgctc ggcccttccg gctggctggt ttattgctga 900taaatctgga gccggtgagc gtgggtctcg cggtatcatt gcagcactgg ggccagatgg 960taagccctcc cgtatcgtag ttatctacac gacggggagt caggcaacta tggatgaacg 1020aaatagacag atcgctgaga taggtgcctc actgattaag cattggtaac tgtcagacca 1080agtttactca tatatacttt agattgattt aaaacttcat ttttaattta aaaggatcta 1140ggtgaagatc ctttttgata atctcatgac caaaatccct taacgtgagt tttcgttcca 1200ctgagcgtca gaccccgtag aaaagatcaa aggatcttct tgagatcctt tttttctgcg 1260cgtaatctgc tgcttgcaaa caaaaaaacc accgctacca gcggtggttt gtttgccgga 1320tcaagagcta ccaactcttt ttccgaaggt aactggcttc agcagagcgc agataccaaa 1380tactgtcctt ctagtgtagc cgtagttagg ccaccacttc aagaactctg tagcaccgcc 1440tacatacctc gctctgctaa tcctgttacc agtggctgct gccagtggcg ataagtcgtg 1500tcttaccggg ttggactcaa gacgatagtt accggataag gcgcagcggt cgggctgaac 1560ggggggttcg tgcacacagc ccagcttgga gcgaacgacc tacaccgaac tgagatacct 1620acagcgtgag ctatgagaaa gcgccacgct tcccgaaggg agaaaggcgg acaggtatcc 1680ggtaagcggc agggtcggaa caggagagcg cacgagggag cttccagggg gaaacgcctg 1740gtatctttat agtcctgtcg ggtttcgcca cctctgactt gagcgtcgat ttttgtgatg 1800ctcgtcaggg gggcggagcc tatggaaaaa cgccagcaac gcggcctttt tacggttcct 1860ggccttttgc tggccttttg ctcacatgtt ctttcctgcg ttatcccctg attctgtgga 1920taaccgtatt accgcctttg agtgagctga taccgctcgc cgcagccgaa cgaccgagcg 1980cagcgagtca gtgagcgagg aagcggaaga gcgcctgatg cggtattttc tccttacgca 2040tctgtgcggt atttcacacc gcatatatgg tgcactctca gtacaatctg ctctgatgcc 2100gcatagttaa gccagtatac actccgctat cgctacgtga ctgggtcatg gctgcgcccc 2160gacacccgcc aacacccgct gacgcgccct gacgggcttg tctgctcccg gcatccgctt 2220acagacaagc tgtgaccgtc tccgggagct gcatgtgtca gaggttttca ccgtcatcac 2280cgaaacgcgc gaggcagcgc tctcccttat gcgactcctg cattaggaag cagcccagta 2340gtaggttgag gccgttgagc accgccgccg caaggaatgg tgcatgcaag gagatggcgc 2400ccaacagtcc cccggccacg gggcctgcca ccatacccac gccgaaacaa gcgctcatga 2460gcccgaagtg gcgagcccga tcttccccat cggtgatgtc ggcgatatag gcgccagcaa 2520ccgcacctgt ggcgccggtg atgccggcca cgatgcgtcc ggcgtagagg atcgagatct 2580agcccgccta atgagcgggc ttttttttag atctcgatcc cgcgaaatta atacgactca 2640ctatagggag accacaacgg tttccctcta gaaataattt tgtttaactt taagaaggag 2700atatacatat ggcagattct gatattaata ttaaaaccgg tactacagat attggaagca 2760atactacagt aaaaacaggt gatttagtca cttatgataa agaaaatggc atgcacaaaa 2820aagtatttta tagttttatc gatgataaaa atcacaataa aaaactgcta gttattagaa 2880caaaaggtac cattgctggt caatatagag tttatagcga agaaggtgct aacaaaagtg 2940gtttagcctg gccttcagcc tttaaggtac agttgcaact acctgataat gaagtagctc 3000aaatatctga ttactatcca agaaattcga ttgatacaaa agagtatatg agtactttaa 3060cttatggatt caacggtaat gttactggtg atgatacagg aaaaattggc ggccttattg 3120gtgcaaatgt ttcgattggt catacactga aatatgttca acctgatttc aaaacaattt 3180tagagagccc aactgataaa aaagtaggct ggaaagtgat atttaacaat atggtgaatc 3240aaaattgggg accatacgat cgagattctt ggaacccggt atatggcaat caacttttca 3300tgaaaactag aaatggttct atgaaagcag cagataactt ccttgatcct aacaaagcaa 3360gttctctatt atcttcaggg ttttcaccag acttcgctac agttattact atggatagaa 3420aagcatccaa acaacaaaca aatatagatg taatatacga acgagttcgt gatgattacc 3480aattgcattg gacttcaaca aattggaaag gtaccaatac taaagataaa tggacagatc 3540gttcttcaga aagatataaa atcgattggg aaaaagaaga aatgacaaat taatgtaaat 3600tatttgtaca tgtacaaata aatataattt ataactttag ccgaaagctt ggatccggct 3660gctaacaaag cccgaaagga agctgagttg gctgctgcca ccgctgagca ataactagca 3720taaccccttg gggcctctaa acgggtcttg aggggttttt tgctgaaagg aggaactata 3780tataattcga gctcggtacc caccccggtt gataatcaga aaagccccaa aaacaggaag 3840attgtataag caaatattta aattgtaaac gttaatattt tgttaaaatt cgcgttaaat 3900ttttgttaaa tcagctcatt ttttaaccaa taggccgaaa tcggcaaaat cccttataaa 3960tcaaaagaat agaccgagat agggttgagt gttgttccag tttggaacaa gagtccagta 4020ttaaagaacg tggactccaa cgtcaaaggg cgaaaaaccg tctatcaggg cgatggccca 4080ctacgtgaac catcacccta atcaagtttt ttggggtcga ggtgccgtaa agcactaaat 4140cggaacccta aagggatgcc ccgatttaga gcttgacggg gaaagccggc gaacgtggcg 4200agaaaggaag ggaagaaagc gaaaggagcg ggcgctaggg cgctggcaag tgtagcggtc 4260acgctgcgcg taaccaccac acccgccgcg cttaatgcgc cgctacaggg cgcgtgggga 4320tcctctagag tcgacctgca ggcatgcaag ctatcccgca agaggcccgg cagtaccggc 4380ataaccaagc ctatgcctac agcatccagg gtgacggtgc cgaggatgac gatgagcgca 4440ttgttagatt tcatacacgg tgcctgactg cgttagcaat ttaactgtga taaactaccg 4500cattaaagct agcttatcga tgataagctg tcaaacatga gaa 45436888DNAArtificial sequencewild-type alpha-hemolysin containing a BspEI cloning site at position 1 (L1) 6atggcagatt ctgatattaa tattaaaacc ggtactacag atattggaag caatacttcc 60ggaacagtaa aaacaggtga tttagtcact tatgataaag aaaatggcat gcacaaaaaa 120gtattttata gttttatcga tgataaaaat cacaataaaa aactgctagt tattagaaca 180aaaggtacca ttgctggtca atatagagtt tatagcgaag aaggtgctaa caaaagtggt 240ttagcctggc cttcagcctt taaggtacag ttgcaactac ctgataatga agtagctcaa 300atatctgatt actatccaag aaattcgatt gatacaaaag agtatatgag tactttaact 360tatggattca acggtaatgt tactggtgat gatacaggaa aaattggcgg ccttattggt 420gcaaatgttt cgattggtca tacactgaaa tatgttcaac ctgatttcaa aacaatttta 480gagagcccaa ctgataaaaa agtaggctgg aaagtgatat ttaacaatat ggtgaatcaa 540aattggggac catacgatcg agattcttgg aacccggtat atggcaatca acttttcatg 600aaaactagaa atggttctat gaaagcagca gataacttcc ttgatcctaa caaagcaagt 660tctctattat cttcagggtt ttcaccagac ttcgctacag ttattactat ggatagaaaa 720gcatccaaac aacaaacaaa tatagatgta atatacgaac gagttcgtga tgattaccaa 780ttgcattgga cttcaacaaa ttggaaaggt accaatacta aagataaatg gacagatcgt 840tcttcagaaa gatataaaat

cgattgggaa aaagaagaaa tgacaaat 8887888DNAArtificial sequencewild-type alpha-hemolysin containing a BspEI cloning site at position 2 (L2a) 7atggcagatt ctgatattaa tattaaaacc ggtactacag atattggaag caatactaca 60gtaaaaacag gtgatttagt cacttatgat aaagaaaatg gcatgcacaa aaaagtattt 120tatagtttta tcgattccgg agataaaaat cacaataaaa aactgctagt tattagaaca 180aaaggtacca ttgctggtca atatagagtt tatagcgaag aaggtgctaa caaaagtggt 240ttagcctggc cttcagcctt taaggtacag ttgcaactac ctgataatga agtagctcaa 300atatctgatt actatccaag aaattcgatt gatacaaaag agtatatgag tactttaact 360tatggattca acggtaatgt tactggtgat gatacaggaa aaattggcgg ccttattggt 420gcaaatgttt cgattggtca tacactgaaa tatgttcaac ctgatttcaa aacaatttta 480gagagcccaa ctgataaaaa agtaggctgg aaagtgatat ttaacaatat ggtgaatcaa 540aattggggac catacgatcg agattcttgg aacccggtat atggcaatca acttttcatg 600aaaactagaa atggttctat gaaagcagca gataacttcc ttgatcctaa caaagcaagt 660tctctattat cttcagggtt ttcaccagac ttcgctacag ttattactat ggatagaaaa 720gcatccaaac aacaaacaaa tatagatgta atatacgaac gagttcgtga tgattaccaa 780ttgcattgga cttcaacaaa ttggaaaggt accaatacta aagataaatg gacagatcgt 840tcttcagaaa gatataaaat cgattgggaa aaagaagaaa tgacaaat 8888888DNAArtificial sequencewild-type alpha-hemolysin containing a BspEI cloning site at position 2 (L2b) 8atggcagatt ctgatattaa tattaaaacc ggtactacag atattggaag caatactaca 60gtaaaaacag gtgatttagt cacttatgat aaagaaaatg gcatgcacaa aaaagtattt 120tatagtttta tcgatgataa aaatcacaat aaatccggaa aactgctagt tattagaaca 180aaaggtacca ttgctggtca atatagagtt tatagcgaag aaggtgctaa caaaagtggt 240ttagcctggc cttcagcctt taaggtacag ttgcaactac ctgataatga agtagctcaa 300atatctgatt actatccaag aaattcgatt gatacaaaag agtatatgag tactttaact 360tatggattca acggtaatgt tactggtgat gatacaggaa aaattggcgg ccttattggt 420gcaaatgttt cgattggtca tacactgaaa tatgttcaac ctgatttcaa aacaatttta 480gagagcccaa ctgataaaaa agtaggctgg aaagtgatat ttaacaatat ggtgaatcaa 540aattggggac catacgatcg agattcttgg aacccggtat atggcaatca acttttcatg 600aaaactagaa atggttctat gaaagcagca gataacttcc ttgatcctaa caaagcaagt 660tctctattat cttcagggtt ttcaccagac ttcgctacag ttattactat ggatagaaaa 720gcatccaaac aacaaacaaa tatagatgta atatacgaac gagttcgtga tgattaccaa 780ttgcattgga cttcaacaaa ttggaaaggt accaatacta aagataaatg gacagatcgt 840tcttcagaaa gatataaaat cgattgggaa aaagaagaaa tgacaaat 8889804DNAE. coliCDS(1)..(804) 9atg aaa ttt gtc tct ttt aat atc aac ggc ctg cgc gcc aga cct cac 48Met Lys Phe Val Ser Phe Asn Ile Asn Gly Leu Arg Ala Arg Pro His1 5 10 15cag ctt gaa gcc atc gtc gaa aag cac caa ccg gat gtg att ggc ctg 96Gln Leu Glu Ala Ile Val Glu Lys His Gln Pro Asp Val Ile Gly Leu 20 25 30cag gag aca aaa gtt cat gac gat atg ttt ccg ctc gaa gag gtg gcg 144Gln Glu Thr Lys Val His Asp Asp Met Phe Pro Leu Glu Glu Val Ala 35 40 45aag ctc ggc tac aac gtg ttt tat cac ggg cag aaa ggc cat tat ggc 192Lys Leu Gly Tyr Asn Val Phe Tyr His Gly Gln Lys Gly His Tyr Gly 50 55 60gtg gcg ctg ctg acc aaa gag acg ccg att gcc gtg cgt cgc ggc ttt 240Val Ala Leu Leu Thr Lys Glu Thr Pro Ile Ala Val Arg Arg Gly Phe65 70 75 80ccc ggt gac gac gaa gag gcg cag cgg cgg att att atg gcg gaa atc 288Pro Gly Asp Asp Glu Glu Ala Gln Arg Arg Ile Ile Met Ala Glu Ile 85 90 95ccc tca ctg ctg ggt aat gtc acc gtg atc aac ggt tac ttc ccg cag 336Pro Ser Leu Leu Gly Asn Val Thr Val Ile Asn Gly Tyr Phe Pro Gln 100 105 110ggt gaa agc cgc gac cat ccg ata aaa ttc ccg gca aaa gcg cag ttt 384Gly Glu Ser Arg Asp His Pro Ile Lys Phe Pro Ala Lys Ala Gln Phe 115 120 125tat cag aat ctg caa aac tac ctg gaa acc gaa ctc aaa cgt gat aat 432Tyr Gln Asn Leu Gln Asn Tyr Leu Glu Thr Glu Leu Lys Arg Asp Asn 130 135 140ccg gta ctg att atg ggc gat atg aat atc agc cct aca gat ctg gat 480Pro Val Leu Ile Met Gly Asp Met Asn Ile Ser Pro Thr Asp Leu Asp145 150 155 160atc ggc att ggc gaa gaa aac cgt aag cgc tgg ctg cgt acc ggt aaa 528Ile Gly Ile Gly Glu Glu Asn Arg Lys Arg Trp Leu Arg Thr Gly Lys 165 170 175tgc tct ttc ctg ccg gaa gag cgc gaa tgg atg gac agg ctg atg agc 576Cys Ser Phe Leu Pro Glu Glu Arg Glu Trp Met Asp Arg Leu Met Ser 180 185 190tgg ggg ttg gtc gat acc ttc cgc cat gcg aat ccg caa aca gca gat 624Trp Gly Leu Val Asp Thr Phe Arg His Ala Asn Pro Gln Thr Ala Asp 195 200 205cgt ttc tca tgg ttt gat tac cgc tca aaa ggt ttt gac gat aac cgt 672Arg Phe Ser Trp Phe Asp Tyr Arg Ser Lys Gly Phe Asp Asp Asn Arg 210 215 220ggt ctg cgc atc gac ctg ctg ctc gcc agc caa ccg ctg gca gaa tgt 720Gly Leu Arg Ile Asp Leu Leu Leu Ala Ser Gln Pro Leu Ala Glu Cys225 230 235 240tgc gta gaa acc ggc atc gac tat gaa atc cgc agc atg gaa aaa ccg 768Cys Val Glu Thr Gly Ile Asp Tyr Glu Ile Arg Ser Met Glu Lys Pro 245 250 255tcc gat cac gcc ccc gtc tgg gcg acc ttc cgc cgc 804Ser Asp His Ala Pro Val Trp Ala Thr Phe Arg Arg 260 26510268PRTE. coli 10Met Lys Phe Val Ser Phe Asn Ile Asn Gly Leu Arg Ala Arg Pro His1 5 10 15Gln Leu Glu Ala Ile Val Glu Lys His Gln Pro Asp Val Ile Gly Leu 20 25 30Gln Glu Thr Lys Val His Asp Asp Met Phe Pro Leu Glu Glu Val Ala 35 40 45Lys Leu Gly Tyr Asn Val Phe Tyr His Gly Gln Lys Gly His Tyr Gly 50 55 60Val Ala Leu Leu Thr Lys Glu Thr Pro Ile Ala Val Arg Arg Gly Phe65 70 75 80Pro Gly Asp Asp Glu Glu Ala Gln Arg Arg Ile Ile Met Ala Glu Ile 85 90 95Pro Ser Leu Leu Gly Asn Val Thr Val Ile Asn Gly Tyr Phe Pro Gln 100 105 110Gly Glu Ser Arg Asp His Pro Ile Lys Phe Pro Ala Lys Ala Gln Phe 115 120 125Tyr Gln Asn Leu Gln Asn Tyr Leu Glu Thr Glu Leu Lys Arg Asp Asn 130 135 140Pro Val Leu Ile Met Gly Asp Met Asn Ile Ser Pro Thr Asp Leu Asp145 150 155 160Ile Gly Ile Gly Glu Glu Asn Arg Lys Arg Trp Leu Arg Thr Gly Lys 165 170 175Cys Ser Phe Leu Pro Glu Glu Arg Glu Trp Met Asp Arg Leu Met Ser 180 185 190Trp Gly Leu Val Asp Thr Phe Arg His Ala Asn Pro Gln Thr Ala Asp 195 200 205Arg Phe Ser Trp Phe Asp Tyr Arg Ser Lys Gly Phe Asp Asp Asn Arg 210 215 220Gly Leu Arg Ile Asp Leu Leu Leu Ala Ser Gln Pro Leu Ala Glu Cys225 230 235 240Cys Val Glu Thr Gly Ile Asp Tyr Glu Ile Arg Ser Met Glu Lys Pro 245 250 255Ser Asp His Ala Pro Val Trp Ala Thr Phe Arg Arg 260 265111425DNAE. coliCDS(1)..(1425) 11atg atg aat gac ggt aag caa caa tct acc ttt ttg ttt cac gat tac 48Met Met Asn Asp Gly Lys Gln Gln Ser Thr Phe Leu Phe His Asp Tyr1 5 10 15gaa acc ttt ggc acg cac ccc gcg tta gat cgc cct gca cag ttc gca 96Glu Thr Phe Gly Thr His Pro Ala Leu Asp Arg Pro Ala Gln Phe Ala 20 25 30gcc att cgc acc gat agc gaa ttc aat gtc atc ggc gaa ccc gaa gtc 144Ala Ile Arg Thr Asp Ser Glu Phe Asn Val Ile Gly Glu Pro Glu Val 35 40 45ttt tac tgc aag ccc gct gat gac tat tta ccc cag cca gga gcc gta 192Phe Tyr Cys Lys Pro Ala Asp Asp Tyr Leu Pro Gln Pro Gly Ala Val 50 55 60tta att acc ggt att acc ccg cag gaa gca cgg gcg aaa gga gaa aac 240Leu Ile Thr Gly Ile Thr Pro Gln Glu Ala Arg Ala Lys Gly Glu Asn65 70 75 80gaa gcc gcg ttt gcc gcc cgt att cac tcg ctt ttt acc gta ccg aag 288Glu Ala Ala Phe Ala Ala Arg Ile His Ser Leu Phe Thr Val Pro Lys 85 90 95acc tgt att ctg ggc tac aac aat gtg cgt ttc gac gac gaa gtc aca 336Thr Cys Ile Leu Gly Tyr Asn Asn Val Arg Phe Asp Asp Glu Val Thr 100 105 110cgc aac att ttt tat cgt aat ttc tac gat cct tac gcc tgg agc tgg 384Arg Asn Ile Phe Tyr Arg Asn Phe Tyr Asp Pro Tyr Ala Trp Ser Trp 115 120 125cag cat gat aac tcg cgc tgg gat tta ctg gat gtt atg cgt gcc tgt 432Gln His Asp Asn Ser Arg Trp Asp Leu Leu Asp Val Met Arg Ala Cys 130 135 140tat gcc ctg cgc ccg gaa gga ata aac tgg cct gaa aat gat gac ggt 480Tyr Ala Leu Arg Pro Glu Gly Ile Asn Trp Pro Glu Asn Asp Asp Gly145 150 155 160cta ccg agc ttt cgc ctt gag cat tta acc aaa gcg aat ggt att gaa 528Leu Pro Ser Phe Arg Leu Glu His Leu Thr Lys Ala Asn Gly Ile Glu 165 170 175cat agc aac gcc cac gat gcg atg gct gat gtg tac gcc act att gcg 576His Ser Asn Ala His Asp Ala Met Ala Asp Val Tyr Ala Thr Ile Ala 180 185 190atg gca aag ctg gta aaa acg cgt cag cca cgc ctg ttt gat tat ctc 624Met Ala Lys Leu Val Lys Thr Arg Gln Pro Arg Leu Phe Asp Tyr Leu 195 200 205ttt acc cat cgt aat aaa cac aaa ctg atg gcg ttg att gat gtt ccg 672Phe Thr His Arg Asn Lys His Lys Leu Met Ala Leu Ile Asp Val Pro 210 215 220cag atg aaa ccc ctg gtg cac gtt tcc gga atg ttt gga gca tgg cgc 720Gln Met Lys Pro Leu Val His Val Ser Gly Met Phe Gly Ala Trp Arg225 230 235 240ggc aat acc agc tgg gtg gca ccg ctg gcg tgg cat cct gaa aat cgc 768Gly Asn Thr Ser Trp Val Ala Pro Leu Ala Trp His Pro Glu Asn Arg 245 250 255aat gcc gta att atg gtg gat ttg gca gga gac att tcg cca tta ctg 816Asn Ala Val Ile Met Val Asp Leu Ala Gly Asp Ile Ser Pro Leu Leu 260 265 270gaa ctg gat agc gac aca ttg cgc gag cgt tta tat acc gca aaa acc 864Glu Leu Asp Ser Asp Thr Leu Arg Glu Arg Leu Tyr Thr Ala Lys Thr 275 280 285gat ctt ggc gat aac gcc gcc gtt ccg gtt aag ctg gtg cat atc aat 912Asp Leu Gly Asp Asn Ala Ala Val Pro Val Lys Leu Val His Ile Asn 290 295 300aaa tgt ccg gtg ctg gcc cag gcg aat acg cta cgc ccg gaa gat gcc 960Lys Cys Pro Val Leu Ala Gln Ala Asn Thr Leu Arg Pro Glu Asp Ala305 310 315 320gac cga ctg gga att aat cgt cag cat tgc ctc gat aac ctg aaa att 1008Asp Arg Leu Gly Ile Asn Arg Gln His Cys Leu Asp Asn Leu Lys Ile 325 330 335ctg cgt gaa aat ccg caa gtg cgc gaa aaa gtg gtg gcg ata ttc gcg 1056Leu Arg Glu Asn Pro Gln Val Arg Glu Lys Val Val Ala Ile Phe Ala 340 345 350gaa gcc gaa ccg ttt acg cct tca gat aac gtg gat gca cag ctt tat 1104Glu Ala Glu Pro Phe Thr Pro Ser Asp Asn Val Asp Ala Gln Leu Tyr 355 360 365aac ggc ttt ttc agt gac gca gat cgt gca gca atg aaa att gtg ctg 1152Asn Gly Phe Phe Ser Asp Ala Asp Arg Ala Ala Met Lys Ile Val Leu 370 375 380gaa acc gag ccg cgt aat tta ccg gca ctg gat atc act ttt gtt gat 1200Glu Thr Glu Pro Arg Asn Leu Pro Ala Leu Asp Ile Thr Phe Val Asp385 390 395 400aaa cgg att gaa aag ctg ttg ttc aat tat cgg gca cgc aac ttc ccg 1248Lys Arg Ile Glu Lys Leu Leu Phe Asn Tyr Arg Ala Arg Asn Phe Pro 405 410 415ggg acg ctg gat tat gcc gag cag caa cgc tgg ctg gag cac cgt cgc 1296Gly Thr Leu Asp Tyr Ala Glu Gln Gln Arg Trp Leu Glu His Arg Arg 420 425 430cag gtc ttc acg cca gag ttt ttg cag ggt tat gct gat gaa ttg cag 1344Gln Val Phe Thr Pro Glu Phe Leu Gln Gly Tyr Ala Asp Glu Leu Gln 435 440 445atg ctg gta caa caa tat gcc gat gac aaa gag aaa gtg gcg ctg tta 1392Met Leu Val Gln Gln Tyr Ala Asp Asp Lys Glu Lys Val Ala Leu Leu 450 455 460aaa gca ctt tgg cag tac gcg gaa gag att gtc 1425Lys Ala Leu Trp Gln Tyr Ala Glu Glu Ile Val465 470 47512475PRTE. coli 12Met Met Asn Asp Gly Lys Gln Gln Ser Thr Phe Leu Phe His Asp Tyr1 5 10 15Glu Thr Phe Gly Thr His Pro Ala Leu Asp Arg Pro Ala Gln Phe Ala 20 25 30Ala Ile Arg Thr Asp Ser Glu Phe Asn Val Ile Gly Glu Pro Glu Val 35 40 45Phe Tyr Cys Lys Pro Ala Asp Asp Tyr Leu Pro Gln Pro Gly Ala Val 50 55 60Leu Ile Thr Gly Ile Thr Pro Gln Glu Ala Arg Ala Lys Gly Glu Asn65 70 75 80Glu Ala Ala Phe Ala Ala Arg Ile His Ser Leu Phe Thr Val Pro Lys 85 90 95Thr Cys Ile Leu Gly Tyr Asn Asn Val Arg Phe Asp Asp Glu Val Thr 100 105 110Arg Asn Ile Phe Tyr Arg Asn Phe Tyr Asp Pro Tyr Ala Trp Ser Trp 115 120 125Gln His Asp Asn Ser Arg Trp Asp Leu Leu Asp Val Met Arg Ala Cys 130 135 140Tyr Ala Leu Arg Pro Glu Gly Ile Asn Trp Pro Glu Asn Asp Asp Gly145 150 155 160Leu Pro Ser Phe Arg Leu Glu His Leu Thr Lys Ala Asn Gly Ile Glu 165 170 175His Ser Asn Ala His Asp Ala Met Ala Asp Val Tyr Ala Thr Ile Ala 180 185 190Met Ala Lys Leu Val Lys Thr Arg Gln Pro Arg Leu Phe Asp Tyr Leu 195 200 205Phe Thr His Arg Asn Lys His Lys Leu Met Ala Leu Ile Asp Val Pro 210 215 220Gln Met Lys Pro Leu Val His Val Ser Gly Met Phe Gly Ala Trp Arg225 230 235 240Gly Asn Thr Ser Trp Val Ala Pro Leu Ala Trp His Pro Glu Asn Arg 245 250 255Asn Ala Val Ile Met Val Asp Leu Ala Gly Asp Ile Ser Pro Leu Leu 260 265 270Glu Leu Asp Ser Asp Thr Leu Arg Glu Arg Leu Tyr Thr Ala Lys Thr 275 280 285Asp Leu Gly Asp Asn Ala Ala Val Pro Val Lys Leu Val His Ile Asn 290 295 300Lys Cys Pro Val Leu Ala Gln Ala Asn Thr Leu Arg Pro Glu Asp Ala305 310 315 320Asp Arg Leu Gly Ile Asn Arg Gln His Cys Leu Asp Asn Leu Lys Ile 325 330 335Leu Arg Glu Asn Pro Gln Val Arg Glu Lys Val Val Ala Ile Phe Ala 340 345 350Glu Ala Glu Pro Phe Thr Pro Ser Asp Asn Val Asp Ala Gln Leu Tyr 355 360 365Asn Gly Phe Phe Ser Asp Ala Asp Arg Ala Ala Met Lys Ile Val Leu 370 375 380Glu Thr Glu Pro Arg Asn Leu Pro Ala Leu Asp Ile Thr Phe Val Asp385 390 395 400Lys Arg Ile Glu Lys Leu Leu Phe Asn Tyr Arg Ala Arg Asn Phe Pro 405 410 415Gly Thr Leu Asp Tyr Ala Glu Gln Gln Arg Trp Leu Glu His Arg Arg 420 425 430Gln Val Phe Thr Pro Glu Phe Leu Gln Gly Tyr Ala Asp Glu Leu Gln 435 440 445Met Leu Val Gln Gln Tyr Ala Asp Asp Lys Glu Lys Val Ala Leu Leu 450 455 460Lys Ala Leu Trp Gln Tyr Ala Glu Glu Ile Val465 470 475131275DNAT. thermophilusCDS(1)..(1275) 13atg ttt cgt cgt aaa gaa gat ctg gat ccg ccg ctg gca ctg ctg ccg 48Met Phe Arg Arg Lys Glu Asp Leu Asp Pro Pro Leu Ala Leu Leu Pro1 5 10 15ctg aaa ggc ctg cgc gaa gcc gcc gca ctg ctg gaa gaa gcg ctg cgt 96Leu Lys Gly Leu Arg Glu Ala Ala Ala Leu Leu Glu Glu Ala Leu Arg 20 25 30caa ggt aaa cgc att cgt gtt cac ggc gac tat gat gcg gat ggc ctg 144Gln Gly Lys Arg Ile Arg Val His Gly Asp Tyr Asp Ala Asp Gly Leu 35 40 45acc ggc acc gcg atc ctg gtt cgt ggt ctg gcc gcc ctg ggt gcg gat 192Thr Gly Thr Ala Ile Leu Val Arg Gly Leu Ala Ala Leu Gly Ala Asp 50 55 60gtt cat ccg ttt atc ccg cac cgc ctg gaa gaa ggc tat ggt gtc ctg 240Val His Pro Phe Ile Pro His Arg Leu Glu Glu Gly Tyr Gly Val Leu65 70 75 80atg gaa cgc gtc ccg gaa cat ctg gaa gcc tcg gac ctg ttt ctg acc 288Met Glu Arg Val Pro Glu His Leu Glu Ala Ser Asp Leu Phe Leu Thr 85 90 95gtt gac tgc ggc att acc aac cat gcg gaa ctg cgc gaa ctg ctg gaa 336Val Asp Cys Gly Ile Thr Asn His Ala Glu Leu Arg Glu Leu Leu Glu 100 105 110aat ggc gtg gaa gtc att

