1. A method for detecting a target sequence, comprising:
a) providing:
i) a sample containing synthetic DNA amplified from genomic DNA, said genomic DNA suspected of containing said target sequence;
ii) oligonucleotides capable of forming an invasive cleavage structure with said synthetic DNA when said genomic DNA contains said target sequence; and
iii) an agent for detecting the presence of an invasive cleavage structure; and
b) exposing said sample to said oligonucleotides and said agent.
2. The method of claim 1, wherein said agent comprises a cleavage agent.
3. The method of claim 1, wherein said genomic DNA is nicked double stranded genomic DNA, and wherein said synthetic DNA is amplified by extension of 3 ends in said nicked double-stranded genomic DNA suspected of containing said target sequence.
4. The method of claim 1, wherein said synthetic DNA amplified from genomic DNA is amplified by extension of multiple primers on said genomic DNA suspected of containing said target sequence.
5. The method of claim 2, wherein said exposing said sample to said oligonucleotides and said agent comprises exposing said sample to said oligonucleotides and said agent under conditions wherein an invasive cleavage structure is formed between said synthetic DNA and said oligonucleotides if said target sequence is present in said genomic DNA, wherein said invasive cleavage structure is cleaved by said cleavage agent.
6. The method of claim 5, further comprising the step of c) detecting said cleavage of said invasive cleavage structure.
7. The method of claim 1, wherein said synthetic DNA comprises a first region and a second region, said second region downstream of and contiguous to said first region, and wherein said oligonucleotides comprise first and second oligonucleotides, said wherein at least a portion of said first oligonucleotide is completely complementary to said first portion of said synthetic DNA and wherein said second oligonucleotide comprises a 3 portion and a 5 portion, wherein said 5 portion is completely complementary to said second portion of said synthetic DNA.
8. The method of claim 7, wherein said 3 portion of said second oligonucleotide comprises a 3 terminal nucleotide not complementary to said target nucleic acid.
9. The method of claim 7, wherein said 3 portion of said second oligonucleotide consists of a single nucleotide not complementary to said target nucleic acid.
10. The method of claim 4, wherein said primers are random primers.
11. The method of claim 4, wherein said primers are exonuclease resistant.
12. The method of claim 6, wherein said detecting the cleavage of said invasive cleavage structure comprises detection of fluorescence.
13. The method of claim 6, wherein said detecting the cleavage of said invasive cleavage structure comprises detection of mass.
14. The method of claim 6, wherein said detecting the cleavage of said invasive cleavage structure comprises detection of fluorescence energy transfer.
15. The method of claim 6, wherein said detecting the cleavage of said invasive cleavage structure comprises detection selected from the group consisting of detection of radioactivity, luminescence, phosphorescence, fluorescence polarization, and charge.
16. The method of claim 1, wherein said synthetic DNA is attached to a solid support.
17. The method of claim 1 wherein said genomic DNA suspected of containing said target sequence is attached to a solid support.
18. The method of claim 7, wherein said first oligonucleotide is attached to a solid support.
19. The method of claim 7, wherein said second oligonucleotide is attached to a solid support.
20. The method of claim 2, wherein said cleavage agent comprises a structure-specific nuclease.
21. The method of claim 20, wherein said structure-specific nuclease comprises a thermostable structure-specific nuclease.
22. The method of claim 20, wherein said structure specific nuclease comprises a 5 nuclease.
23. The method of claim 22, wherein said 5-nuclease comprises a thermostable 5-nuclease.
24. The method of claim 22, wherein a portion of the amino acid sequence of said nuclease is homologous to a portion of the amino acid sequence of a thermostable DNA polymerase derived from a thermophilic organism.
25. The method of claim 24, wherein said thermophilic organism is selected from the group consisting of Thermus aquaticus, Thermus flavus, and Thermus thermophilus.
26. The method of claim 22, wherein said 5-nuclease comprises a FEN nuclease.
27. The method of claim 23, wherein said thermostable 5 nuclease comprises a thermostable FEN nuclease.
28. The method of claim 27, wherein said wherein a portion of the amino acid sequence of said nuclease is homologous to a portion of the amino acid sequence of a thermostable FEN nuclease derived from a thermophilic organism.
29. The method of claim 28, wherein said thermophilic organism is from an Archaebacterial species.
30. The method of claim 29, wherein said Archaebacterial species is selected from the group consisting of Methanococcus jannaschii, Pyrococcus furiosus, Pyrococcus woesei, Methanobacterium thermoautotrophicum, and Archaeoglobus fulgidus.
31. A nucleic acid treatment kit comprising oligonucleotides capable of forming an invasive cleavage structure with synthetic DNA amplified from genomic DNA suspected of containing a target sequence when said genomic DNA contains a target sequence.
