4C
First Claim
1. A method for analysing the frequency of interaction of a target nucleotide sequence with one or more nucleotide sequences of interest (eg. one or more genomic loci) comprising the steps of:
- (a) providing a sample of cross-linked DNA;
(b) digesting the cross-linked DNA with a primary restriction enzyme;
(c) ligating the cross-linked nucleotide sequences;
(d) reversing the cross linking;
(e) optionally digesting the nucleotide sequences with a secondary restriction enzyme;
(f) optionally ligating one or more DNA sequences of known nucleotide composition to the available secondary restriction enzyme digestion site(s) that flank the one or more nucleotide sequences of interest;
(g) amplifying the one or more nucleotide sequences of interest using at least two oligonucleotide primers, wherein each primer hybridises to the DNA sequences that flank the nucleotide sequences of interest;
(h) hybridising the amplified sequence(s) to an array; and
(i) determining the frequency of interaction between the DNA sequences.
0 Assignments
0 Petitions
Accused Products
Abstract
The present invention relates in one aspect to a method for analysing the frequency of interaction of a target nucleotide sequence with one or more nucleotide sequences of interest (eg. one or more genomic loci) comprising the steps of: (a) providing a sample of cross-linked DNA; (b) digesting the cross-linked DNA with a primary restriction enzyme; (c) ligating the cross-linked nucleotide sequences; (d) reversing the cross linking; (e) digesting the nucleotide sequences with a secondary restriction enzyme; (f) ligating one or more DNA sequences of known nucleotide composition to the available secondary restriction enzyme digestion site(s) that flank the one or more nucleotide sequences of interest; (g) amplifying the one or more nucleotide sequences of interest using at least two oligonucleotide primers, wherein each primer hybridises to the DNA sequences that flank the nucleotide sequences of interest; (h) hybridising the amplified sequence(s) to an array or sequencing the amplified sequences; and (i) determining the frequency of interaction between the DNA sequences.
-
Citations
99 Claims
-
1. A method for analysing the frequency of interaction of a target nucleotide sequence with one or more nucleotide sequences of interest (eg. one or more genomic loci) comprising the steps of:
-
(a) providing a sample of cross-linked DNA;
(b) digesting the cross-linked DNA with a primary restriction enzyme;
(c) ligating the cross-linked nucleotide sequences;
(d) reversing the cross linking;
(e) optionally digesting the nucleotide sequences with a secondary restriction enzyme;
(f) optionally ligating one or more DNA sequences of known nucleotide composition to the available secondary restriction enzyme digestion site(s) that flank the one or more nucleotide sequences of interest;
(g) amplifying the one or more nucleotide sequences of interest using at least two oligonucleotide primers, wherein each primer hybridises to the DNA sequences that flank the nucleotide sequences of interest;
(h) hybridising the amplified sequence(s) to an array; and
(i) determining the frequency of interaction between the DNA sequences. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 90)
-
-
13. A method for analysing the frequency of interaction of a target nucleotide sequence with one or more nucleotide sequences (e.g. one or more genomic loci) comprising the steps of:
-
(a) providing a sample of cross-linked DNA;
(b) digesting the cross-linked DNA with a primary restriction enzyme;
(c) ligating the cross-linked nucleotide sequences;
(d) reversing the cross linking;
(e) optionally digesting the nucleotide sequences with a secondary restriction enzyme;
(f) circularising the nucleotide sequences;
(g) amplifying the one or more nucleotide sequences that are ligated to the target nucleotide sequence;
(h) optionally hybridising the amplified sequences to an array; and
(i) determining the frequency of interaction between the DNA sequences. - View Dependent Claims (95)
-
- 14. A circularised nucleotide sequence comprising a first and a second nucleotide sequence, wherein each end of the first and a second nucleotide sequences are separated by different restriction enzyme recognition sites, and wherein said first nucleotide sequence is a target nucleotide sequence and said second nucleotide sequence is obtainable by cross-linking genomic DNA.
-
15. A method for preparing a circularised nucleotide sequence comprising the steps of:
-
(a) providing a sample of cross-linked DNA;
(b) digesting the cross-linked DNA with a primary restriction enzyme;
(c) ligating the cross-linked nucleotide sequences;
(d) reversing the cross linking;
(e) optionally digesting the nucleotide sequences with a secondary restriction enzyme; and
(f) circularising the nucleotide sequences. - View Dependent Claims (43, 45, 77, 80, 84, 87, 97)
-
- 18. A set of probes complementary in sequence to the nucleic acid sequence adjacent to each one of the primary restriction enzyme recognition sites of a primary restriction enzyme in genomic DNA.
-
30. A process for preparing a set of probes comprising the steps of:
-
(a) identifying each one of the primary restriction enzyme recognition sites for a primary restriction enzyme in genomic DNA;
(b) designing probes that are capable of hybridising to the sequence adjacent each one of the primary restriction enzyme recognition sites in the genomic DNA;
(c) synthesising the probes; and
(d) combining the probes together to form a set of probes or substantially a set of probes. - View Dependent Claims (31, 32, 99)
-
-
34. An array comprising the set of probes complementary in sequence to the nucleic acid sequence adjacent to each one of the primary restriction enzyme recognition sites of a primary restriction enzyme in genomic DNA or obtained or obtainable by the process comprising the steps of:
- (a) identifying each one of the primary restriction enzyme recognition sites for a primary restriction enzyme in genomic DNA;
(b) designing probes that are capable of hybridising to the sequence adjacent each one of the primary restriction enzyme recognition sites in the genomic DNA;
(c) synthesising the probes; and
(d) combining the probes together to form a set of probes or substantially a set of probes. - View Dependent Claims (36, 38, 40, 42)
- (a) identifying each one of the primary restriction enzyme recognition sites for a primary restriction enzyme in genomic DNA;
-
89. A method for analysing the frequency of interaction of one or more target nucleotide sequences with one or more nucleotide sequences of interest (eg. one or more genomic loci) comprising the steps of:
-
(a) providing a sample of cross-linked DNA;
(b) digesting the cross-linked DNA with a primary restriction enzyme;
(c) ligating the cross-linked nucleotide sequences;
(d) reversing the cross linking; and
(e) sequencing the ligated nucleotide sequences.
-
-
91. (canceled)
-
92. (canceled)
-
93. (canceled)
-
94. (canceled)
Specification