gtt acc gat cat cat acg ccg ggc aaa acg 384Asn Gly Val Glu Val Ile Val Thr Asp His His Thr Pro Gly Lys Thr 115 120 125ccg ccg ccg ggt ctg gtc gtg cat ccg gcg ctg acg ccg gat ctg aaa 432Pro Pro Pro Gly Leu Val Val His Pro Ala Leu Thr Pro Asp Leu Lys 130 135 140gaa aaa ccg acc ggc gca ggc gtg gcg ttt ctg ctg ctg tgg gca ctg 480Glu Lys Pro Thr Gly Ala Gly Val Ala Phe Leu Leu Leu Trp Ala Leu145 150 155 160cat gaa cgc ctg ggc ctg ccg ccg ccg ctg gaa tac gcg gac ctg gca 528His Glu Arg Leu Gly Leu Pro Pro Pro Leu Glu Tyr Ala Asp Leu Ala 165 170 175gcc gtt ggc acc att gcc gac gtt gcc ccg ctg tgg ggt tgg aat cgt 576Ala Val Gly Thr Ile Ala Asp Val Ala Pro Leu Trp Gly Trp Asn Arg 180 185 190gca ctg gtg aaa gaa ggt ctg gca cgc atc ccg gct tca tct tgg gtg 624Ala Leu Val Lys Glu Gly Leu Ala Arg Ile Pro Ala Ser Ser Trp Val 195 200 205ggc ctg cgt ctg ctg gct gaa gcc gtg ggc tat acc ggc aaa gcg gtc 672Gly Leu Arg Leu Leu Ala Glu Ala Val Gly Tyr Thr Gly Lys Ala Val 210 215 220gaa gtc gct ttc cgc atc gcg ccg cgc atc aat gcg gct tcc cgc ctg 720Glu Val Ala Phe Arg Ile Ala Pro Arg Ile Asn Ala Ala Ser Arg Leu225 230 235 240ggc gaa gcg gaa aaa gcc ctg cgc ctg ctg ctg acg gat gat gcg gca 768Gly Glu Ala Glu Lys Ala Leu Arg Leu Leu Leu Thr Asp Asp Ala Ala 245 250 255gaa gct cag gcg ctg gtc ggc gaa ctg cac cgt ctg aac gcc cgt cgt 816Glu Ala Gln Ala Leu Val Gly Glu Leu His Arg Leu Asn Ala Arg Arg 260 265 270cag acc ctg gaa gaa gcg atg ctg cgc aaa ctg ctg ccg cag gcc gac 864Gln Thr Leu Glu Glu Ala Met Leu Arg Lys Leu Leu Pro Gln Ala Asp 275 280 285ccg gaa gcg aaa gcc atc gtt ctg ctg gac ccg gaa ggc cat ccg ggt 912Pro Glu Ala Lys Ala Ile Val Leu Leu Asp Pro Glu Gly His Pro Gly 290 295 300gtt atg ggt att gtg gcc tct cgc atc ctg gaa gcg acc ctg cgc ccg 960Val Met Gly Ile Val Ala Ser Arg Ile Leu Glu Ala Thr Leu Arg Pro305 310 315 320gtc ttt ctg gtg gcc cag ggc aaa ggc acc gtg cgt tcg ctg gct ccg 1008Val Phe Leu Val Ala Gln Gly Lys Gly Thr Val Arg Ser Leu Ala Pro 325 330 335att tcc gcc gtc gaa gca ctg cgc agc gcg gaa gat ctg ctg ctg cgt 1056Ile Ser Ala Val Glu Ala Leu Arg Ser Ala Glu Asp Leu Leu Leu Arg 340 345 350tat ggt ggt cat aaa gaa gcg gcg ggt ttc gca atg gat gaa gcg ctg 1104Tyr Gly Gly His Lys Glu Ala Ala Gly Phe Ala Met Asp Glu Ala Leu 355 360 365ttt ccg gcg ttc aaa gca cgc gtt gaa gcg tat gcc gca cgt ttc ccg 1152Phe Pro Ala Phe Lys Ala Arg Val Glu Ala Tyr Ala Ala Arg Phe Pro 370 375 380gat ccg gtt cgt gaa gtg gca ctg ctg gat ctg ctg ccg gaa ccg ggc 1200Asp Pro Val Arg Glu Val Ala Leu Leu Asp Leu Leu Pro Glu Pro Gly385 390 395 400ctg ctg ccg cag gtg ttc cgt gaa ctg gca ctg ctg gaa ccg tat ggt 1248Leu Leu Pro Gln Val Phe Arg Glu Leu Ala Leu Leu Glu Pro Tyr Gly 405 410 415gaa ggt aac ccg gaa ccg ctg ttc ctg 1275Glu Gly Asn Pro Glu Pro Leu Phe Leu 420 42514425PRTT. thermophilus 14Met Phe Arg Arg Lys Glu Asp Leu Asp Pro Pro Leu Ala Leu Leu Pro1 5 10 15Leu Lys Gly Leu Arg Glu Ala Ala Ala Leu Leu Glu Glu Ala Leu Arg 20 25 30Gln Gly Lys Arg Ile Arg Val His Gly Asp Tyr Asp Ala Asp Gly Leu 35 40 45Thr Gly Thr Ala Ile Leu Val Arg Gly Leu Ala Ala Leu Gly Ala Asp 50 55 60Val His Pro Phe Ile Pro His Arg Leu Glu Glu Gly Tyr Gly Val Leu65 70 75 80Met Glu Arg Val Pro Glu His Leu Glu Ala Ser Asp Leu Phe Leu Thr 85 90 95Val Asp Cys Gly Ile Thr Asn His Ala Glu Leu Arg Glu Leu Leu Glu 100 105 110Asn Gly Val Glu Val Ile Val Thr Asp His His Thr Pro Gly Lys Thr 115 120 125Pro Pro Pro Gly Leu Val Val His Pro Ala Leu Thr Pro Asp Leu Lys 130 135 140Glu Lys Pro Thr Gly Ala Gly Val Ala Phe Leu Leu Leu Trp Ala Leu145 150 155 160His Glu Arg Leu Gly Leu Pro Pro Pro Leu Glu Tyr Ala Asp Leu Ala 165 170 175Ala Val Gly Thr Ile Ala Asp Val Ala Pro Leu Trp Gly Trp Asn Arg 180 185 190Ala Leu Val Lys Glu Gly Leu Ala Arg Ile Pro Ala Ser Ser Trp Val 195 200 205Gly Leu Arg Leu Leu Ala Glu Ala Val Gly Tyr Thr Gly Lys Ala Val 210 215 220Glu Val Ala Phe Arg Ile Ala Pro Arg Ile Asn Ala Ala Ser Arg Leu225 230 235 240Gly Glu Ala Glu Lys Ala Leu Arg Leu Leu Leu Thr Asp Asp Ala Ala 245 250 255Glu Ala Gln Ala Leu Val Gly Glu Leu His Arg Leu Asn Ala Arg Arg 260 265 270Gln Thr Leu Glu Glu Ala Met Leu Arg Lys Leu Leu Pro Gln Ala Asp 275 280 285Pro Glu Ala Lys Ala Ile Val Leu Leu Asp Pro Glu Gly His Pro Gly 290 295 300Val Met Gly Ile Val Ala Ser Arg Ile Leu Glu Ala Thr Leu Arg Pro305 310 315 320Val Phe Leu Val Ala Gln Gly Lys Gly Thr Val Arg Ser Leu Ala Pro 325 330 335Ile Ser Ala Val Glu Ala Leu Arg Ser Ala Glu Asp Leu Leu Leu Arg 340 345 350Tyr Gly Gly His Lys Glu Ala Ala Gly Phe Ala Met Asp Glu Ala Leu 355 360 365Phe Pro Ala Phe Lys Ala Arg Val Glu Ala Tyr Ala Ala Arg Phe Pro 370 375 380Asp Pro Val Arg Glu Val Ala Leu Leu Asp Leu Leu Pro Glu Pro Gly385 390 395 400Leu Leu Pro Gln Val Phe Arg Glu Leu Ala Leu Leu Glu Pro Tyr Gly 405 410 415Glu Gly Asn Pro Glu Pro Leu Phe Leu 420 42515738DNABacteriophageCDS(31)..(708) 15tccggaagcg gctctggtag tggttctggc atg aca ccg gac att atc ctg cag 54 Met Thr Pro Asp Ile Ile Leu Gln 1 5cgt acc ggg atc gat gtg aga gct gtc gaa cag ggg gat gat gcg tgg 102Arg Thr Gly Ile Asp Val Arg Ala Val Glu Gln Gly Asp Asp Ala Trp 10 15 20cac aaa tta cgg ctc ggc gtc atc acc gct tca gaa gtt cac aac gtg 150His Lys Leu Arg Leu Gly Val Ile Thr Ala Ser Glu Val His Asn Val25 30 35 40ata gca aaa ccc cgc tcc gga aag aag tgg cct gac atg aaa atg tcc 198Ile Ala Lys Pro Arg Ser Gly Lys Lys Trp Pro Asp Met Lys Met Ser 45 50 55tac ttc cac acc ctg ctt gct gag gtt tgc acc ggt gtg gct ccg gaa 246Tyr Phe His Thr Leu Leu Ala Glu Val Cys Thr Gly Val Ala Pro Glu 60 65 70gtt aac gct aaa gca ctg gcc tgg gga aaa cag tac gag aac gac gcc 294Val Asn Ala Lys Ala Leu Ala Trp Gly Lys Gln Tyr Glu Asn Asp Ala 75 80 85aga acc ctg ttt gaa ttc act tcc ggc gtg aat gtt act gaa tcc ccg 342Arg Thr Leu Phe Glu Phe Thr Ser Gly Val Asn Val Thr Glu Ser Pro 90 95 100atc atc tat cgc gac gaa agt atg cgt acc gcc tgc tct ccc gat ggt 390Ile Ile Tyr Arg Asp Glu Ser Met Arg Thr Ala Cys Ser Pro Asp Gly105 110 115 120tta tgc agt gac ggc aac ggc ctt gaa ctg aaa tgc ccg ttt acc tcc 438Leu Cys Ser Asp Gly Asn Gly Leu Glu Leu Lys Cys Pro Phe Thr Ser 125 130 135cgg gat ttc atg aag ttc cgg ctc ggt ggt ttc gag gcc ata aag tca 486Arg Asp Phe Met Lys Phe Arg Leu Gly Gly Phe Glu Ala Ile Lys Ser 140 145 150gct tac atg gcc cag gtg cag tac agc atg tgg gtg acg cga aaa aat 534Ala Tyr Met Ala Gln Val Gln Tyr Ser Met Trp Val Thr Arg Lys Asn 155 160 165gcc tgg tac ttt gcc aac tat gac ccg cgt atg aag cgt gaa ggc ctg 582Ala Trp Tyr Phe Ala Asn Tyr Asp Pro Arg Met Lys Arg Glu Gly Leu 170 175 180cat tat gtc gtg att gag cgg gat gaa aag tac atg gcg agt ttt gac 630His Tyr Val Val Ile Glu Arg Asp Glu Lys Tyr Met Ala Ser Phe Asp185 190 195 200gag atc gtg ccg gag ttc atc gaa aaa atg gac gag gca ctg gct gaa 678Glu Ile Val Pro Glu Phe Ile Glu Lys Met Asp Glu Ala Leu Ala Glu 205 210 215att ggt ttt gta ttt ggg gag caa tgg cga tctggctctg gttccggcag 728Ile Gly Phe Val Phe Gly Glu Gln Trp Arg 220 225cggttccgga 73816226PRTBacteriophage 16Met Thr Pro Asp Ile Ile Leu Gln Arg Thr Gly Ile Asp Val Arg Ala1 5 10 15Val Glu Gln Gly Asp Asp Ala Trp His Lys Leu Arg Leu Gly Val Ile 20 25 30Thr Ala Ser Glu Val His Asn Val Ile Ala Lys Pro Arg Ser Gly Lys 35 40 45Lys Trp Pro Asp Met Lys Met Ser Tyr Phe His Thr Leu Leu Ala Glu 50 55 60Val Cys Thr Gly Val Ala Pro Glu Val Asn Ala Lys Ala Leu Ala Trp65 70 75 80Gly Lys Gln Tyr Glu Asn Asp Ala Arg Thr Leu Phe Glu Phe Thr Ser 85 90 95Gly Val Asn Val Thr Glu Ser Pro Ile Ile Tyr Arg Asp Glu Ser Met 100 105 110Arg Thr Ala Cys Ser Pro Asp Gly Leu Cys Ser Asp Gly Asn Gly Leu 115 120 125Glu Leu Lys Cys Pro Phe Thr Ser Arg Asp Phe Met Lys Phe Arg Leu 130 135 140Gly Gly Phe Glu Ala Ile Lys Ser Ala Tyr Met Ala Gln Val Gln Tyr145 150 155 160Ser Met Trp Val Thr Arg Lys Asn Ala Trp Tyr Phe Ala Asn Tyr Asp 165 170 175Pro Arg Met Lys Arg Glu Gly Leu His Tyr Val Val Ile Glu Arg Asp 180 185 190Glu Lys Tyr Met Ala Ser Phe Asp Glu Ile Val Pro Glu Phe Ile Glu 195 200 205Lys Met Asp Glu Ala Leu Ala Glu Ile Gly Phe Val Phe Gly Glu Gln 210 215 220Trp Arg225171794DNAArtificial sequenceHL-wt-EcoExoIII-L1-H6 17atg gca gat tct gat att aat att aaa acc ggt act aca gat att gga 48 Ala Asp Ser Asp Ile Asn Ile Lys Thr Gly Thr Thr Asp Ile Gly 1 5 10 15agc aat act tcc gga agc ggc tct ggt agt ggt tct ggc atg aaa ttt 96Ser Asn Thr Ser Gly Ser Gly Ser Gly Ser Gly Ser Gly Met Lys Phe 20 25 30gtt agc ttc aat atc aac ggc ctg cgc gcg cgc ccg cat cag ctg gaa 144Val Ser Phe Asn Ile Asn Gly Leu Arg Ala Arg Pro His Gln Leu Glu 35 40 45gcg att gtg gaa aaa cat cag ccg gat gtt att ggt ctg cag gaa acc 192Ala Ile Val Glu Lys His Gln Pro Asp Val Ile Gly Leu Gln Glu Thr 50 55 60aaa gtt cac gat gat atg ttt ccg ctg gaa gaa gtg gcg aaa ctg ggc 240Lys Val His Asp Asp Met Phe Pro Leu Glu Glu Val Ala Lys Leu Gly 65 70 75tat aac gtg ttt tat cat ggc cag aaa ggt cat tat ggc gtg gcc ctg 288Tyr Asn Val Phe Tyr His Gly Gln Lys Gly His Tyr Gly Val Ala Leu80 85 90 95ctg acc aaa gaa acc ccg atc gcg gtt cgt cgt ggt ttt ccg ggt gat 336Leu Thr Lys Glu Thr Pro Ile Ala Val Arg Arg Gly Phe Pro Gly Asp 100 105 110gat gaa gaa gcg cag cgt cgt att att atg gcg gaa att ccg agc ctg 384Asp Glu Glu Ala Gln Arg Arg Ile Ile Met Ala Glu Ile Pro Ser Leu 115 120 125ctg ggc aat gtg acc gtt att aac ggc tat ttt ccg cag ggc gaa agc 432Leu Gly Asn Val Thr Val Ile Asn Gly Tyr Phe Pro Gln Gly Glu Ser 130 135 140cgt gat cat ccg att aaa ttt ccg gcc aaa gcg cag ttc tat cag aac 480Arg Asp His Pro Ile Lys Phe Pro Ala Lys Ala Gln Phe Tyr Gln Asn 145 150 155ctg cag aac tat ctg gaa acc gaa ctg aaa cgt gat aat ccg gtg ctg 528Leu Gln Asn Tyr Leu Glu Thr Glu Leu Lys Arg Asp Asn Pro Val Leu160 165 170 175atc atg ggc gat atg aac att agc ccg acc gat ctg gat att ggc att 576Ile Met Gly Asp Met Asn Ile Ser Pro Thr Asp Leu Asp Ile Gly Ile 180 185 190ggc gaa gaa aac cgt aaa cgc tgg ctg cgt acc ggt aaa tgc agc ttt 624Gly Glu Glu Asn Arg Lys Arg Trp Leu Arg Thr Gly Lys Cys Ser Phe 195 200 205ctg ccg gaa gaa cgt gaa tgg atg gat cgc ctg atg agc tgg ggc ctg 672Leu Pro Glu Glu Arg Glu Trp Met Asp Arg Leu Met Ser Trp Gly Leu 210 215 220gtg gat acc ttt cgt cat gcg aac ccg cag acc gcc gat cgc ttt agc 720Val Asp Thr Phe Arg His Ala Asn Pro Gln Thr Ala Asp Arg Phe Ser 225 230 235tgg ttt gat tat cgc agc aaa ggt ttt gat gat aac cgt ggc ctg cgc 768Trp Phe Asp Tyr Arg Ser Lys Gly Phe Asp Asp Asn Arg Gly Leu Arg240 245 250 255att gat ctg ctg ctg gcg agc cag ccg ctg gcg gaa tgc tgc gtt gaa 816Ile Asp Leu Leu Leu Ala Ser Gln Pro Leu Ala Glu Cys Cys Val Glu 260 265 270acc ggt att gat tat gaa att cgc agc atg gaa aaa ccg agc gat cac 864Thr Gly Ile Asp Tyr Glu Ile Arg Ser Met Glu Lys Pro Ser Asp His 275 280 285gcc ccg gtg tgg gcg acc ttt cgc cgc tct ggc tct ggt tcc ggc agc 912Ala Pro Val Trp Ala Thr Phe Arg Arg Ser Gly Ser Gly Ser Gly Ser 290 295 300ggt tcc gga aca gta aaa aca ggt gat tta gtc act tat gat aaa gaa 960Gly Ser Gly Thr Val Lys Thr Gly Asp Leu Val Thr Tyr Asp Lys Glu 305 310 315aat ggc atg cac aaa aaa gta ttt tat agt ttt atc gat gat aaa aat 1008Asn Gly Met His Lys Lys Val Phe Tyr Ser Phe Ile Asp Asp Lys Asn320 325 330 335cac aat aaa aaa ctg cta gtt att aga aca aaa ggt acc att gct ggt 1056His Asn Lys Lys Leu Leu Val Ile Arg Thr Lys Gly Thr Ile Ala Gly 340 345 350caa tat aga gtt tat agc gaa gaa ggt gct aac aaa agt ggt tta gcc 1104Gln Tyr Arg Val Tyr Ser Glu Glu Gly Ala Asn Lys Ser Gly Leu Ala 355 360 365tgg cct tca gcc ttt aag gta cag ttg caa cta cct gat aat gaa gta 1152Trp Pro Ser Ala Phe Lys Val Gln Leu Gln Leu Pro Asp Asn Glu Val 370 375 380gct caa ata tct gat tac tat cca aga aat tcg att gat aca aaa gag 1200Ala Gln Ile Ser Asp Tyr Tyr Pro Arg Asn Ser Ile Asp Thr Lys Glu 385 390 395tat atg agt act tta act tat gga ttc aac ggt aat gtt act ggt gat 1248Tyr Met Ser Thr Leu Thr Tyr Gly Phe Asn Gly Asn Val Thr Gly Asp400 405 410 415gat aca gga aaa att ggc ggc ctt att ggt gca aat gtt tcg att ggt 1296Asp Thr Gly Lys Ile Gly Gly Leu Ile Gly Ala Asn Val Ser Ile Gly 420 425 430cat aca ctg aaa tat gtt caa cct gat ttc aaa aca att tta gag agc 1344His Thr Leu Lys Tyr Val Gln Pro Asp Phe Lys Thr Ile Leu Glu Ser 435 440 445cca act gat aaa aaa gta ggc tgg aaa gtg ata ttt aac aat atg gtg 1392Pro Thr Asp Lys Lys Val Gly Trp Lys Val Ile Phe Asn Asn Met Val 450 455 460aat caa aat tgg gga cca tac gat cga gat tct tgg aac ccg gta tat 1440Asn Gln Asn Trp Gly Pro Tyr Asp Arg Asp Ser Trp Asn Pro Val Tyr 465 470 475ggc aat caa ctt ttc atg aaa act aga aat ggt tct atg aaa gca gca 1488Gly Asn Gln Leu Phe Met Lys Thr Arg Asn Gly Ser Met Lys Ala Ala480 485 490 495gat aac ttc ctt gat cct aac aaa gca agt tct cta tta tct tca ggg 1536Asp Asn Phe Leu Asp Pro Asn Lys Ala Ser Ser Leu Leu Ser Ser Gly 500 505 510ttt tca cca gac ttc gct aca gtt att act atg gat aga aaa gca tcc 1584Phe Ser Pro Asp Phe Ala Thr Val Ile Thr Met Asp Arg Lys Ala Ser 515 520 525aaa caa caa aca aat ata gat gta ata tac gaa cga gtt cgt gat gat 1632Lys Gln Gln Thr Asn Ile Asp Val Ile Tyr Glu Arg Val Arg Asp Asp 530 535 540tac caa ttg cat tgg act tca aca aat tgg aaa ggt acc aat act aaa 1680Tyr Gln Leu His Trp Thr Ser Thr Asn Trp Lys Gly Thr Asn Thr Lys 545 550 555gat aaa tgg aca gat cgt tct tca gaa aga tat aaa atc gat tgg gaa