32. The kit of claim 31, wherein said synthetic DNA amplified from genomic DNA comprising a target sequence comprises a first region and a second region, said second region downstream of and contiguous to said first region, the kit comprising:
a) a first oligonucleotide, wherein at least a portion of said first oligonucleotide is completely complementary to said first portion of said first target nucleic acid; and
b) a second oligonucleotide comprising a 3 portion and a 5 portion, wherein said 5 portion is completely complementary to said second portion of said target nucleic acid.
33. The kit of claim 32, further comprising a cleavage agent.
34. The kit of claim 32, wherein said kit further comprises a solid support.
35. The kit of claim 34, wherein said first oligonucleotide is attached to said solid support.
36. The kit of claim 34, wherein said second oligonucleotide is attached to said solid support.
37. The kit of claim 33, wherein said cleavage agent comprises a structure-specific nuclease.
38. The kit of claim 37, wherein said structure-specific nuclease comprises a thermostable structure-specific nuclease.
39. The kit of claim 33, wherein said cleavage agent comprises a 5 nuclease.
40. The kit of claim 39, wherein said 5 nuclease comprises a thermostable 5 nuclease.
41. The kit of claim 40, wherein a portion of the amino acid sequence of said nuclease is homologous to a portion of the amino acid sequence of a thermostable DNA polymerase derived from a thermophilic organism.
42. The kit of claim 41, wherein said thermophilic organism is selected from the group consisting of Thermus aquaticus, Thermus flavus, and Thermus thermophilus.
43. The kit of claim 37, wherein said structure-specific nuclease comprises a FEN-1 endonuclease.
44. The kit of claim 38, wherein said thermostable structure-specific nuclease comprises a thermostable FEN nuclease.
45. The kit of claim 44, wherein said wherein a portion of the amino acid sequence of said nuclease is homologous to a portion of the amino acid sequence of a thermostable FEN nuclease derived from a thermophilic organism.
46. The kit of claim 45, wherein said thermophilic organism is from an Archaebacterial species.
47. The kit of claim 46, wherein said Archaebacterial species is selected from the group consisting of Methanococcus jannaschii, Pyrococcus furiosus, Pyrococcus woesei, Methanobacterium thermoautotrophicum, and Archaeoglobus fulgidus.
48. The kit of claim 31, further comprising a buffer solution.
49. The kit of claim 48, wherein said buffer solution comprises a source of divalent cations.
50. The kit of claim 49, wherein said divalent cation is selected from the group consisting of Mn2 and Mg2 ions.
51. The kit of claim 31, further comprising said target nucleic acid.
52. The kit of claim 31, further comprising amplification primers.
53. A kit for detecting the presence of a synthetic DNA comprising a FEN-1 endonuclease and amplification primers.
The claims below are in addition to those above.
All refrences to claim(s) which appear below refer to the numbering after this setence.
1. A method and device to produce character output to a computer or other device independent of the use of key combinations, and to reduce the number of key presses required to operate a computer or other device, comprising:
a. providing a Memory which stores operating program instructions for handling data input and code output, and
b. said memory also containing a Character Map which identifies the appropriate character codes for each character, and
c. said Character Map stores, at individual addresses in said memory, uppercase character codes for producing uppercase versions of alphabet characters, and
d. said Character Map stores, at individual addresses in said memory, lowercase character codes for producing lowercase versions of alphabet characters, and
e. said Character Map stores, at individual addresses in said memory, all-lowercase character codes for producing all-lowercase versions of whole words and
f. said Character Map stores, at individual addresses in said memory, leading-uppercase character codes for producing leading-uppercase words, such as those beginning a sentence, and
g. said Character Map stores, at individual addresses in said memory, character codes for producing partial words such as word endings (suffixes), and
h. said Character Map stores, at individual addresses in said memory, character codes for producing punctuation marks, and
i. said Character Map stores, at individual addresses in said memory, character codes for producing symbols, and
j. said Character Map stores, at individual addresses in said memory, character codes for producing numbers.
2. Providing a Processor which outputs the appropriate character code or codes from the individual addresses in the memory of claim 1.
3. Providing a Keyboard for operator input and code output, comprising:
a. the Memory of claim 1, and
b. said keyboard having a separate key location for each individual address in said memory, and
c. said keyboard having all uppercase alphabet character keys in a separate, single row, and
d. said keyboard having all lowercase alphabet character keys in a separate, single row, and
e. said keyboard providing a Key Matrix which energizes a key location as that particular key location is activated by a key press, and
f. the Processor of claim 2 providing a means to determine and produce the appropriate character code output based on which key location has been energized.