1728Asp Lys Trp Thr Asp Arg Ser Ser Glu Arg Tyr Lys Ile Asp Trp Glu560 565 570 575aaa gaa gaa atg aca aat ggt ggt tcg ggc tca tct ggt ggc tcg agt 1776Lys Glu Glu Met Thr Asn Gly Gly Ser Gly Ser Ser Gly Gly Ser Ser 580 585 590cac cat cat cat cac cac 1794His His His His His His 59518597PRTArtificial sequenceHL-wt-EcoExoIII-L1-H6 18Ala Asp Ser Asp Ile Asn Ile Lys Thr Gly Thr Thr Asp Ile Gly Ser1 5 10 15Asn Thr Ser Gly Ser Gly Ser Gly Ser Gly Ser Gly Met Lys Phe Val 20 25 30Ser Phe Asn Ile Asn Gly Leu Arg Ala Arg Pro His Gln Leu Glu Ala 35 40 45Ile Val Glu Lys His Gln Pro Asp Val Ile Gly Leu Gln Glu Thr Lys 50 55 60Val His Asp Asp Met Phe Pro Leu Glu Glu Val Ala Lys Leu Gly Tyr65 70 75 80Asn Val Phe Tyr His Gly Gln Lys Gly His Tyr Gly Val Ala Leu Leu 85 90 95Thr Lys Glu Thr Pro Ile Ala Val Arg Arg Gly Phe Pro Gly Asp Asp 100 105 110Glu Glu Ala Gln Arg Arg Ile Ile Met Ala Glu Ile Pro Ser Leu Leu 115 120 125Gly Asn Val Thr Val Ile Asn Gly Tyr Phe Pro Gln Gly Glu Ser Arg 130 135 140Asp His Pro Ile Lys Phe Pro Ala Lys Ala Gln Phe Tyr Gln Asn Leu145 150 155 160Gln Asn Tyr Leu Glu Thr Glu Leu Lys Arg Asp Asn Pro Val Leu Ile 165 170 175Met Gly Asp Met Asn Ile Ser Pro Thr Asp Leu Asp Ile Gly Ile Gly 180 185 190Glu Glu Asn Arg Lys Arg Trp Leu Arg Thr Gly Lys Cys Ser Phe Leu 195 200 205Pro Glu Glu Arg Glu Trp Met Asp Arg Leu Met Ser Trp Gly Leu Val 210 215 220Asp Thr Phe Arg His Ala Asn Pro Gln Thr Ala Asp Arg Phe Ser Trp225 230 235 240Phe Asp Tyr Arg Ser Lys Gly Phe Asp Asp Asn Arg Gly Leu Arg Ile 245 250 255Asp Leu Leu Leu Ala Ser Gln Pro Leu Ala Glu Cys Cys Val Glu Thr 260 265 270Gly Ile Asp Tyr Glu Ile Arg Ser Met Glu Lys Pro Ser Asp His Ala 275 280 285Pro Val Trp Ala Thr Phe Arg Arg Ser Gly Ser Gly Ser Gly Ser Gly 290 295 300Ser Gly Thr Val Lys Thr Gly Asp Leu Val Thr Tyr Asp Lys Glu Asn305 310 315 320Gly Met His Lys Lys Val Phe Tyr Ser Phe Ile Asp Asp Lys Asn His 325 330 335Asn Lys Lys Leu Leu Val Ile Arg Thr Lys Gly Thr Ile Ala Gly Gln 340 345 350Tyr Arg Val Tyr Ser Glu Glu Gly Ala Asn Lys Ser Gly Leu Ala Trp 355 360 365Pro Ser Ala Phe Lys Val Gln Leu Gln Leu Pro Asp Asn Glu Val Ala 370 375 380Gln Ile Ser Asp Tyr Tyr Pro Arg Asn Ser Ile Asp Thr Lys Glu Tyr385 390 395 400Met Ser Thr Leu Thr Tyr Gly Phe Asn Gly Asn Val Thr Gly Asp Asp 405 410 415Thr Gly Lys Ile Gly Gly Leu Ile Gly Ala Asn Val Ser Ile Gly His 420 425 430Thr Leu Lys Tyr Val Gln Pro Asp Phe Lys Thr Ile Leu Glu Ser Pro 435 440 445Thr Asp Lys Lys Val Gly Trp Lys Val Ile Phe Asn Asn Met Val Asn 450 455 460Gln Asn Trp Gly Pro Tyr Asp Arg Asp Ser Trp Asn Pro Val Tyr Gly465 470 475 480Asn Gln Leu Phe Met Lys Thr Arg Asn Gly Ser Met Lys Ala Ala Asp 485 490 495Asn Phe Leu Asp Pro Asn Lys Ala Ser Ser Leu Leu Ser Ser Gly Phe 500 505 510Ser Pro Asp Phe Ala Thr Val Ile Thr Met Asp Arg Lys Ala Ser Lys 515 520 525Gln Gln Thr Asn Ile Asp Val Ile Tyr Glu Arg Val Arg Asp Asp Tyr 530 535 540Gln Leu His Trp Thr Ser Thr Asn Trp Lys Gly Thr Asn Thr Lys Asp545 550 555 560Lys Trp Thr Asp Arg Ser Ser Glu Arg Tyr Lys Ile Asp Trp Glu Lys 565 570 575Glu Glu Met Thr Asn Gly Gly Ser Gly Ser Ser Gly Gly Ser Ser His 580 585 590His His His His His 595191794DNAArtificial sequenceHL-RQC-EcoExoIII-L1-H6 19atg gca gat tct gat att aat att aaa acc ggt act aca gat att gga 48 Ala Asp Ser Asp Ile Asn Ile Lys Thr Gly Thr Thr Asp Ile Gly 1 5 10 15agc aat act tcc gga agc ggc tct ggt agt ggt tct ggc atg aaa ttt 96Ser Asn Thr Ser Gly Ser Gly Ser Gly Ser Gly Ser Gly Met Lys Phe 20 25 30gtt agc ttc aat atc aac ggc ctg cgc gcg cgc ccg cat cag ctg gaa 144Val Ser Phe Asn Ile Asn Gly Leu Arg Ala Arg Pro His Gln Leu Glu 35 40 45gcg att gtg gaa aaa cat cag ccg gat gtt att ggt ctg cag gaa acc 192Ala Ile Val Glu Lys His Gln Pro Asp Val Ile Gly Leu Gln Glu Thr 50 55 60aaa gtt cac gat gat atg ttt ccg ctg gaa gaa gtg gcg aaa ctg ggc 240Lys Val His Asp Asp Met Phe Pro Leu Glu Glu Val Ala Lys Leu Gly 65 70 75tat aac gtg ttt tat cat ggc cag aaa ggt cat tat ggc gtg gcc ctg 288Tyr Asn Val Phe Tyr His Gly Gln Lys Gly His Tyr Gly Val Ala Leu80 85 90 95ctg acc aaa gaa acc ccg atc gcg gtt cgt cgt ggt ttt ccg ggt gat 336Leu Thr Lys Glu Thr Pro Ile Ala Val Arg Arg Gly Phe Pro Gly Asp 100 105 110gat gaa gaa gcg cag cgt cgt att att atg gcg gaa att ccg agc ctg 384Asp Glu Glu Ala Gln Arg Arg Ile Ile Met Ala Glu Ile Pro Ser Leu 115 120 125ctg ggc aat gtg acc gtt att aac ggc tat ttt ccg cag ggc gaa agc 432Leu Gly Asn Val Thr Val Ile Asn Gly Tyr Phe Pro Gln Gly Glu Ser 130 135 140cgt gat cat ccg att aaa ttt ccg gcc aaa gcg cag ttc tat cag aac 480Arg Asp His Pro Ile Lys Phe Pro Ala Lys Ala Gln Phe Tyr Gln Asn 145 150 155ctg cag aac tat ctg gaa acc gaa ctg aaa cgt gat aat ccg gtg ctg 528Leu Gln Asn Tyr Leu Glu Thr Glu Leu Lys Arg Asp Asn Pro Val Leu160 165 170 175atc atg ggc gat atg aac att agc ccg acc gat ctg gat att ggc att 576Ile Met Gly Asp Met Asn Ile Ser Pro Thr Asp Leu Asp Ile Gly Ile 180 185 190ggc gaa gaa aac cgt aaa cgc tgg ctg cgt acc ggt aaa tgc agc ttt 624Gly Glu Glu Asn Arg Lys Arg Trp Leu Arg Thr Gly Lys Cys Ser Phe 195 200 205ctg ccg gaa gaa cgt gaa tgg atg gat cgc ctg atg agc tgg ggc ctg 672Leu Pro Glu Glu Arg Glu Trp Met Asp Arg Leu Met Ser Trp Gly Leu 210 215 220gtg gat acc ttt cgt cat gcg aac ccg cag acc gcc gat cgc ttt agc 720Val Asp Thr Phe Arg His Ala Asn Pro Gln Thr Ala Asp Arg Phe Ser 225 230 235tgg ttt gat tat cgc agc aaa ggt ttt gat gat aac cgt ggc ctg cgc 768Trp Phe Asp Tyr Arg Ser Lys Gly Phe Asp Asp Asn Arg Gly Leu Arg240 245 250 255att gat ctg ctg ctg gcg agc cag ccg ctg gcg gaa tgc tgc gtt gaa 816Ile Asp Leu Leu Leu Ala Ser Gln Pro Leu Ala Glu Cys Cys Val Glu 260 265 270acc ggt att gat tat gaa att cgc agc atg gaa aaa ccg agc gat cac 864Thr Gly Ile Asp Tyr Glu Ile Arg Ser Met Glu Lys Pro Ser Asp His 275 280 285gcc ccg gtg tgg gcg acc ttt cgc cgc tct ggc tct ggt tcc ggc agc 912Ala Pro Val Trp Ala Thr Phe Arg Arg Ser Gly Ser Gly Ser Gly Ser 290 295 300ggt tcc gga aca gta aaa aca ggt gat tta gtc act tat gat aaa gaa 960Gly Ser Gly Thr Val Lys Thr Gly Asp Leu Val Thr Tyr Asp Lys Glu 305 310 315aat ggc atg cac aaa aaa gta ttt tat agt ttt atc gat gat aaa aat 1008Asn Gly Met His Lys Lys Val Phe Tyr Ser Phe Ile Asp Asp Lys Asn320 325 330 335cac aat aaa aaa ctg cta gtt att aga aca aaa ggt acc att gct ggt 1056His Asn Lys Lys Leu Leu Val Ile Arg Thr Lys Gly Thr Ile Ala Gly 340 345 350caa tat aga gtt tat agc gaa gaa ggt gct aac aaa agt ggt tta gcc 1104Gln Tyr Arg Val Tyr Ser Glu Glu Gly Ala Asn Lys Ser Gly Leu Ala 355 360 365tgg cct tca gcc ttt aag gta cag ttg caa cta cct gat aat gaa gta 1152Trp Pro Ser Ala Phe Lys Val Gln Leu Gln Leu Pro Asp Asn Glu Val 370 375 380gct caa ata tct gat tac tat cca aga aat tcg att gat aca aaa gag 1200Ala Gln Ile Ser Asp Tyr Tyr Pro Arg Asn Ser Ile Asp Thr Lys Glu 385 390 395tat agg agt act tta act tat gga ttc aac ggt aat gtt act ggt gat 1248Tyr Arg Ser Thr Leu Thr Tyr Gly Phe Asn Gly Asn Val Thr Gly Asp400 405 410 415gat aca gga aaa att ggc ggc tgt att ggt gca caa gtt tcg att ggt 1296Asp Thr Gly Lys Ile Gly Gly Cys Ile Gly Ala Gln Val Ser Ile Gly 420 425 430cat aca ctg aaa tat gtt caa cct gat ttc aaa aca att tta gag agc 1344His Thr Leu Lys Tyr Val Gln Pro Asp Phe Lys Thr Ile Leu Glu Ser 435 440 445cca act gat aaa aaa gta ggc tgg aaa gtg ata ttt aac aat atg gtg 1392Pro Thr Asp Lys Lys Val Gly Trp Lys Val Ile Phe Asn Asn Met Val 450 455 460aat caa aat tgg gga cca tac gat cga gat tct tgg aac ccg gta tat 1440Asn Gln Asn Trp Gly Pro Tyr Asp Arg Asp Ser Trp Asn Pro Val Tyr 465 470 475ggc aat caa ctt ttc atg aaa act aga aat ggt tct atg aaa gca gca 1488Gly Asn Gln Leu Phe Met Lys Thr Arg Asn Gly Ser Met Lys Ala Ala480 485 490 495gat aac ttc ctt gat cct aac aaa gca agt tct cta tta tct tca ggg 1536Asp Asn Phe Leu Asp Pro Asn Lys Ala Ser Ser Leu Leu Ser Ser Gly 500 505 510ttt tca cca gac ttc gct aca gtt att act atg gat aga aaa gca tcc 1584Phe Ser Pro Asp Phe Ala Thr Val Ile Thr Met Asp Arg Lys Ala Ser 515 520 525aaa caa caa aca aat ata gat gta ata tac gaa cga gtt cgt gat gat 1632Lys Gln Gln Thr Asn Ile Asp Val Ile Tyr Glu Arg Val Arg Asp Asp 530 535 540tac caa ttg cat tgg act tca aca aat tgg aaa ggt acc aat act aaa 1680Tyr Gln Leu His Trp Thr Ser Thr Asn Trp Lys Gly Thr Asn Thr Lys 545 550 555gat aaa tgg aca gat cgt tct tca gaa aga tat aaa atc gat tgg gaa 1728Asp Lys Trp Thr Asp Arg Ser Ser Glu Arg Tyr Lys Ile Asp Trp Glu560 565 570 575aaa gaa gaa atg aca aat ggt ggt tcg ggc tca tct ggt ggc tcg agt 1776Lys Glu Glu Met Thr Asn Gly Gly Ser Gly Ser Ser Gly Gly Ser Ser 580 585 590cac cat cat cat cac cac 1794His His His His His His 59520597PRTArtificial sequenceHL-RQC-EcoExoIII-L1-H6 20Ala Asp Ser Asp Ile Asn Ile Lys Thr Gly Thr Thr Asp Ile Gly Ser1 5 10 15Asn Thr Ser Gly Ser Gly Ser Gly Ser Gly Ser Gly Met Lys Phe Val 20 25 30Ser Phe Asn Ile Asn Gly Leu Arg Ala Arg Pro His Gln Leu Glu Ala 35 40 45Ile Val Glu Lys His Gln Pro Asp Val Ile Gly Leu Gln Glu Thr Lys 50 55 60Val His Asp Asp Met Phe Pro Leu Glu Glu Val Ala Lys Leu Gly Tyr65 70 75 80Asn Val Phe Tyr His Gly Gln Lys Gly His Tyr Gly Val Ala Leu Leu 85 90 95Thr Lys Glu Thr Pro Ile Ala Val Arg Arg Gly Phe Pro Gly Asp Asp 100 105 110Glu Glu Ala Gln Arg Arg Ile Ile Met Ala Glu Ile Pro Ser Leu Leu 115 120 125Gly Asn Val Thr Val Ile Asn Gly Tyr Phe Pro Gln Gly Glu Ser Arg 130 135 140Asp His Pro Ile Lys Phe Pro Ala Lys Ala Gln Phe Tyr Gln Asn Leu145 150 155 160Gln Asn Tyr Leu Glu Thr Glu Leu Lys Arg Asp Asn Pro Val Leu Ile 165 170 175Met Gly Asp Met Asn Ile Ser Pro Thr Asp Leu Asp Ile Gly Ile Gly 180 185 190Glu Glu Asn Arg Lys Arg Trp Leu Arg Thr Gly Lys Cys Ser Phe Leu 195 200 205Pro Glu Glu Arg Glu Trp Met Asp Arg Leu Met Ser Trp Gly Leu Val 210 215 220Asp Thr Phe Arg His Ala Asn Pro Gln Thr Ala Asp Arg Phe Ser Trp225 230 235 240Phe Asp Tyr Arg Ser Lys Gly Phe Asp Asp Asn Arg Gly Leu Arg Ile 245 250 255Asp Leu Leu Leu Ala Ser Gln Pro Leu Ala Glu Cys Cys Val Glu Thr 260 265 270Gly Ile Asp Tyr Glu Ile Arg Ser Met Glu Lys Pro Ser Asp His Ala 275 280 285Pro Val Trp Ala Thr Phe Arg Arg Ser Gly Ser Gly Ser Gly Ser Gly 290 295 300Ser Gly Thr Val Lys Thr Gly Asp Leu Val Thr Tyr Asp Lys Glu Asn305 310 315 320Gly Met His Lys Lys Val Phe Tyr Ser Phe Ile Asp Asp Lys Asn His 325 330 335Asn Lys Lys Leu Leu Val Ile Arg Thr Lys Gly Thr Ile Ala Gly Gln 340 345 350Tyr Arg Val Tyr Ser Glu Glu Gly Ala Asn Lys Ser Gly Leu Ala Trp 355 360 365Pro Ser Ala Phe Lys Val Gln Leu Gln Leu Pro Asp Asn Glu Val Ala 370 375 380Gln Ile Ser Asp Tyr Tyr Pro Arg Asn Ser Ile Asp Thr Lys Glu Tyr385 390 395 400Arg Ser Thr Leu Thr Tyr Gly Phe Asn Gly Asn Val Thr Gly Asp Asp 405 410 415Thr Gly Lys Ile Gly Gly Cys Ile Gly Ala Gln Val Ser Ile Gly His 420 425 430Thr Leu Lys Tyr Val Gln Pro Asp Phe Lys Thr Ile Leu Glu Ser Pro 435 440 445Thr Asp Lys Lys Val Gly Trp Lys Val Ile Phe Asn Asn Met Val Asn 450 455 460Gln Asn Trp Gly Pro Tyr Asp Arg Asp Ser Trp Asn Pro Val Tyr Gly465 470 475 480Asn Gln Leu Phe Met Lys Thr Arg Asn Gly Ser Met Lys Ala Ala Asp 485 490 495Asn Phe Leu Asp Pro Asn Lys Ala Ser Ser Leu Leu Ser Ser Gly Phe 500 505 510Ser Pro Asp Phe Ala Thr Val Ile Thr Met Asp Arg Lys Ala Ser Lys 515 520 525Gln Gln Thr Asn Ile Asp Val Ile Tyr Glu Arg Val Arg Asp Asp Tyr 530 535 540Gln Leu His Trp Thr Ser Thr Asn Trp Lys Gly Thr Asn Thr Lys Asp545 550 555 560Lys Trp Thr Asp Arg Ser Ser Glu Arg Tyr Lys Ile Asp Trp Glu Lys 565 570 575Glu Glu Met Thr Asn Gly Gly Ser Gly Ser Ser Gly Gly Ser Ser His 580 585 590His His His His His 595212415DNAArtificial sequenceHL-RQC-EcoExoI-L1-H6 21atg gca gat tct gat att aat att aaa acc ggt act aca gat att gga 48 Ala Asp Ser Asp Ile Asn Ile Lys Thr Gly Thr Thr Asp Ile Gly 1 5 10 15agc aat act tcc gga agc ggc tct ggt agt ggt tct ggc atg atg aac 96Ser Asn Thr Ser Gly Ser Gly Ser Gly Ser Gly Ser Gly Met Met Asn 20 25 30gat ggc aaa cag cag agc acc ttc ctg ttt cat gat tat gaa acc ttc 144Asp Gly Lys Gln Gln Ser Thr Phe Leu Phe His Asp Tyr Glu Thr Phe 35 40 45ggt acc cat ccg gcc ctg gat cgt ccg gcg cag ttt gcg gcc att cgc 192Gly Thr His Pro Ala Leu Asp Arg Pro Ala Gln Phe Ala Ala Ile Arg 50 55 60acc gat agc gaa ttc aat gtg att ggc gaa ccg gaa gtg ttt tat tgc 240Thr Asp Ser Glu Phe Asn Val Ile Gly Glu Pro Glu Val Phe Tyr Cys 65 70 75aaa ccg gcc gat gat tat ctg ccg cag ccg ggt gcg gtg ctg att acc 288Lys Pro Ala Asp Asp Tyr Leu Pro Gln Pro Gly Ala Val Leu Ile Thr80 85 90 95ggt att acc ccg cag gaa gcg cgc gcg aaa ggt gaa aac gaa gcg gcg 336Gly Ile Thr Pro Gln Glu Ala Arg Ala Lys Gly Glu Asn Glu Ala Ala 100 105 110ttt gcc gcg cgc att cat agc ctg ttt acc gtg ccg aaa acc tgc att 384Phe Ala Ala Arg Ile His Ser Leu Phe Thr Val Pro Lys Thr Cys Ile 115 120 125ctg ggc tat aac aat gtg cgc ttc gat gat gaa gtt acc cgt aat atc 432Leu Gly Tyr Asn Asn Val Arg Phe Asp Asp Glu Val Thr Arg Asn Ile 130

135 140ttt tat cgt aac ttt tat gat ccg tat gcg tgg agc tgg cag cat gat 480Phe Tyr Arg Asn Phe Tyr Asp Pro Tyr Ala Trp Ser Trp Gln His Asp 145 150 155aac agc cgt tgg gat ctg ctg gat gtg atg cgc gcg tgc tat gcg ctg 528Asn Ser Arg Trp Asp Leu Leu Asp Val Met Arg Ala Cys Tyr Ala Leu160 165 170 175cgc ccg gaa ggc att aat tgg ccg gaa aac gat gat ggc ctg ccg agc 576Arg Pro Glu Gly Ile Asn Trp Pro Glu Asn Asp Asp Gly Leu Pro Ser 180 185 190ttt cgt ctg gaa cat ctg acc aaa gcc aac ggc att gaa cat agc aat 624Phe Arg Leu Glu His Leu Thr Lys Ala Asn Gly Ile Glu His Ser Asn 195 200 205gcc cat gat gcg atg gcc gat gtt tat gcg acc att gcg atg gcg aaa 672Ala His Asp Ala Met Ala Asp Val Tyr Ala Thr Ile Ala Met Ala Lys 210 215 220ctg gtt aaa acc cgt cag ccg cgc ctg ttt gat tat ctg ttt acc cac 720Leu Val Lys Thr Arg Gln Pro Arg Leu Phe Asp Tyr Leu Phe Thr His 225 230 235cgt aac aaa cac aaa ctg atg gcg ctg att gat gtt ccg cag atg aaa 768Arg Asn Lys His Lys Leu Met Ala Leu Ile Asp Val Pro Gln Met Lys240 245 250 255ccg ctg gtg cat gtg agc ggc atg ttt ggc gcc tgg cgc ggc aac acc 816Pro Leu Val His Val Ser Gly Met Phe Gly Ala Trp Arg Gly Asn Thr 260 265 270agc tgg gtg gcc ccg ctg gcc tgg cac ccg gaa aat cgt aac gcc gtg 864Ser Trp Val Ala Pro Leu Ala Trp His Pro Glu Asn Arg Asn Ala Val 275 280 285att atg gtt gat ctg gcc ggt gat att agc ccg ctg ctg gaa ctg gat 912Ile Met Val Asp Leu Ala Gly Asp Ile Ser Pro Leu Leu Glu Leu Asp 290 295 300agc gat acc ctg cgt gaa cgc ctg tat acc gcc aaa acc gat ctg ggc 960Ser Asp Thr Leu Arg Glu Arg Leu Tyr Thr Ala Lys Thr Asp Leu Gly 305 310 315gat aat gcc gcc gtg ccg gtg aaa ctg gtt cac att aac aaa tgc ccg 1008Asp Asn Ala Ala Val Pro Val Lys Leu Val His Ile Asn Lys Cys Pro320 325 330 335gtg ctg gcc cag gcg aac acc ctg cgc ccg gaa gat gcg gat cgt ctg 1056Val Leu Ala Gln Ala Asn Thr Leu Arg Pro Glu Asp Ala Asp Arg Leu 340 345 350ggt att aat cgc cag cat tgt ctg gat aat ctg aaa atc ctg cgt gaa 1104Gly Ile Asn Arg Gln His Cys Leu Asp Asn Leu Lys Ile Leu Arg Glu 355 360 365aac ccg cag gtg cgt gaa aaa gtg gtg gcg atc ttc gcg gaa gcg gaa 1152Asn Pro Gln Val Arg Glu Lys Val Val Ala Ile Phe Ala Glu Ala Glu 370 375 380ccg ttc acc ccg agc gat aac gtg gat gcg cag ctg tat aac ggc ttc 1200Pro Phe Thr Pro Ser Asp Asn Val Asp Ala Gln Leu Tyr Asn Gly Phe 385 390 395ttt agc gat gcc gat cgc gcg gcg atg aaa atc gtt ctg gaa acc gaa 1248Phe Ser Asp Ala Asp Arg Ala Ala Met Lys Ile Val Leu Glu Thr Glu400 405 410 415ccg cgc aat ctg ccg gcg ctg gat att acc ttt gtt gat aaa cgt att 1296Pro Arg Asn Leu Pro Ala Leu Asp Ile Thr Phe Val Asp Lys Arg Ile 420 425 430gaa aaa ctg ctg ttt aat tat cgt gcg cgc aat ttt ccg ggt acc ctg 1344Glu Lys Leu Leu Phe Asn Tyr Arg Ala Arg Asn Phe Pro Gly Thr Leu 435 440 445gat tat gcc gaa cag cag cgt tgg ctg gaa cat cgt cgt cag gtt ttc 1392Asp Tyr Ala Glu Gln Gln Arg Trp Leu Glu His Arg Arg Gln Val Phe 450 455 460acc ccg gaa ttt ctg cag ggt tat gcg gat gaa ctg cag atg ctg gtt 1440Thr Pro Glu Phe Leu Gln Gly Tyr Ala Asp Glu Leu Gln Met Leu Val 465 470 475cag cag tat gcc gat gat aaa gaa aaa gtg gcg ctg ctg aaa gcg ctg 1488Gln Gln Tyr Ala Asp Asp Lys Glu Lys Val Ala Leu Leu Lys Ala Leu480 485 490 495tgg cag tat gcg gaa gaa atc gtt tct ggc tct ggt tcc ggc agc ggt 1536Trp Gln Tyr Ala Glu Glu Ile Val Ser Gly Ser Gly Ser Gly Ser Gly 500 505 510tcc gga aca gta aaa aca ggt gat tta gtc act tat gat aaa gaa aat 1584Ser Gly Thr Val Lys Thr Gly Asp Leu Val Thr Tyr Asp Lys Glu Asn 515 520 525ggc atg cac aaa aaa gta ttt tat agt ttt atc gat gat aaa aat cac 1632Gly Met His Lys Lys Val Phe Tyr Ser Phe Ile Asp Asp Lys Asn His 530 535 540aat aaa aaa ctg cta gtt att aga aca aaa ggt acc att gct ggt caa 1680Asn Lys Lys Leu Leu Val Ile Arg Thr Lys Gly Thr Ile Ala Gly Gln 545 550 555tat aga gtt tat agc gaa gaa ggt gct aac aaa agt ggt tta gcc tgg 1728Tyr Arg Val Tyr Ser Glu Glu Gly Ala Asn Lys Ser Gly Leu Ala Trp560 565 570 575cct tca gcc ttt aag gta cag ttg caa cta cct gat aat gaa gta gct 1776Pro Ser Ala Phe Lys Val Gln Leu Gln Leu Pro Asp Asn Glu Val Ala 580 585 590caa ata tct gat tac tat cca aga aat tcg att gat aca aaa gag tat 1824Gln Ile Ser Asp Tyr Tyr Pro Arg Asn Ser Ile Asp Thr Lys Glu Tyr 595 600 605agg agt act tta act tat gga ttc aac ggt aat gtt act ggt gat gat 1872Arg Ser Thr Leu Thr Tyr Gly Phe Asn Gly Asn Val Thr Gly Asp Asp 610 615 620aca gga aaa att ggc ggc tgt att ggt gca caa gtt tcg att ggt cat 1920Thr Gly Lys Ile Gly Gly Cys Ile Gly Ala Gln Val Ser Ile Gly His 625 630 635aca ctg aaa tat gtt caa cct gat ttc aaa aca att tta gag agc cca 1968Thr Leu Lys Tyr Val Gln Pro Asp Phe Lys Thr Ile Leu Glu Ser Pro640 645 650 655act gat aaa aaa gta ggc tgg aaa gtg ata ttt aac aat atg gtg aat 2016Thr Asp Lys Lys Val Gly Trp Lys Val Ile Phe Asn Asn Met Val Asn 660 665 670caa aat tgg gga cca tac gat cga gat tct tgg aac ccg gta tat ggc 2064Gln Asn Trp Gly Pro Tyr Asp Arg Asp Ser Trp Asn Pro Val Tyr Gly 675 680 685aat caa ctt ttc atg aaa act aga aat ggt tct atg aaa gca gca gat 2112Asn Gln Leu Phe Met Lys Thr Arg Asn Gly Ser Met Lys Ala Ala Asp 690 695 700aac ttc ctt gat cct aac aaa gca agt tct cta tta tct tca ggg ttt 2160Asn Phe Leu Asp Pro Asn Lys Ala Ser Ser Leu Leu Ser Ser Gly Phe 705 710 715tca cca gac ttc gct aca gtt att act atg gat aga aaa gca tcc aaa 2208Ser Pro Asp Phe Ala Thr Val Ile Thr Met Asp Arg Lys Ala Ser Lys720 725 730 735caa caa aca aat ata gat gta ata tac gaa cga gtt cgt gat gat tac 2256Gln Gln Thr Asn Ile Asp Val Ile Tyr Glu Arg Val Arg Asp Asp Tyr 740 745 750caa ttg cat tgg act tca aca aat tgg aaa ggt acc aat act aaa gat 2304Gln Leu His Trp Thr Ser Thr Asn Trp Lys Gly Thr Asn Thr Lys Asp 755 760 765aaa tgg aca gat cgt tct tca gaa aga tat aaa atc gat tgg gaa aaa 2352Lys Trp Thr Asp Arg Ser Ser Glu Arg Tyr Lys Ile Asp Trp Glu Lys 770 775 780gaa gaa atg aca aat ggt ggt tcg ggc tca tct ggt ggc tcg agt cac 2400Glu Glu Met Thr Asn Gly Gly Ser Gly Ser Ser Gly Gly Ser Ser His 785 790 795cat cat cat cac cac 2415His His His His His80022804PRTArtificial sequenceHL-RQC-EcoExoI-L1-H6 22Ala Asp Ser Asp Ile Asn Ile Lys Thr Gly Thr Thr Asp Ile Gly Ser1 5 10 15Asn Thr Ser Gly Ser Gly Ser Gly Ser Gly Ser Gly Met Met Asn Asp 20 25 30Gly Lys Gln Gln Ser Thr Phe Leu Phe His Asp Tyr Glu Thr Phe Gly 35 40 45Thr His Pro Ala Leu Asp Arg Pro Ala Gln Phe Ala Ala Ile Arg Thr 50 55 60Asp Ser Glu Phe Asn Val Ile Gly Glu Pro Glu Val Phe Tyr Cys Lys65 70 75 80Pro Ala Asp Asp Tyr Leu Pro Gln Pro Gly Ala Val Leu Ile Thr Gly 85 90 95Ile Thr Pro Gln Glu Ala Arg Ala Lys Gly Glu Asn Glu Ala Ala Phe 100 105 110Ala Ala Arg Ile His Ser Leu Phe Thr Val Pro Lys Thr Cys Ile Leu 115 120 125Gly Tyr Asn Asn Val Arg Phe Asp Asp Glu Val Thr Arg Asn Ile Phe 130 135 140Tyr Arg Asn Phe Tyr Asp Pro Tyr Ala Trp Ser Trp Gln His Asp Asn145 150 155 160Ser Arg Trp Asp Leu Leu Asp Val Met Arg Ala Cys Tyr Ala Leu Arg 165 170 175Pro Glu Gly Ile Asn Trp Pro Glu Asn Asp Asp Gly Leu Pro Ser Phe 180 185 190Arg Leu Glu His Leu Thr Lys Ala Asn Gly Ile Glu His Ser Asn Ala 195 200 205His Asp Ala Met Ala Asp Val Tyr Ala Thr Ile Ala Met Ala Lys Leu 210 215 220Val Lys Thr Arg Gln Pro Arg Leu Phe Asp Tyr Leu Phe Thr His Arg225 230 235 240Asn Lys His Lys Leu Met Ala Leu Ile Asp Val Pro Gln Met Lys Pro 245 250 255Leu Val His Val Ser Gly Met Phe Gly Ala Trp Arg Gly Asn Thr Ser 260 265 270Trp Val Ala Pro Leu Ala Trp His Pro Glu Asn Arg Asn Ala Val Ile 275 280 285Met Val Asp Leu Ala Gly Asp Ile Ser Pro Leu Leu Glu Leu Asp Ser 290 295 300Asp Thr Leu Arg Glu Arg Leu Tyr Thr Ala Lys Thr Asp Leu Gly Asp305 310 315 320Asn Ala Ala Val Pro Val Lys Leu Val His Ile Asn Lys Cys Pro Val 325 330 335Leu Ala Gln Ala Asn Thr Leu Arg Pro Glu Asp Ala Asp Arg Leu Gly 340 345 350Ile Asn Arg Gln His Cys Leu Asp Asn Leu Lys Ile Leu Arg Glu Asn 355 360 365Pro Gln Val Arg Glu Lys Val Val Ala Ile Phe Ala Glu Ala Glu Pro 370 375 380Phe Thr Pro Ser Asp Asn Val Asp Ala Gln Leu Tyr Asn Gly Phe Phe385 390 395 400Ser Asp Ala Asp Arg Ala Ala Met Lys Ile Val Leu Glu Thr Glu Pro 405 410 415Arg Asn Leu Pro Ala Leu Asp Ile Thr Phe Val Asp Lys Arg Ile Glu 420 425 430Lys Leu Leu Phe Asn Tyr Arg Ala Arg Asn Phe Pro Gly Thr Leu Asp 435 440 445Tyr Ala Glu Gln Gln Arg Trp Leu Glu His Arg Arg Gln Val Phe Thr 450 455 460Pro Glu Phe Leu Gln Gly Tyr Ala Asp Glu Leu Gln Met Leu Val Gln465 470 475 480Gln Tyr Ala Asp Asp Lys Glu Lys Val Ala Leu Leu Lys Ala Leu Trp 485 490 495Gln Tyr Ala Glu Glu Ile Val Ser Gly Ser Gly Ser Gly Ser Gly Ser 500 505 510Gly Thr Val Lys Thr Gly Asp Leu Val Thr Tyr Asp Lys Glu Asn Gly 515 520 525Met His Lys Lys Val Phe Tyr Ser Phe Ile Asp Asp Lys Asn His Asn 530 535 540Lys Lys Leu Leu Val Ile Arg Thr Lys Gly Thr Ile Ala Gly Gln Tyr545 550 555 560Arg Val Tyr Ser Glu Glu Gly Ala Asn Lys Ser Gly Leu Ala Trp Pro 565 570 575Ser Ala Phe Lys Val Gln Leu Gln Leu Pro Asp Asn Glu Val Ala Gln 580 585 590Ile Ser Asp Tyr Tyr Pro Arg Asn Ser Ile Asp Thr Lys Glu Tyr Arg 595 600 605Ser Thr Leu Thr Tyr Gly Phe Asn Gly Asn Val Thr Gly Asp Asp Thr 610 615 620Gly Lys Ile Gly Gly Cys Ile Gly Ala Gln Val Ser Ile Gly His Thr625 630 635 640Leu Lys Tyr Val Gln Pro Asp Phe Lys Thr Ile Leu Glu Ser Pro Thr 645 650 655Asp Lys Lys Val Gly Trp Lys Val Ile Phe Asn Asn Met Val Asn Gln 660 665 670Asn Trp Gly Pro Tyr Asp Arg Asp Ser Trp Asn Pro Val Tyr Gly Asn 675 680 685Gln Leu Phe Met Lys Thr Arg Asn Gly Ser Met Lys Ala Ala Asp Asn 690 695 700Phe Leu Asp Pro Asn Lys Ala Ser Ser Leu Leu Ser Ser Gly Phe Ser705 710 715 720Pro Asp Phe Ala Thr Val Ile Thr Met Asp Arg Lys Ala Ser Lys Gln 725 730 735Gln Thr Asn Ile Asp Val Ile Tyr Glu Arg Val Arg Asp Asp Tyr Gln 740 745 750Leu His Trp Thr Ser Thr Asn Trp Lys Gly Thr Asn Thr Lys Asp Lys 755 760 765Trp Thr Asp Arg Ser Ser Glu Arg Tyr Lys Ile Asp Trp Glu Lys Glu 770 775 780Glu Met Thr Asn Gly Gly Ser Gly Ser Ser Gly Gly Ser Ser His His785 790 795 800His His His His232265DNAArtificial sequenceHL-RQC-TthRecJ-L1-H6 23atg gca gat tct gat att aat att aaa acc ggt act aca gat att gga 48 Ala Asp Ser Asp Ile Asn Ile Lys Thr Gly Thr Thr Asp Ile Gly 1 5 10 15agc aat act tcc gga agc ggc tct ggt agt ggt tct ggc atg ttt cgt 96Ser Asn Thr Ser Gly Ser Gly Ser Gly Ser Gly Ser Gly Met Phe Arg 20 25 30cgt aaa gaa gat ctg gat ccg ccg ctg gca ctg ctg ccg ctg aaa ggc 144Arg Lys Glu Asp Leu Asp Pro Pro Leu Ala Leu Leu Pro Leu Lys Gly 35 40 45ctg cgc gaa gcc gcc gca ctg ctg gaa gaa gcg ctg cgt caa ggt aaa 192Leu Arg Glu Ala Ala Ala Leu Leu Glu Glu Ala Leu Arg Gln Gly Lys 50 55 60cgc att cgt gtt cac ggc gac tat gat gcg gat ggc ctg acc ggc acc 240Arg Ile Arg Val His Gly Asp Tyr Asp Ala Asp Gly Leu Thr Gly Thr 65 70 75gcg atc ctg gtt cgt ggt ctg gcc gcc ctg ggt gcg gat gtt cat ccg 288Ala Ile Leu Val Arg Gly Leu Ala Ala Leu Gly Ala Asp Val His Pro80 85 90 95ttt atc ccg cac cgc ctg gaa gaa ggc tat ggt gtc ctg atg gaa cgc 336Phe Ile Pro His Arg Leu Glu Glu Gly Tyr Gly Val Leu Met Glu Arg 100 105 110gtc ccg gaa cat ctg gaa gcc tcg gac ctg ttt ctg acc gtt gac tgc 384Val Pro Glu His Leu Glu Ala Ser Asp Leu Phe Leu Thr Val Asp Cys 115 120 125ggc att acc aac cat gcg gaa ctg cgc gaa ctg ctg gaa aat ggc gtg 432Gly Ile Thr Asn His Ala Glu Leu Arg Glu Leu Leu Glu Asn Gly Val 130 135 140gaa gtc att gtt acc gat cat cat acg ccg ggc aaa acg ccg ccg ccg 480Glu Val Ile Val Thr Asp His His Thr Pro Gly Lys Thr Pro Pro Pro 145 150 155ggt ctg gtc gtg cat ccg gcg ctg acg ccg gat ctg aaa gaa aaa ccg 528Gly Leu Val Val His Pro Ala Leu Thr Pro Asp Leu Lys Glu Lys Pro160 165 170 175acc ggc gca ggc gtg gcg ttt ctg ctg ctg tgg gca ctg cat gaa cgc 576Thr Gly Ala Gly Val Ala Phe Leu Leu Leu Trp Ala Leu His Glu Arg 180 185 190ctg ggc ctg ccg ccg ccg ctg gaa tac gcg gac ctg gca gcc gtt ggc 624Leu Gly Leu Pro Pro Pro Leu Glu Tyr Ala Asp Leu Ala Ala Val Gly 195 200 205acc att gcc gac gtt gcc ccg ctg tgg ggt tgg aat cgt gca ctg gtg 672Thr Ile Ala Asp Val Ala Pro Leu Trp Gly Trp Asn Arg Ala Leu Val 210 215 220aaa gaa ggt ctg gca cgc atc ccg gct tca tct tgg gtg ggc ctg cgt 720Lys Glu Gly Leu Ala Arg Ile Pro Ala Ser Ser Trp Val Gly Leu Arg 225 230 235ctg ctg gct gaa gcc gtg ggc tat acc ggc aaa gcg gtc gaa gtc gct 768Leu Leu Ala Glu Ala Val Gly Tyr Thr Gly Lys Ala Val Glu Val Ala240 245 250 255ttc cgc atc gcg ccg cgc atc aat gcg gct tcc cgc ctg ggc gaa gcg 816Phe Arg Ile Ala Pro Arg Ile Asn Ala Ala Ser Arg Leu Gly Glu Ala 260 265 270gaa aaa gcc ctg cgc ctg ctg ctg acg gat gat gcg gca gaa gct cag 864Glu Lys Ala Leu Arg Leu Leu Leu Thr Asp Asp Ala Ala Glu Ala Gln 275 280 285gcg ctg gtc ggc gaa ctg cac cgt ctg aac gcc cgt cgt cag acc ctg 912Ala Leu Val Gly Glu Leu His Arg Leu Asn Ala Arg Arg Gln Thr Leu 290 295 300gaa gaa gcg atg ctg cgc aaa ctg ctg ccg cag gcc gac ccg gaa gcg 960Glu Glu Ala Met Leu Arg Lys Leu Leu Pro Gln Ala Asp Pro Glu Ala 305 310 315aaa gcc atc gtt ctg ctg gac ccg gaa ggc cat ccg ggt gtt atg ggt 1008Lys Ala Ile Val Leu Leu Asp Pro Glu Gly His Pro Gly Val Met Gly320 325 330 335att gtg gcc tct cgc atc ctg gaa gcg acc ctg cgc ccg gtc ttt ctg 1056Ile Val Ala Ser Arg Ile Leu Glu Ala Thr Leu Arg Pro Val Phe Leu 340 345 350gtg gcc cag ggc aaa ggc acc gtg cgt tcg ctg gct ccg att tcc gcc 1104Val Ala Gln Gly Lys Gly Thr Val Arg Ser Leu Ala Pro Ile Ser Ala

355 360 365gtc gaa gca ctg cgc agc gcg gaa gat ctg ctg ctg cgt tat ggt ggt 1152Val Glu Ala Leu Arg Ser Ala Glu Asp Leu Leu Leu Arg Tyr Gly Gly 370 375 380cat aaa gaa gcg gcg ggt ttc gca atg gat gaa gcg ctg ttt ccg gcg 1200His Lys Glu Ala Ala Gly Phe Ala Met Asp Glu Ala Leu Phe Pro Ala 385 390 395ttc aaa gca cgc gtt gaa gcg tat gcc gca cgt ttc ccg gat ccg gtt 1248Phe Lys Ala Arg Val Glu Ala Tyr Ala Ala Arg Phe Pro Asp Pro Val400 405 410 415cgt gaa gtg gca ctg ctg gat ctg ctg ccg gaa ccg ggc ctg ctg ccg 1296Arg Glu Val Ala Leu Leu Asp Leu Leu Pro Glu Pro Gly Leu Leu Pro 420 425 430cag gtg ttc cgt gaa ctg gca ctg ctg gaa ccg tat ggt gaa ggt aac 1344Gln Val Phe Arg Glu Leu Ala Leu Leu Glu Pro Tyr Gly Glu Gly Asn 435 440 445ccg gaa ccg ctg ttc ctg tct ggc tct ggt tcc ggc agc ggt tcc gga 1392Pro Glu Pro Leu Phe Leu Ser Gly Ser Gly Ser Gly Ser Gly Ser Gly 450 455 460aca gta aaa aca ggt gat tta gtc act tat gat aaa gaa aat ggc atg 1440Thr Val Lys Thr Gly Asp Leu Val Thr Tyr Asp Lys Glu Asn Gly Met 465 470 475cac aaa aaa gta ttt tat agt ttt atc gat gat aaa aat cac aat aaa 1488His Lys Lys Val Phe Tyr Ser Phe Ile Asp Asp Lys Asn His Asn Lys480 485 490 495aaa ctg cta gtt att aga aca aaa ggt acc att gct ggt caa tat aga 1536Lys Leu Leu Val Ile Arg Thr Lys Gly Thr Ile Ala Gly Gln Tyr Arg 500 505 510gtt tat agc gaa gaa ggt gct aac aaa agt ggt tta gcc tgg cct tca 1584Val Tyr Ser Glu Glu Gly Ala Asn Lys Ser Gly Leu Ala Trp Pro Ser 515 520 525gcc ttt aag gta cag ttg caa cta cct gat aat gaa gta gct caa ata 1632Ala Phe Lys Val Gln Leu Gln Leu Pro Asp Asn Glu Val Ala Gln Ile 530 535 540tct gat tac tat cca aga aat tcg att gat aca aaa gag tat agg agt 1680Ser Asp Tyr Tyr Pro Arg Asn Ser Ile Asp Thr Lys Glu Tyr Arg Ser 545 550 555act tta act tat gga ttc aac ggt aat gtt act ggt gat gat aca gga 1728Thr Leu Thr Tyr Gly Phe Asn Gly Asn Val Thr Gly Asp Asp Thr Gly560 565 570 575aaa att ggc ggc tgt att ggt gca caa gtt tcg att ggt cat aca ctg 1776Lys Ile Gly Gly Cys Ile Gly Ala Gln Val Ser Ile Gly His Thr Leu 580 585 590aaa tat gtt caa cct gat ttc aaa aca att tta gag agc cca act gat 1824Lys Tyr Val Gln Pro Asp Phe Lys Thr Ile Leu Glu Ser Pro Thr Asp 595 600 605aaa aaa gta ggc tgg aaa gtg ata ttt aac aat atg gtg aat caa aat 1872Lys Lys Val Gly Trp Lys Val Ile Phe Asn Asn Met Val Asn Gln Asn 610 615 620tgg gga cca tac gat cga gat tct tgg aac ccg gta tat ggc aat caa 1920Trp Gly Pro Tyr Asp Arg Asp Ser Trp Asn Pro Val Tyr Gly Asn Gln 625 630 635ctt ttc atg aaa act aga aat ggt tct atg aaa gca gca gat aac ttc 1968Leu Phe Met Lys Thr Arg Asn Gly Ser Met Lys Ala Ala Asp Asn Phe640 645 650 655ctt gat cct aac aaa gca agt tct cta tta tct tca ggg ttt tca cca 2016Leu Asp Pro Asn Lys Ala Ser Ser Leu Leu Ser Ser Gly Phe Ser Pro 660 665 670gac ttc gct aca gtt att act atg gat aga aaa gca tcc aaa caa caa 2064Asp Phe Ala Thr Val Ile Thr Met Asp Arg Lys Ala Ser Lys Gln Gln 675 680 685aca aat ata gat gta ata tac gaa cga gtt cgt gat gat tac caa ttg 2112Thr Asn Ile Asp Val Ile Tyr Glu Arg Val Arg Asp Asp Tyr Gln Leu 690 695 700cat tgg act tca aca aat tgg aaa ggt acc aat act aaa gat aaa tgg 2160His Trp Thr Ser Thr Asn Trp Lys Gly Thr Asn Thr Lys Asp Lys Trp 705 710 715aca gat cgt tct tca gaa aga tat aaa atc gat tgg gaa aaa gaa gaa 2208Thr Asp Arg Ser Ser Glu Arg Tyr Lys Ile Asp Trp Glu Lys Glu Glu720 725 730 735atg aca aat ggt ggt tcg ggc tca tct ggt ggc tcg agt cac cat cat 2256Met Thr Asn Gly Gly Ser Gly Ser Ser Gly Gly Ser Ser His His His 740 745 750cat cac cac 2265His His His24754PRTArtificial sequenceHL-RQC-TthRecJ-L1-H6 24Ala Asp Ser Asp Ile Asn Ile Lys Thr Gly Thr Thr Asp Ile Gly Ser1 5 10 15Asn Thr Ser Gly Ser Gly Ser Gly Ser Gly Ser Gly Met Phe Arg Arg 20 25 30Lys Glu Asp Leu Asp Pro Pro Leu Ala Leu Leu Pro Leu Lys Gly Leu 35 40 45Arg Glu Ala Ala Ala Leu Leu Glu Glu Ala Leu Arg Gln Gly Lys Arg 50 55 60Ile Arg Val His Gly Asp Tyr Asp Ala Asp Gly Leu Thr Gly Thr Ala65 70 75 80Ile Leu Val Arg Gly Leu Ala Ala Leu Gly Ala Asp Val His Pro Phe 85 90 95Ile Pro His Arg Leu Glu Glu Gly Tyr Gly Val Leu Met Glu Arg Val 100 105 110Pro Glu His Leu Glu Ala Ser Asp Leu Phe Leu Thr Val Asp Cys Gly 115 120 125Ile Thr Asn His Ala Glu Leu Arg Glu Leu Leu Glu Asn Gly Val Glu 130 135 140Val Ile Val Thr Asp His His Thr Pro Gly Lys Thr Pro Pro Pro Gly145 150 155 160Leu Val Val His Pro Ala Leu Thr Pro Asp Leu Lys Glu Lys Pro Thr 165 170 175Gly Ala Gly Val Ala Phe Leu Leu Leu Trp Ala Leu His Glu Arg Leu 180 185 190Gly Leu Pro Pro Pro Leu Glu Tyr Ala Asp Leu Ala Ala Val Gly Thr 195 200 205Ile Ala Asp Val Ala Pro Leu Trp Gly Trp Asn Arg Ala Leu Val Lys 210 215 220Glu Gly Leu Ala Arg Ile Pro Ala Ser Ser Trp Val Gly Leu Arg Leu225 230 235 240Leu Ala Glu Ala Val Gly Tyr Thr Gly Lys Ala Val Glu Val Ala Phe 245 250 255Arg Ile Ala Pro Arg Ile Asn Ala Ala Ser Arg Leu Gly Glu Ala Glu 260 265 270Lys Ala Leu Arg Leu Leu Leu Thr Asp Asp Ala Ala Glu Ala Gln Ala 275 280 285Leu Val Gly Glu Leu His Arg Leu Asn Ala Arg Arg Gln Thr Leu Glu 290 295 300Glu Ala Met Leu Arg Lys Leu Leu Pro Gln Ala Asp Pro Glu Ala Lys305 310 315 320Ala Ile Val Leu Leu Asp Pro Glu Gly His Pro Gly Val Met Gly Ile 325 330 335Val Ala Ser Arg Ile Leu Glu Ala Thr Leu Arg Pro Val Phe Leu Val 340 345 350Ala Gln Gly Lys Gly Thr Val Arg Ser Leu Ala Pro Ile Ser Ala Val 355 360 365Glu Ala Leu Arg Ser Ala Glu Asp Leu Leu Leu Arg Tyr Gly Gly His 370 375 380Lys Glu Ala Ala Gly Phe Ala Met Asp Glu Ala Leu Phe Pro Ala Phe385 390 395 400Lys Ala Arg Val Glu Ala Tyr Ala Ala Arg Phe Pro Asp Pro Val Arg 405 410 415Glu Val Ala Leu Leu Asp Leu Leu Pro Glu Pro Gly Leu Leu Pro Gln 420 425 430Val Phe Arg Glu Leu Ala Leu Leu Glu Pro Tyr Gly Glu Gly Asn Pro 435 440 445Glu Pro Leu Phe Leu Ser Gly Ser Gly Ser Gly Ser Gly Ser Gly Thr 450 455 460Val Lys Thr Gly Asp Leu Val Thr Tyr Asp Lys Glu Asn Gly Met His465 470 475 480Lys Lys Val Phe Tyr Ser Phe Ile Asp Asp Lys Asn His Asn Lys Lys 485 490 495Leu Leu Val Ile Arg Thr Lys Gly Thr Ile Ala Gly Gln Tyr Arg Val 500 505 510Tyr Ser Glu Glu Gly Ala Asn Lys Ser Gly Leu Ala Trp Pro Ser Ala 515 520 525Phe Lys Val Gln Leu Gln Leu Pro Asp Asn Glu Val Ala Gln Ile Ser 530 535 540Asp Tyr Tyr Pro Arg Asn Ser Ile Asp Thr Lys Glu Tyr Arg Ser Thr545 550 555 560Leu Thr Tyr Gly Phe Asn Gly Asn Val Thr Gly Asp Asp Thr Gly Lys 565 570 575Ile Gly Gly Cys Ile Gly Ala Gln Val Ser Ile Gly His Thr Leu Lys 580 585 590Tyr Val Gln Pro Asp Phe Lys Thr Ile Leu Glu Ser Pro Thr Asp Lys 595 600 605Lys Val Gly Trp Lys Val Ile Phe Asn Asn Met Val Asn Gln Asn Trp 610 615 620Gly Pro Tyr Asp Arg Asp Ser Trp Asn Pro Val Tyr Gly Asn Gln Leu625 630 635 640Phe Met Lys Thr Arg Asn Gly Ser Met Lys Ala Ala Asp Asn Phe Leu 645 650 655Asp Pro Asn Lys Ala Ser Ser Leu Leu Ser Ser Gly Phe Ser Pro Asp 660 665 670Phe Ala Thr Val Ile Thr Met Asp Arg Lys Ala Ser Lys Gln Gln Thr 675 680 685Asn Ile Asp Val Ile Tyr Glu Arg Val Arg Asp Asp Tyr Gln Leu His 690 695 700Trp Thr Ser Thr Asn Trp Lys Gly Thr Asn Thr Lys Asp Lys Trp Thr705 710 715 720Asp Arg Ser Ser Glu Arg Tyr Lys Ile Asp Trp Glu Lys Glu Glu Met 725 730 735Thr Asn Gly Gly Ser Gly Ser Ser Gly Gly Ser Ser His His His His 740 745 750His His251785DNAArtificial sequenceHL-RQC-EcoExoIII-L2-D45-N47delta-H6 25atg gca gat tct gat att aat att aaa acc ggt act aca gat att gga 48 Ala Asp Ser Asp Ile Asn Ile Lys Thr Gly Thr Thr Asp Ile Gly 1 5 10 15agc aat act aca gta aaa aca ggt gat tta gtc act tat gat aaa gaa 96Ser Asn Thr Thr Val Lys Thr Gly Asp Leu Val Thr Tyr Asp Lys Glu 20 25 30aat ggc atg cac aaa aaa gta ttt tat agt ttt atc gat tcc gga agc 144Asn Gly Met His Lys Lys Val Phe Tyr Ser Phe Ile Asp Ser Gly Ser 35 40 45ggc tct ggt agt ggt tct ggc atg aaa ttt gtt agc ttc aat atc aac 192Gly Ser Gly Ser Gly Ser Gly Met Lys Phe Val Ser Phe Asn Ile Asn 50 55 60ggc ctg cgc gcg cgc ccg cat cag ctg gaa gcg att gtg gaa aaa cat 240Gly Leu Arg Ala Arg Pro His Gln Leu Glu Ala Ile Val Glu Lys His 65 70 75cag ccg gat gtt att ggt ctg cag gaa acc aaa gtt cac gat gat atg 288Gln Pro Asp Val Ile Gly Leu Gln Glu Thr Lys Val His Asp Asp Met80 85 90 95ttt ccg ctg gaa gaa gtg gcg aaa ctg ggc tat aac gtg ttt tat cat 336Phe Pro Leu Glu Glu Val Ala Lys Leu Gly Tyr Asn Val Phe Tyr His 100 105 110ggc cag aaa ggt cat tat ggc gtg gcc ctg ctg acc aaa gaa acc ccg 384Gly Gln Lys Gly His Tyr Gly Val Ala Leu Leu Thr Lys Glu Thr Pro 115 120 125atc gcg gtt cgt cgt ggt ttt ccg ggt gat gat gaa gaa gcg cag cgt 432Ile Ala Val Arg Arg Gly Phe Pro Gly Asp Asp Glu Glu Ala Gln Arg 130 135 140cgt att att atg gcg gaa att ccg agc ctg ctg ggc aat gtg acc gtt 480Arg Ile Ile Met Ala Glu Ile Pro Ser Leu Leu Gly Asn Val Thr Val 145 150 155att aac ggc tat ttt ccg cag ggc gaa agc cgt gat cat ccg att aaa 528Ile Asn Gly Tyr Phe Pro Gln Gly Glu Ser Arg Asp His Pro Ile Lys160 165 170 175ttt ccg gcc aaa gcg cag ttc tat cag aac ctg cag aac tat ctg gaa 576Phe Pro Ala Lys Ala Gln Phe Tyr Gln Asn Leu Gln Asn Tyr Leu Glu 180 185 190acc gaa ctg aaa cgt gat aat ccg gtg ctg atc atg ggc gat atg aac 624Thr Glu Leu Lys Arg Asp Asn Pro Val Leu Ile Met Gly Asp Met Asn 195 200 205att agc ccg acc gat ctg gat att ggc att ggc gaa gaa aac cgt aaa 672Ile Ser Pro Thr Asp Leu Asp Ile Gly Ile Gly Glu Glu Asn Arg Lys 210 215 220cgc tgg ctg cgt acc ggt aaa tgc agc ttt ctg ccg gaa gaa cgt gaa 720Arg Trp Leu Arg Thr Gly Lys Cys Ser Phe Leu Pro Glu Glu Arg Glu 225 230 235tgg atg gat cgc ctg atg agc tgg ggc ctg gtg gat acc ttt cgt cat 768Trp Met Asp Arg Leu Met Ser Trp Gly Leu Val Asp Thr Phe Arg His240 245 250 255gcg aac ccg cag acc gcc gat cgc ttt agc tgg ttt gat tat cgc agc 816Ala Asn Pro Gln Thr Ala Asp Arg Phe Ser Trp Phe Asp Tyr Arg Ser 260 265 270aaa ggt ttt gat gat aac cgt ggc ctg cgc att gat ctg ctg ctg gcg 864Lys Gly Phe Asp Asp Asn Arg Gly Leu Arg Ile Asp Leu Leu Leu Ala 275 280 285agc cag ccg ctg gcg gaa tgc tgc gtt gaa acc ggt att gat tat gaa 912Ser Gln Pro Leu Ala Glu Cys Cys Val Glu Thr Gly Ile Asp Tyr Glu 290 295 300att cgc agc atg gaa aaa ccg agc gat cac gcc ccg gtg tgg gcg acc 960Ile Arg Ser Met Glu Lys Pro Ser Asp His Ala Pro Val Trp Ala Thr 305 310 315ttt cgc cgc tct ggc tct ggt tcc ggc agc ggt tcc gga cac aat aaa 1008Phe Arg Arg Ser Gly Ser Gly Ser Gly Ser Gly Ser Gly His Asn Lys320 325 330 335aaa ctg cta gtt att aga aca aaa ggt acc att gct ggt caa tat aga 1056Lys Leu Leu Val Ile Arg Thr Lys Gly Thr Ile Ala Gly Gln Tyr Arg 340 345 350gtt tat agc gaa gaa ggt gct aac aaa agt ggt tta gcc tgg cct tca 1104Val Tyr Ser Glu Glu Gly Ala Asn Lys Ser Gly Leu Ala Trp Pro Ser 355 360 365gcc ttt aag gta cag ttg caa cta cct gat aat gaa gta gct caa ata 1152Ala Phe Lys Val Gln Leu Gln Leu Pro Asp Asn Glu Val Ala Gln Ile 370 375 380tct gat tac tat cca aga aat tcg att gat aca aaa gag tat agg agt 1200Ser Asp Tyr Tyr Pro Arg Asn Ser Ile Asp Thr Lys Glu Tyr Arg Ser 385 390 395act tta act tat gga ttc aac ggt aat gtt act ggt gat gat aca gga 1248Thr Leu Thr Tyr Gly Phe Asn Gly Asn Val Thr Gly Asp Asp Thr Gly400 405 410 415aaa att ggc ggc tgt att ggt gca caa gtt tcg att ggt cat aca ctg 1296Lys Ile Gly Gly Cys Ile Gly Ala Gln Val Ser Ile Gly His Thr Leu 420 425 430aaa tat gtt caa cct gat ttc aaa aca att tta gag agc cca act gat 1344Lys Tyr Val Gln Pro Asp Phe Lys Thr Ile Leu Glu Ser Pro Thr Asp 435 440 445aaa aaa gta ggc tgg aaa gtg ata ttt aac aat atg gtg aat caa aat 1392Lys Lys Val Gly Trp Lys Val Ile Phe Asn Asn Met Val Asn Gln Asn 450 455 460tgg gga cca tac gat cga gat tct tgg aac ccg gta tat ggc aat caa 1440Trp Gly Pro Tyr Asp Arg Asp Ser Trp Asn Pro Val Tyr Gly Asn Gln 465 470 475ctt ttc atg aaa act aga aat ggt tct atg aaa gca gca gat aac ttc 1488Leu Phe Met Lys Thr Arg Asn Gly Ser Met Lys Ala Ala Asp Asn Phe480 485 490 495ctt gat cct aac aaa gca agt tct cta tta tct tca ggg ttt tca cca 1536Leu Asp Pro Asn Lys Ala Ser Ser Leu Leu Ser Ser Gly Phe Ser Pro 500 505 510gac ttc gct aca gtt att act atg gat aga aaa gca tcc aaa caa caa 1584Asp Phe Ala Thr Val Ile Thr Met Asp Arg Lys Ala Ser Lys Gln Gln 515 520 525aca aat ata gat gta ata tac gaa cga gtt cgt gat gat tac caa ttg 1632Thr Asn Ile Asp Val Ile Tyr Glu Arg Val Arg Asp Asp Tyr Gln Leu 530 535 540cat tgg act tca aca aat tgg aaa ggt acc aat act aaa gat aaa tgg 1680His Trp Thr Ser Thr Asn Trp Lys Gly Thr Asn Thr Lys Asp Lys Trp 545 550 555aca gat cgt tct tca gaa aga tat aaa atc gat tgg gaa aaa gaa gaa 1728Thr Asp Arg Ser Ser Glu Arg Tyr Lys Ile Asp Trp Glu Lys Glu Glu560 565 570 575atg aca aat ggt ggt tcg ggc tca tct ggt ggc tcg agt cac cat cat 1776Met Thr Asn Gly Gly Ser Gly Ser Ser Gly Gly Ser Ser His His His 580 585 590cat cac cac 1785His His His26594PRTArtificial sequenceHL-RQC-EcoExoIII-L2-D45-N47delta-H6 26Ala Asp Ser Asp Ile Asn Ile Lys Thr Gly Thr Thr Asp Ile Gly Ser1 5 10 15Asn Thr Thr Val Lys Thr Gly Asp Leu Val Thr Tyr Asp Lys Glu Asn 20 25 30Gly Met His Lys Lys Val Phe Tyr Ser Phe Ile Asp Ser Gly Ser Gly 35 40 45Ser Gly Ser Gly Ser Gly Met Lys Phe Val Ser Phe Asn Ile Asn Gly 50 55 60Leu Arg Ala Arg Pro His Gln Leu Glu Ala Ile Val Glu Lys His Gln65 70 75 80Pro Asp Val Ile Gly Leu Gln Glu Thr Lys Val His Asp Asp Met Phe 85

90 95Pro Leu Glu Glu Val Ala Lys Leu Gly Tyr Asn Val Phe Tyr His Gly 100 105 110Gln Lys Gly His Tyr Gly Val Ala Leu Leu Thr Lys Glu Thr Pro Ile 115 120 125Ala Val Arg Arg Gly Phe Pro Gly Asp Asp Glu Glu Ala Gln Arg Arg 130 135 140Ile Ile Met Ala Glu Ile Pro Ser Leu Leu Gly Asn Val Thr Val Ile145 150 155 160Asn Gly Tyr Phe Pro Gln Gly Glu Ser Arg Asp His Pro Ile Lys Phe 165 170 175Pro Ala Lys Ala Gln Phe Tyr Gln Asn Leu Gln Asn Tyr Leu Glu Thr 180 185 190Glu Leu Lys Arg Asp Asn Pro Val Leu Ile Met Gly Asp Met Asn Ile 195 200 205Ser Pro Thr Asp Leu Asp Ile Gly Ile Gly Glu Glu Asn Arg Lys Arg 210 215 220Trp Leu Arg Thr Gly Lys Cys Ser Phe Leu Pro Glu Glu Arg Glu Trp225 230 235 240Met Asp Arg Leu Met Ser Trp Gly Leu Val Asp Thr Phe Arg His Ala 245 250 255Asn Pro Gln Thr Ala Asp Arg Phe Ser Trp Phe Asp Tyr Arg Ser Lys 260 265 270Gly Phe Asp Asp Asn Arg Gly Leu Arg Ile Asp Leu Leu Leu Ala Ser 275 280 285Gln Pro Leu Ala Glu Cys Cys Val Glu Thr Gly Ile Asp Tyr Glu Ile 290 295 300Arg Ser Met Glu Lys Pro Ser Asp His Ala Pro Val Trp Ala Thr Phe305 310 315 320Arg Arg Ser Gly Ser Gly Ser Gly Ser Gly Ser Gly His Asn Lys Lys 325 330 335Leu Leu Val Ile Arg Thr Lys Gly Thr Ile Ala Gly Gln Tyr Arg Val 340 345 350Tyr Ser Glu Glu Gly Ala Asn Lys Ser Gly Leu Ala Trp Pro Ser Ala 355 360 365Phe Lys Val Gln Leu Gln Leu Pro Asp Asn Glu Val Ala Gln Ile Ser 370 375 380Asp Tyr Tyr Pro Arg Asn Ser Ile Asp Thr Lys Glu Tyr Arg Ser Thr385 390 395 400Leu Thr Tyr Gly Phe Asn Gly Asn Val Thr Gly Asp Asp Thr Gly Lys 405 410 415Ile Gly Gly Cys Ile Gly Ala Gln Val Ser Ile Gly His Thr Leu Lys 420 425 430Tyr Val Gln Pro Asp Phe Lys Thr Ile Leu Glu Ser Pro Thr Asp Lys 435 440 445Lys Val Gly Trp Lys Val Ile Phe Asn Asn Met Val Asn Gln Asn Trp 450 455 460Gly Pro Tyr Asp Arg Asp Ser Trp Asn Pro Val Tyr Gly Asn Gln Leu465 470 475 480Phe Met Lys Thr Arg Asn Gly Ser Met Lys Ala Ala Asp Asn Phe Leu 485 490 495Asp Pro Asn Lys Ala Ser Ser Leu Leu Ser Ser Gly Phe Ser Pro Asp 500 505 510Phe Ala Thr Val Ile Thr Met Asp Arg Lys Ala Ser Lys Gln Gln Thr 515 520 525Asn Ile Asp Val Ile Tyr Glu Arg Val Arg Asp Asp Tyr Gln Leu His 530 535 540Trp Thr Ser Thr Asn Trp Lys Gly Thr Asn Thr Lys Asp Lys Trp Thr545 550 555 560Asp Arg Ser Ser Glu Arg Tyr Lys Ile Asp Trp Glu Lys Glu Glu Met 565 570 575Thr Asn Gly Gly Ser Gly Ser Ser Gly Gly Ser Ser His His His His 580 585 590His His272364DNAArtificial sequenceHL-RQC-EcoExoI-Cter-{SG}8-H6 27atg gca gat tct gat att aat att aaa acc ggt act aca gat att gga 48 Ala Asp Ser Asp Ile Asn Ile Lys Thr Gly Thr Thr Asp Ile Gly 1 5 10 15agc aat act aca gta aaa aca ggt gat tta gtc act tat gat aaa gaa 96Ser Asn Thr Thr Val Lys Thr Gly Asp Leu Val Thr Tyr Asp Lys Glu 20 25 30aat ggc atg cac aaa aaa gta ttt tat agt ttt atc gat gat aaa aat 144Asn Gly Met His Lys Lys Val Phe Tyr Ser Phe Ile Asp Asp Lys Asn 35 40 45cac aat aaa aaa ctg cta gtt att aga aca aaa ggt acc att gct ggt 192His Asn Lys Lys Leu Leu Val Ile Arg Thr Lys Gly Thr Ile Ala Gly 50 55 60caa tat aga gtt tat agc gaa gaa ggt gct aac aaa agt ggt tta gcc 240Gln Tyr Arg Val Tyr Ser Glu Glu Gly Ala Asn Lys Ser Gly Leu Ala 65 70 75tgg cct tca gcc ttt aag gta cag ttg caa cta cct gat aat gaa gta 288Trp Pro Ser Ala Phe Lys Val Gln Leu Gln Leu Pro Asp Asn Glu Val80 85 90 95gct caa ata tct gat tac tat cca aga aat tcg att gat aca aaa gag 336Ala Gln Ile Ser Asp Tyr Tyr Pro Arg Asn Ser Ile Asp Thr Lys Glu 100 105 110tat agg agt act tta act tat gga ttc aac ggt aat gtt act ggt gat 384Tyr Arg Ser Thr Leu Thr Tyr Gly Phe Asn Gly Asn Val Thr Gly Asp 115 120 125gat aca gga aaa att ggc ggc tgt att ggt gca caa gtt tcg att ggt 432Asp Thr Gly Lys Ile Gly Gly Cys Ile Gly Ala Gln Val Ser Ile Gly 130 135 140cat aca ctg aaa tat gtt caa cct gat ttc aaa aca att tta gag agc 480His Thr Leu Lys Tyr Val Gln Pro Asp Phe Lys Thr Ile Leu Glu Ser 145 150 155cca act gat aaa aaa gta ggc tgg aaa gtg ata ttt aac aat atg gtg 528Pro Thr Asp Lys Lys Val Gly Trp Lys Val Ile Phe Asn Asn Met Val160 165 170 175aat caa aat tgg gga cca tac gat cga gat tct tgg aac ccg gta tat 576Asn Gln Asn Trp Gly Pro Tyr Asp Arg Asp Ser Trp Asn Pro Val Tyr 180 185 190ggc aat caa ctt ttc atg aaa act aga aat ggt tct atg aaa gca gca 624Gly Asn Gln Leu Phe Met Lys Thr Arg Asn Gly Ser Met Lys Ala Ala 195 200 205gat aac ttc ctt gat cct aac aaa gca agt tct cta tta tct tca ggg 672Asp Asn Phe Leu Asp Pro Asn Lys Ala Ser Ser Leu Leu Ser Ser Gly 210 215 220ttt tca cca gac ttc gct aca gtt att act atg gat aga aaa gca tcc 720Phe Ser Pro Asp Phe Ala Thr Val Ile Thr Met Asp Arg Lys Ala Ser 225 230 235aaa caa caa aca aat ata gat gta ata tac gaa cga gtt cgt gat gat 768Lys Gln Gln Thr Asn Ile Asp Val Ile Tyr Glu Arg Val Arg Asp Asp240 245 250 255tac caa ttg cat tgg act tca aca aat tgg aaa ggt acc aat act aaa 816Tyr Gln Leu His Trp Thr Ser Thr Asn Trp Lys Gly Thr Asn Thr Lys 260 265 270gat aaa tgg aca gat cgt tct tca gaa aga tat aaa atc gat tgg gaa 864Asp Lys Trp Thr Asp Arg Ser Ser Glu Arg Tyr Lys Ile Asp Trp Glu 275 280 285aaa gaa gaa atg aca aat tcc ggt agc ggc tct ggt tct ggc tct ggt 912Lys Glu Glu Met Thr Asn Ser Gly Ser Gly Ser Gly Ser Gly Ser Gly 290 295 300tcc ggc agc ggt tcc gga cag agc acc ttc ctg ttt cat gat tat gaa 960Ser Gly Ser Gly Ser Gly Gln Ser Thr Phe Leu Phe His Asp Tyr Glu 305 310 315acc ttc ggt acc cat ccg gcc ctg gat cgt ccg gcg cag ttt gcg gcc 1008Thr Phe Gly Thr His Pro Ala Leu Asp Arg Pro Ala Gln Phe Ala Ala320 325 330 335att cgc acc gat agc gaa ttc aat gtg att ggc gaa ccg gaa gtg ttt 1056Ile Arg Thr Asp Ser Glu Phe Asn Val Ile Gly Glu Pro Glu Val Phe 340 345 350tat tgc aaa ccg gcc gat gat tat ctg ccg cag ccg ggt gcg gtg ctg 1104Tyr Cys Lys Pro Ala Asp Asp Tyr Leu Pro Gln Pro Gly Ala Val Leu 355 360 365att acc ggt att acc ccg cag gaa gcg cgc gcg aaa ggt gaa aac gaa 1152Ile Thr Gly Ile Thr Pro Gln Glu Ala Arg Ala Lys Gly Glu Asn Glu 370 375 380gcg gcg ttt gcc gcg cgc att cat agc ctg ttt acc gtg ccg aaa acc 1200Ala Ala Phe Ala Ala Arg Ile His Ser Leu Phe Thr Val Pro Lys Thr 385 390 395tgc att ctg ggc tat aac aat gtg cgc ttc gat gat gaa gtt acc cgt 1248Cys Ile Leu Gly Tyr Asn Asn Val Arg Phe Asp Asp Glu Val Thr Arg400 405 410 415aat atc ttt tat cgt aac ttt tat gat ccg tat gcg tgg agc tgg cag 1296Asn Ile Phe Tyr Arg Asn Phe Tyr Asp Pro Tyr Ala Trp Ser Trp Gln 420 425 430cat gat aac agc cgt tgg gat ctg ctg gat gtg atg cgc gcg tgc tat 1344His Asp Asn Ser Arg Trp Asp Leu Leu Asp Val Met Arg Ala Cys Tyr 435 440 445gcg ctg cgc ccg gaa ggc att aat tgg ccg gaa aac gat gat ggc ctg 1392Ala Leu Arg Pro Glu Gly Ile Asn Trp Pro Glu Asn Asp Asp Gly Leu 450 455 460ccg agc ttt cgt ctg gaa cat ctg acc aaa gcc aac ggc att gaa cat 1440Pro Ser Phe Arg Leu Glu His Leu Thr Lys Ala Asn Gly Ile Glu His 465 470 475agc aat gcc cat gat gcg atg gcc gat gtt tat gcg acc att gcg atg 1488Ser Asn Ala His Asp Ala Met Ala Asp Val Tyr Ala Thr Ile Ala Met480 485 490 495gcg aaa ctg gtt aaa acc cgt cag ccg cgc ctg ttt gat tat ctg ttt 1536Ala Lys Leu Val Lys Thr Arg Gln Pro Arg Leu Phe Asp Tyr Leu Phe 500 505 510acc cac cgt aac aaa cac aaa ctg atg gcg ctg att gat gtt ccg cag 1584Thr His Arg Asn Lys His Lys Leu Met Ala Leu Ile Asp Val Pro Gln 515 520 525atg aaa ccg ctg gtg cat gtg agc ggc atg ttt ggc gcc tgg cgc ggc 1632Met Lys Pro Leu Val His Val Ser Gly Met Phe Gly Ala Trp Arg Gly 530 535 540aac acc agc tgg gtg gcc ccg ctg gcc tgg cac ccg gaa aat cgt aac 1680Asn Thr Ser Trp Val Ala Pro Leu Ala Trp His Pro Glu Asn Arg Asn 545 550 555gcc gtg att atg gtt gat ctg gcc ggt gat att agc ccg ctg ctg gaa 1728Ala Val Ile Met Val Asp Leu Ala Gly Asp Ile Ser Pro Leu Leu Glu560 565 570 575ctg gat agc gat acc ctg cgt gaa cgc ctg tat acc gcc aaa acc gat 1776Leu Asp Ser Asp Thr Leu Arg Glu Arg Leu Tyr Thr Ala Lys Thr Asp 580 585 590ctg ggc gat aat gcc gcc gtg ccg gtg aaa ctg gtt cac att aac aaa 1824Leu Gly Asp Asn Ala Ala Val Pro Val Lys Leu Val His Ile Asn Lys 595 600 605tgc ccg gtg ctg gcc cag gcg aac acc ctg cgc ccg gaa gat gcg gat 1872Cys Pro Val Leu Ala Gln Ala Asn Thr Leu Arg Pro Glu Asp Ala Asp 610 615 620cgt ctg ggt att aat cgc cag cat tgt ctg gat aat ctg aaa atc ctg 1920Arg Leu Gly Ile Asn Arg Gln His Cys Leu Asp Asn Leu Lys Ile Leu 625 630 635cgt gaa aac ccg cag gtg cgt gaa aaa gtg gtg gcg atc ttc gcg gaa 1968Arg Glu Asn Pro Gln Val Arg Glu Lys Val Val Ala Ile Phe Ala Glu640 645 650 655gcg gaa ccg ttc acc ccg agc gat aac gtg gat gcg cag ctg tat aac 2016Ala Glu Pro Phe Thr Pro Ser Asp Asn Val Asp Ala Gln Leu Tyr Asn 660 665 670ggc ttc ttt agc gat gcc gat cgc gcg gcg atg aaa atc gtt ctg gaa 2064Gly Phe Phe Ser Asp Ala Asp Arg Ala Ala Met Lys Ile Val Leu Glu 675 680 685acc gaa ccg cgc aat ctg ccg gcg ctg gat att acc ttt gtt gat aaa 2112Thr Glu Pro Arg Asn Leu Pro Ala Leu Asp Ile Thr Phe Val Asp Lys 690 695 700cgt att gaa aaa ctg ctg ttt aat tat cgt gcg cgc aat ttt ccg ggt 2160Arg Ile Glu Lys Leu Leu Phe Asn Tyr Arg Ala Arg Asn Phe Pro Gly 705 710 715acc ctg gat tat gcc gaa cag cag cgt tgg ctg gaa cat cgt cgt cag 2208Thr Leu Asp Tyr Ala Glu Gln Gln Arg Trp Leu Glu His Arg Arg Gln720 725 730 735gtt ttc acc ccg gaa ttt ctg cag ggt tat gcg gat gaa ctg cag atg 2256Val Phe Thr Pro Glu Phe Leu Gln Gly Tyr Ala Asp Glu Leu Gln Met 740 745 750ctg gtt cag cag tat gcc gat gat aaa gaa aaa gtg gcg ctg ctg aaa 2304Leu Val Gln Gln Tyr Ala Asp Asp Lys Glu Lys Val Ala Leu Leu Lys 755 760 765gcg ctg tgg cag tat gcg gaa gaa atc gtt tct ggc tct ggt cac cat 2352Ala Leu Trp Gln Tyr Ala Glu Glu Ile Val Ser Gly Ser Gly His His 770 775 780cat cat cac cac 2364His His His His 78528787PRTArtificial sequenceHL-RQC-EcoExoI-Cter-{SG}8-H6 28Ala Asp Ser Asp Ile Asn Ile Lys Thr Gly Thr Thr Asp Ile Gly Ser1 5 10 15Asn Thr Thr Val Lys Thr Gly Asp Leu Val Thr Tyr Asp Lys Glu Asn 20 25 30Gly Met His Lys Lys Val Phe Tyr Ser Phe Ile Asp Asp Lys Asn His 35 40 45Asn Lys Lys Leu Leu Val Ile Arg Thr Lys Gly Thr Ile Ala Gly Gln 50 55 60Tyr Arg Val Tyr Ser Glu Glu Gly Ala Asn Lys Ser Gly Leu Ala Trp65 70 75 80Pro Ser Ala Phe Lys Val Gln Leu Gln Leu Pro Asp Asn Glu Val Ala 85 90 95Gln Ile Ser Asp Tyr Tyr Pro Arg Asn Ser Ile Asp Thr Lys Glu Tyr 100 105 110Arg Ser Thr Leu Thr Tyr Gly Phe Asn Gly Asn Val Thr Gly Asp Asp 115 120 125Thr Gly Lys Ile Gly Gly Cys Ile Gly Ala Gln Val Ser Ile Gly His 130 135 140Thr Leu Lys Tyr Val Gln Pro Asp Phe Lys Thr Ile Leu Glu Ser Pro145 150 155 160Thr Asp Lys Lys Val Gly Trp Lys Val Ile Phe Asn Asn Met Val Asn 165 170 175Gln Asn Trp Gly Pro Tyr Asp Arg Asp Ser Trp Asn Pro Val Tyr Gly 180 185 190Asn Gln Leu Phe Met Lys Thr Arg Asn Gly Ser Met Lys Ala Ala Asp 195 200 205Asn Phe Leu Asp Pro Asn Lys Ala Ser Ser Leu Leu Ser Ser Gly Phe 210 215 220Ser Pro Asp Phe Ala Thr Val Ile Thr Met Asp Arg Lys Ala Ser Lys225 230 235 240Gln Gln Thr Asn Ile Asp Val Ile Tyr Glu Arg Val Arg Asp Asp Tyr 245 250 255Gln Leu His Trp Thr Ser Thr Asn Trp Lys Gly Thr Asn Thr Lys Asp 260 265 270Lys Trp Thr Asp Arg Ser Ser Glu Arg Tyr Lys Ile Asp Trp Glu Lys 275 280 285Glu Glu Met Thr Asn Ser Gly Ser Gly Ser Gly Ser Gly Ser Gly Ser 290 295 300Gly Ser Gly Ser Gly Gln Ser Thr Phe Leu Phe His Asp Tyr Glu Thr305 310 315 320Phe Gly Thr His Pro Ala Leu Asp Arg Pro Ala Gln Phe Ala Ala Ile 325 330 335Arg Thr Asp Ser Glu Phe Asn Val Ile Gly Glu Pro Glu Val Phe Tyr 340 345 350Cys Lys Pro Ala Asp Asp Tyr Leu Pro Gln Pro Gly Ala Val Leu Ile 355 360 365Thr Gly Ile Thr Pro Gln Glu Ala Arg Ala Lys Gly Glu Asn Glu Ala 370 375 380Ala Phe Ala Ala Arg Ile His Ser Leu Phe Thr Val Pro Lys Thr Cys385 390 395 400Ile Leu Gly Tyr Asn Asn Val Arg Phe Asp Asp Glu Val Thr Arg Asn 405 410 415Ile Phe Tyr Arg Asn Phe Tyr Asp Pro Tyr Ala Trp Ser Trp Gln His 420 425 430Asp Asn Ser Arg Trp Asp Leu Leu Asp Val Met Arg Ala Cys Tyr Ala 435 440 445Leu Arg Pro Glu Gly Ile Asn Trp Pro Glu Asn Asp Asp Gly Leu Pro 450 455 460Ser Phe Arg Leu Glu His Leu Thr Lys Ala Asn Gly Ile Glu His Ser465 470 475 480Asn Ala His Asp Ala Met Ala Asp Val Tyr Ala Thr Ile Ala Met Ala 485 490 495Lys Leu Val Lys Thr Arg Gln Pro Arg Leu Phe Asp Tyr Leu Phe Thr 500 505 510His Arg Asn Lys His Lys Leu Met Ala Leu Ile Asp Val Pro Gln Met 515 520 525Lys Pro Leu Val His Val Ser Gly Met Phe Gly Ala Trp Arg Gly Asn 530 535 540Thr Ser Trp Val Ala Pro Leu Ala Trp His Pro Glu Asn Arg Asn Ala545 550 555 560Val Ile Met Val Asp Leu Ala Gly Asp Ile Ser Pro Leu Leu Glu Leu 565 570 575Asp Ser Asp Thr Leu Arg Glu Arg Leu Tyr Thr Ala Lys Thr Asp Leu 580 585 590Gly Asp Asn Ala Ala Val Pro Val Lys Leu Val His Ile Asn Lys Cys 595 600 605Pro Val Leu Ala Gln Ala Asn Thr Leu Arg Pro Glu Asp Ala Asp Arg 610 615 620Leu Gly Ile Asn Arg Gln His Cys Leu Asp Asn Leu Lys Ile Leu Arg625 630 635 640Glu Asn Pro Gln Val Arg Glu Lys Val Val Ala Ile Phe Ala Glu Ala 645 650 655Glu Pro Phe Thr Pro Ser Asp Asn Val Asp Ala Gln Leu Tyr Asn Gly 660 665 670Phe Phe Ser Asp Ala Asp Arg Ala Ala Met Lys Ile Val Leu Glu Thr 675 680

685Glu Pro Arg Asn Leu Pro Ala Leu Asp Ile Thr Phe Val Asp Lys Arg 690 695 700Ile Glu Lys Leu Leu Phe Asn Tyr Arg Ala Arg Asn Phe Pro Gly Thr705 710 715 720Leu Asp Tyr Ala Glu Gln Gln Arg Trp Leu Glu His Arg Arg Gln Val 725 730 735Phe Thr Pro Glu Phe Leu Gln Gly Tyr Ala Asp Glu Leu Gln Met Leu 740 745 750Val Gln Gln Tyr Ala Asp Asp Lys Glu Lys Val Ala Leu Leu Lys Ala 755 760 765Leu Trp Gln Tyr Ala Glu Glu Ile Val Ser Gly Ser Gly His His His 770 775 780His His His785292370DNAArtificial sequenceHL-RQC-EcoExoI-Cter-DG{SG}8-H6 29atg gca gat tct gat att aat att aaa acc ggt act aca gat att gga 48 Ala Asp Ser Asp Ile Asn Ile Lys Thr Gly Thr Thr Asp Ile Gly 1 5 10 15agc aat act aca gta aaa aca ggt gat tta gtc act tat gat aaa gaa 96Ser Asn Thr Thr Val Lys Thr Gly Asp Leu Val Thr Tyr Asp Lys Glu 20 25 30aat ggc atg cac aaa aaa gta ttt tat agt ttt atc gat gat aaa aat 144Asn Gly Met His Lys Lys Val Phe Tyr Ser Phe Ile Asp Asp Lys Asn 35 40 45cac aat aaa aaa ctg cta gtt att aga aca aaa ggt acc att gct ggt 192His Asn Lys Lys Leu Leu Val Ile Arg Thr Lys Gly Thr Ile Ala Gly 50 55 60caa tat aga gtt tat agc gaa gaa ggt gct aac aaa agt ggt tta gcc 240Gln Tyr Arg Val Tyr Ser Glu Glu Gly Ala Asn Lys Ser Gly Leu Ala 65 70 75tgg cct tca gcc ttt aag gta cag ttg caa cta cct gat aat gaa gta 288Trp Pro Ser Ala Phe Lys Val Gln Leu Gln Leu Pro Asp Asn Glu Val80 85 90 95gct caa ata tct gat tac tat cca aga aat tcg att gat aca aaa gag 336Ala Gln Ile Ser Asp Tyr Tyr Pro Arg Asn Ser Ile Asp Thr Lys Glu 100 105 110tat agg agt act tta act tat gga ttc aac ggt aat gtt act ggt gat 384Tyr Arg Ser Thr Leu Thr Tyr Gly Phe Asn Gly Asn Val Thr Gly Asp 115 120 125gat aca gga aaa att ggc ggc tgt att ggt gca caa gtt tcg att ggt 432Asp Thr Gly Lys Ile Gly Gly Cys Ile Gly Ala Gln Val Ser Ile Gly 130 135 140cat aca ctg aaa tat gtt caa cct gat ttc aaa aca att tta gag agc 480His Thr Leu Lys Tyr Val Gln Pro Asp Phe Lys Thr Ile Leu Glu Ser 145 150 155cca act gat aaa aaa gta ggc tgg aaa gtg ata ttt aac aat atg gtg 528Pro Thr Asp Lys Lys Val Gly Trp Lys Val Ile Phe Asn Asn Met Val160 165 170 175aat caa aat tgg gga cca tac gat cga gat tct tgg aac ccg gta tat 576Asn Gln Asn Trp Gly Pro Tyr Asp Arg Asp Ser Trp Asn Pro Val Tyr 180 185 190ggc aat caa ctt ttc atg aaa act aga aat ggt tct atg aaa gca gca 624Gly Asn Gln Leu Phe Met Lys Thr Arg Asn Gly Ser Met Lys Ala Ala 195 200 205gat aac ttc ctt gat cct aac aaa gca agt tct cta tta tct tca ggg 672Asp Asn Phe Leu Asp Pro Asn Lys Ala Ser Ser Leu Leu Ser Ser Gly 210 215 220ttt tca cca gac ttc gct aca gtt att act atg gat aga aaa gca tcc 720Phe Ser Pro Asp Phe Ala Thr Val Ile Thr Met Asp Arg Lys Ala Ser 225 230 235aaa caa caa aca aat ata gat gta ata tac gaa cga gtt cgt gat gat 768Lys Gln Gln Thr Asn Ile Asp Val Ile Tyr Glu Arg Val Arg Asp Asp240 245 250 255tac caa ttg cat tgg act tca aca aat tgg aaa ggt acc aat act aaa 816Tyr Gln Leu His Trp Thr Ser Thr Asn Trp Lys Gly Thr Asn Thr Lys 260 265 270gat aaa tgg aca gat cgt tct tca gaa aga tat aaa atc gat tgg gaa 864Asp Lys Trp Thr Asp Arg Ser Ser Glu Arg Tyr Lys Ile Asp Trp Glu 275 280 285aaa gaa gaa atg aca aat gat ggc tcc ggt agc ggc tct ggt tct ggc 912Lys Glu Glu Met Thr Asn Asp Gly Ser Gly Ser Gly Ser Gly Ser Gly 290 295 300tct ggt tcc ggc agc ggt tcc gga cag agc acc ttc ctg ttt cat gat 960Ser Gly Ser Gly Ser Gly Ser Gly Gln Ser Thr Phe Leu Phe His Asp 305 310 315tat gaa acc ttc ggt acc cat ccg gcc ctg gat cgt ccg gcg cag ttt 1008Tyr Glu Thr Phe Gly Thr His Pro Ala Leu Asp Arg Pro Ala Gln Phe320 325 330 335gcg gcc att cgc acc gat agc gaa ttc aat gtg att ggc gaa ccg gaa 1056Ala Ala Ile Arg Thr Asp Ser Glu Phe Asn Val Ile Gly Glu Pro Glu 340 345 350gtg ttt tat tgc aaa ccg gcc gat gat tat ctg ccg cag ccg ggt gcg 1104Val Phe Tyr Cys Lys Pro Ala Asp Asp Tyr Leu Pro Gln Pro Gly Ala 355 360 365gtg ctg att acc ggt att acc ccg cag gaa gcg cgc gcg aaa ggt gaa 1152Val Leu Ile Thr Gly Ile Thr Pro Gln Glu Ala Arg Ala Lys Gly Glu 370 375 380aac gaa gcg gcg ttt gcc gcg cgc att cat agc ctg ttt acc gtg ccg 1200Asn Glu Ala Ala Phe Ala Ala Arg Ile His Ser Leu Phe Thr Val Pro 385 390 395aaa acc tgc att ctg ggc tat aac aat gtg cgc ttc gat gat gaa gtt 1248Lys Thr Cys Ile Leu Gly Tyr Asn Asn Val Arg Phe Asp Asp Glu Val400 405 410 415acc cgt aat atc ttt tat cgt aac ttt tat gat ccg tat gcg tgg agc 1296Thr Arg Asn Ile Phe Tyr Arg Asn Phe Tyr Asp Pro Tyr Ala Trp Ser 420 425 430tgg cag cat gat aac agc cgt tgg gat ctg ctg gat gtg atg cgc gcg 1344Trp Gln His Asp Asn Ser Arg Trp Asp Leu Leu Asp Val Met Arg Ala 435 440 445tgc tat gcg ctg cgc ccg gaa ggc att aat tgg ccg gaa aac gat gat 1392Cys Tyr Ala Leu Arg Pro Glu Gly Ile Asn Trp Pro Glu Asn Asp Asp 450 455 460ggc ctg ccg agc ttt cgt ctg gaa cat ctg acc aaa gcc aac ggc att 1440Gly Leu Pro Ser Phe Arg Leu Glu His Leu Thr Lys Ala Asn Gly Ile 465 470 475gaa cat agc aat gcc cat gat gcg atg gcc gat gtt tat gcg acc att 1488Glu His Ser Asn Ala His Asp Ala Met Ala Asp Val Tyr Ala Thr Ile480 485 490 495gcg atg gcg aaa ctg gtt aaa acc cgt cag ccg cgc ctg ttt gat tat 1536Ala Met Ala Lys Leu Val Lys Thr Arg Gln Pro Arg Leu Phe Asp Tyr 500 505 510ctg ttt acc cac cgt aac aaa cac aaa ctg atg gcg ctg att gat gtt 1584Leu Phe Thr His Arg Asn Lys His Lys Leu Met Ala Leu Ile Asp Val 515 520 525ccg cag atg aaa ccg ctg gtg cat gtg agc ggc atg ttt ggc gcc tgg 1632Pro Gln Met Lys Pro Leu Val His Val Ser Gly Met Phe Gly Ala Trp 530 535 540cgc ggc aac acc agc tgg gtg gcc ccg ctg gcc tgg cac ccg gaa aat 1680Arg Gly Asn Thr Ser Trp Val Ala Pro Leu Ala Trp His Pro Glu Asn 545 550 555cgt aac gcc gtg att atg gtt gat ctg gcc ggt gat att agc ccg ctg 1728Arg Asn Ala Val Ile Met Val Asp Leu Ala Gly Asp Ile Ser Pro Leu560 565 570 575ctg gaa ctg gat agc gat acc ctg cgt gaa cgc ctg tat acc gcc aaa 1776Leu Glu Leu Asp Ser Asp Thr Leu Arg Glu Arg Leu Tyr Thr Ala Lys 580 585 590acc gat ctg ggc gat aat gcc gcc gtg ccg gtg aaa ctg gtt cac att 1824Thr Asp Leu Gly Asp Asn Ala Ala Val Pro Val Lys Leu Val His Ile 595 600 605aac aaa tgc ccg gtg ctg gcc cag gcg aac acc ctg cgc ccg gaa gat 1872Asn Lys Cys Pro Val Leu Ala Gln Ala Asn Thr Leu Arg Pro Glu Asp 610 615 620gcg gat cgt ctg ggt att aat cgc cag cat tgt ctg gat aat ctg aaa 1920Ala Asp Arg Leu Gly Ile Asn Arg Gln His Cys Leu Asp Asn Leu Lys 625 630 635atc ctg cgt gaa aac ccg cag gtg cgt gaa aaa gtg gtg gcg atc ttc 1968Ile Leu Arg Glu Asn Pro Gln Val Arg Glu Lys Val Val Ala Ile Phe640 645 650 655gcg gaa gcg gaa ccg ttc acc ccg agc gat aac gtg gat gcg cag ctg 2016Ala Glu Ala Glu Pro Phe Thr Pro Ser Asp Asn Val Asp Ala Gln Leu 660 665 670tat aac ggc ttc ttt agc gat gcc gat cgc gcg gcg atg aaa atc gtt 2064Tyr Asn Gly Phe Phe Ser Asp Ala Asp Arg Ala Ala Met Lys Ile Val 675 680 685ctg gaa acc gaa ccg cgc aat ctg ccg gcg ctg gat att acc ttt gtt 2112Leu Glu Thr Glu Pro Arg Asn Leu Pro Ala Leu Asp Ile Thr Phe Val 690 695 700gat aaa cgt att gaa aaa ctg ctg ttt aat tat cgt gcg cgc aat ttt 2160Asp Lys Arg Ile Glu Lys Leu Leu Phe Asn Tyr Arg Ala Arg Asn Phe 705 710 715ccg ggt acc ctg gat tat gcc gaa cag cag cgt tgg ctg gaa cat cgt 2208Pro Gly Thr Leu Asp Tyr Ala Glu Gln Gln Arg Trp Leu Glu His Arg720 725 730 735cgt cag gtt ttc acc ccg gaa ttt ctg cag ggt tat gcg gat gaa ctg 2256Arg Gln Val Phe Thr Pro Glu Phe Leu Gln Gly Tyr Ala Asp Glu Leu 740 745 750cag atg ctg gtt cag cag tat gcc gat gat aaa gaa aaa gtg gcg ctg 2304Gln Met Leu Val Gln Gln Tyr Ala Asp Asp Lys Glu Lys Val Ala Leu 755 760 765ctg aaa gcg ctg tgg cag tat gcg gaa gaa atc gtt tct ggc tct ggt 2352Leu Lys Ala Leu Trp Gln Tyr Ala Glu Glu Ile Val Ser Gly Ser Gly 770 775 780cac cat cat cat cac cac 2370His His His His His His 78530789PRTArtificial sequenceSynthetic Construct 30Ala Asp Ser Asp Ile Asn Ile Lys Thr Gly Thr Thr Asp Ile Gly Ser1 5 10 15Asn Thr Thr Val Lys Thr Gly Asp Leu Val Thr Tyr Asp Lys Glu Asn 20 25 30Gly Met His Lys Lys Val Phe Tyr Ser Phe Ile Asp Asp Lys Asn His 35 40 45Asn Lys Lys Leu Leu Val Ile Arg Thr Lys Gly Thr Ile Ala Gly Gln 50 55 60Tyr Arg Val Tyr Ser Glu Glu Gly Ala Asn Lys Ser Gly Leu Ala Trp65 70 75 80Pro Ser Ala Phe Lys Val Gln Leu Gln Leu Pro Asp Asn Glu Val Ala 85 90 95Gln Ile Ser Asp Tyr Tyr Pro Arg Asn Ser Ile Asp Thr Lys Glu Tyr 100 105 110Arg Ser Thr Leu Thr Tyr Gly Phe Asn Gly Asn Val Thr Gly Asp Asp 115 120 125Thr Gly Lys Ile Gly Gly Cys Ile Gly Ala Gln Val Ser Ile Gly His 130 135 140Thr Leu Lys Tyr Val Gln Pro Asp Phe Lys Thr Ile Leu Glu Ser Pro145 150 155 160Thr Asp Lys Lys Val Gly Trp Lys Val Ile Phe Asn Asn Met Val Asn 165 170 175Gln Asn Trp Gly Pro Tyr Asp Arg Asp Ser Trp Asn Pro Val Tyr Gly 180 185 190Asn Gln Leu Phe Met Lys Thr Arg Asn Gly Ser Met Lys Ala Ala Asp 195 200 205Asn Phe Leu Asp Pro Asn Lys Ala Ser Ser Leu Leu Ser Ser Gly Phe 210 215 220Ser Pro Asp Phe Ala Thr Val Ile Thr Met Asp Arg Lys Ala Ser Lys225 230 235 240Gln Gln Thr Asn Ile Asp Val Ile Tyr Glu Arg Val Arg Asp Asp Tyr 245 250 255Gln Leu His Trp Thr Ser Thr Asn Trp Lys Gly Thr Asn Thr Lys Asp 260 265 270Lys Trp Thr Asp Arg Ser Ser Glu Arg Tyr Lys Ile Asp Trp Glu Lys 275 280 285Glu Glu Met Thr Asn Asp Gly Ser Gly Ser Gly Ser Gly Ser Gly Ser 290 295 300Gly Ser Gly Ser Gly Ser Gly Gln Ser Thr Phe Leu Phe His Asp Tyr305 310 315 320Glu Thr Phe Gly Thr His Pro Ala Leu Asp Arg Pro Ala Gln Phe Ala 325 330 335Ala Ile Arg Thr Asp Ser Glu Phe Asn Val Ile Gly Glu Pro Glu Val 340 345 350Phe Tyr Cys Lys Pro Ala Asp Asp Tyr Leu Pro Gln Pro Gly Ala Val 355 360 365Leu Ile Thr Gly Ile Thr Pro Gln Glu Ala Arg Ala Lys Gly Glu Asn 370 375 380Glu Ala Ala Phe Ala Ala Arg Ile His Ser Leu Phe Thr Val Pro Lys385 390 395 400Thr Cys Ile Leu Gly Tyr Asn Asn Val Arg Phe Asp Asp Glu Val Thr 405 410 415Arg Asn Ile Phe Tyr Arg Asn Phe Tyr Asp Pro Tyr Ala Trp Ser Trp 420 425 430Gln His Asp Asn Ser Arg Trp Asp Leu Leu Asp Val Met Arg Ala Cys 435 440 445Tyr Ala Leu Arg Pro Glu Gly Ile Asn Trp Pro Glu Asn Asp Asp Gly 450 455 460Leu Pro Ser Phe Arg Leu Glu His Leu Thr Lys Ala Asn Gly Ile Glu465 470 475 480His Ser Asn Ala His Asp Ala Met Ala Asp Val Tyr Ala Thr Ile Ala 485 490 495Met Ala Lys Leu Val Lys Thr Arg Gln Pro Arg Leu Phe Asp Tyr Leu 500 505 510Phe Thr His Arg Asn Lys His Lys Leu Met Ala Leu Ile Asp Val Pro 515 520 525Gln Met Lys Pro Leu Val His Val Ser Gly Met Phe Gly Ala Trp Arg 530 535 540Gly Asn Thr Ser Trp Val Ala Pro Leu Ala Trp His Pro Glu Asn Arg545 550 555 560Asn Ala Val Ile Met Val Asp Leu Ala Gly Asp Ile Ser Pro Leu Leu 565 570 575Glu Leu Asp Ser Asp Thr Leu Arg Glu Arg Leu Tyr Thr Ala Lys Thr 580 585 590Asp Leu Gly Asp Asn Ala Ala Val Pro Val Lys Leu Val His Ile Asn 595 600 605Lys Cys Pro Val Leu Ala Gln Ala Asn Thr Leu Arg Pro Glu Asp Ala 610 615 620Asp Arg Leu Gly Ile Asn Arg Gln His Cys Leu Asp Asn Leu Lys Ile625 630 635 640Leu Arg Glu Asn Pro Gln Val Arg Glu Lys Val Val Ala Ile Phe Ala 645 650 655Glu Ala Glu Pro Phe Thr Pro Ser Asp Asn Val Asp Ala Gln Leu Tyr 660 665 670Asn Gly Phe Phe Ser Asp Ala Asp Arg Ala Ala Met Lys Ile Val Leu 675 680 685Glu Thr Glu Pro Arg Asn Leu Pro Ala Leu Asp Ile Thr Phe Val Asp 690 695 700Lys Arg Ile Glu Lys Leu Leu Phe Asn Tyr Arg Ala Arg Asn Phe Pro705 710 715 720Gly Thr Leu Asp Tyr Ala Glu Gln Gln Arg Trp Leu Glu His Arg Arg 725 730 735Gln Val Phe Thr Pro Glu Phe Leu Gln Gly Tyr Ala Asp Glu Leu Gln 740 745 750Met Leu Val Gln Gln Tyr Ala Asp Asp Lys Glu Lys Val Ala Leu Leu 755 760 765Lys Ala Leu Trp Gln Tyr Ala Glu Glu Ile Val Ser Gly Ser Gly His 770 775 780His His His His His7853150DNAArtificial sequenceoligonucleotide for exonuclease assay 31gcaacagagc tgatggatca aatgcattag gtaaacatgt tacgtcgtaa 503255DNAArtificial sequenceoligonucleotide for exonuclease assay 32cgatcttacg acgtaacatg tttacctaat gcatttgatc catcagctct gttgc 55

Claims

1. A construct comprising a transmembrane protein pore subunit and a nucleic acid handling enzyme, wherein the subunit is covalently attached to the enzyme, wherein the subunit retains its ability to form a pore and wherein the enzyme retains its ability to handle nucleic acids.

2. A construct according to claim 1, wherein (a) the enzyme is attached to the subunit at more than one point; (b) the enzyme is genetically fused to the subunit; (c) the amino acid sequence of the enzyme is added in frame into the amino acid sequence of the subunit; or (d) the enzyme is chemically fused to the subunit.

3-5. (canceled)

6. A construct according to claim 1, wherein the enzyme is attached to the pore by one or more linkers, optionally amino acid linkers.

7. (canceled)

8. A construct according to claim 1, wherein the subunit is derived from .alpha.-hemolysin (.alpha.-HL) or the subunit comprises the sequence shown SEQ ID NO: 2 or a variant thereof.

9. (canceled)

10. A construct according to claim 1, wherein the nucleic acid handling enzyme is (a) a nuclease and wherein the nuclease is optionally a member of any of the Enzyme Classification (EC) groups 3.1.11, 3.1.13, 3.1.14, 3.1.15, 3.1.16, 3.1.21, 3.1.22, 3.1.25, 3.1.26, 3.1.27, 3.1.30 and 3.1.31; (b) an exonuclease and wherein the enzyme optionally comprises the sequence shown in any one of SEQ ID NOs: 10, 12, 14 and 16 or a variant thereof; (c) is a polymerase and wherein the polymerase is optionally (i) a member of any of the Enzyme Classification (EC) groups 2.7.7.6, 2.7.7.7, 2.7.7.19, 2.7.7.48 and 2.7.7.49 or (ii) a DNA-dependent DNA polymerase, an RNA-dependent DNA polymerase, a DNA-dependent RNA polymerase or an RNA-dependent RNA polymerase; (d) is a helicase and wherein the helicase is optionally (i) a member of any of the Enzyme Classification (EC) groups 3.6.1.- and 2.7.7 or (ii) an ATP-dependent DNA helicase, an ATP-dependent RNA helicase or an ATP-independent RNA helicase; or (e) is a topoisomerase and wherein the helicase is optionally (i) a member of any of the Enzyme Classification (EC) groups 5.99.1.2 and 5.99.1.3 or (ii) a gyrase.

11-13. (canceled)

14. A construct according to claim 1, wherein the construct comprises the sequence shown in any one of SEQ ID NOs: 18, 20, 22, 24, 26, 28 and 30 or a variant thereof.

15-19. (canceled)

20. A polynucleotide sequence which encodes a construct according to claim 2, wherein the polynucleotide optionally comprises the sequence shown in any one of SEQ ID NOs: 17, 19, 21, 23, 25, 27 and 29 or a variant thereof.

21. (canceled)

22. A modified pore for use in sequencing nucleic acids, comprising at least one construct comprises a transmembrane protein pore subunit and a nucleic acid handling enzyme, wherein the subunit is covalently attached to the enzyme, wherein the subunit retains its ability to form a pore and wherein the enzyme retains its ability to handle nucleic acids, wherein the pore optionally comprises a construct of claim 4 and six subunits comprising the sequence shown SEQ ID NO: 2 or a variant thereof.

23. (canceled)

24. A pore according to claim 22, wherein (a) all seven subunits have a glutamine at position 139 of SEQ ID NO: 2 and one of the subunits has a cysteine at position 135; (b) all seven subunits have an arginine at position 113 of SEQ ID NO: 2; and/or (c) the pore comprises a molecular adaptor that facilitates an interaction between the pore and one or more nucleotide(s) and wherein the molecular adaptor is optionally (i) a cyclodextrin or a derivative thereof or (ii) heptakis-6-amino-.beta.-cyclodextrin (am.sub.7-.beta.CD), 6-monodeoxy-6-monoamino-.beta.-cyclodextrin (am.sub.1-.beta. CD) or heptakis-(6-deoxy-6-guanidino)-cyclodextrin (gu.sub.7-.beta.CD).

25-28. (canceled)

29. A kit for producing a modified pore for use in sequencing nucleic acids, comprising: (a) at least one construct comprising a transmembrane protein pore subunit and a nucleic acid handling enzyme, wherein the subunit is covalently attached to the enzyme, wherein the subunit retains its ability to form a pore and wherein the enzyme retains its ability to handle nucleic acids and the remaining subunits needed to form a pore; or (b) at least one polynucleotide according to claim 7 and polynucleotide sequences encoding any remaining subunits needed to form a pore.

30. A kit according to claim 29, wherein the kit comprises: (a) a construct comprising a transmembrane protein pore subunit and a nucleic acid handling enzyme, wherein the subunit is covalently attached to the enzyme, wherein the subunit retains its ability to form a pore, wherein the enzyme retains its ability to handle nucleic acids, and wherein the subunit is derived from .alpha.-hemolysin (.alpha.-HL) or the subunit comprises the sequence shown SEQ ID NO: 2 or a variant thereof and six subunits each comprising the sequence shown in SEQ ID NO: 2 or a variant thereof.

31-32. (canceled)

33. A method of producing a construct according to claim 1, comprising: (a) covalently attaching a nucleic acid handling enzyme to a transmembrane protein pore subunit; and (b) determining whether or not the resulting construct is capable of forming a pore and handling nucleic acids, wherein the enzyme is optionally attached to the subunit before the subunit forms part of a pore (post expression modification) or after the subunit has formed part of a pore (post oligomerisation modification) and/or wherein step (a) optionally comprises: (i) providing a polynucleotide that encodes the construct, wherein the polynucleotide optionally comprises the sequence shown in any one of SEQ ID NOs: 17, 19, 21, 23, 25, 27 and 29 or a variant thereof; and (ii) expressing the polynucleotide sequence.

34-35. (canceled)

36. A method of producing a modified pore according to claim 22, comprising: (a) covalently attaching a nucleic acid handling enzyme to a transmembrane protein pore; and (b) determining whether or not the resulting pore is capable of handling nucleic acids and detecting nucleotides; or comprising: (a) allowing at least one construct to form a pore with other suitable subunits, wherein the construct comprises a transmembrane protein pore subunit and a nucleic acid handling enzyme, wherein the subunit is covalently attached to the enzyme, wherein the subunit retains its ability to form a pore and wherein the enzyme retains its ability to handle nucleic acids; and (b) determining whether or not the resulting pore is capable of handling nucleic acids and detecting nucleotides.

37. (canceled)

38. A method of purifying a transmembrane pore comprising at least one construct according to claim 1, comprising: (a) providing the at least one construct and the other subunits required to form the pore; (b) oligomerising the at least one construct and other subunits on synthetic lipid vesicles; and (c) contacting the vesicles with a non-ionic surfactant; and (d) recovering the oligomerised pore, wherein the synthetic vesicles optionally comprise 30% cholesterol, 30% phosphatidylcholine (PC), 20% phosphatidylethanolamine (PE), 10% sphingomyelin (SM) and 10% phosphatidylserine (PS) and/or wherein the non-ionic surfactant is optionally an Octyl Glucoside (OG) or DoDecyl Maltoside (DDM) detergent.

39-40. (canceled)

41. A method of sequencing a target nucleic acid sequence, comprising: (a) contacting the target sequence with a pore according to claim 24, which comprises an exonuclease, such that the exonuclease digests an individual nucleotide from one end of the target sequence; (b) contacting the nucleotide with the pore so that the nucleotide interacts with the adaptor; (c) measuring the current passing through the pore during the interaction and thereby determining the identity of the nucleotide; and (d) repeating steps (a) to (c) at the same end of the target sequence and thereby determining the sequence of the target sequence.

42. A method of sequencing a target nucleic acid sequence, comprising: (a) contacting the target sequence with a pore according to claim 22 so that the enzyme pushes or pulls the target sequence through the pore and a proportion of the nucleotides in the target sequence interacts with the pore; and (b) measuring the current passing through the pore during each interaction and thereby determining the sequence of the target sequence.

43. A kit according to claim 29, wherein the kit comprises a polynucleotide encoding a construct comprising a transmembrane protein pore subunit and a nucleic acid handling enzyme, wherein the subunit is covalently attached to the enzyme, wherein the subunit retains its ability to form a pore and wherein the enzyme retains its ability to handle nucleic acids, and six polynucleotides each encoding a subunit comprising the sequence shown in SEQ ID NO: 2 or a variant thereof.