Method of preparation of nanopore and uses thereof
This disclosure provides systems and methods for sequencing nucleic acids using nucleotide analogues and translocation of tags from incorporated nucleotide analogues through a nanopore. In aspects, this disclosure is related to composition, method, and system for sequencing a nucleic acid using tag molecules and detection of translocation through a nanopore of tags released from incorporation of the molecule.
1. A tagged nucleotide, wherein the nucleotide comprises a tag capable of being cleaved in a nucleotide polymerization event and detected with the aid of a nanopore, wherein the tagged nucleotide has the structure:
wherein the tag comprises an oligonucleotide which comprises nucleotides having natural bases and (i) at least one abasic site or (ii) at least one nucleotide having a modified base;
wherein R 1 is OH, wherein R 2 is H or OH, wherein X is a linker and may comprise O, NH, S, or CH 2 , wherein Z is O, S, or BH 3 , wherein the base is adenine, guanine, cytosine, thymine, uracil, or a derivative of one of these bases, wherein n is 1, 2, 3, or 4.
2. The tagged nucleotide of claim 1 , wherein the tag does not comprise a fluorophore.
3. The tagged nucleotide of claim 1 , wherein the tag is detectable by its charge, shape, size, or any combination thereof.
4. The tagged nucleotide of claim 1 , wherein the tag comprises an additional identifiable moiety.
5. The tagged nucleotide of claim 4 , wherein the additional identifiable moiety is a coumarin-based dye.
6. A composition comprising four different types of the tagged nucleotide of claim 1 , wherein the base of a first type of tagged nucleotide is adenine or a derivative thereof, the base of a second type of tagged nucleotide is guanine or a derivative thereof, the base of a third type of tagged nucleotide is cytosine or a derivative thereof, and the base of a fourth type of tagged nucleotide is thymine or a derivative thereof or uracil or a derivative thereof, and wherein the tag on each type of tagged nucleotide is different from the tag on each of the other three types of tagged nucleotide.
7. The tagged nucleotide of claim 1 , wherein the tag further comprises one or more of ethylene glycol, an amino acid, a carbohydrate, a peptide, a dye, a chemiluminescent compound, a mononucleotide, a dinucleotide, a trinucleotide, a tetranucleotide, a pentanucleotide, a hexanucleotide, an aliphatic acid, an aromatic acid, an alcohol, a thiol group, a cyano group, a nitro group, an alkyl group, an alkenyl group, an alkynyl group, an azido group, or a combination thereof.
8. The tagged nucleotide of claim 1 , wherein the oligonucleotide has a length of approximately 30 bases.
9. The tagged nucleotide of claim 1 , wherein n is four.
10. The tagged nucleotide of claim 1 , wherein the oligonucleotide comprises a 5′-OH, and the 5′-OH of said oligonucleotide is attached to the terminal phosphate of the tagged nucleotide analogue.
11. The tagged nucleotide of claim 1 , wherein the oligonucleotide comprises at least one abasic site.
12. The tagged nucleotide of claim 1 , wherein the oligonucleotide comprises at least one nucleotide having a modified base.
13. The tagged nucleotide of claim 1 , wherein the tag has a charge which is reverse in sign relative to the charge on the rest of the tagged nucleotide.
14. The tagged nucleotide of claim 13 , wherein the magnitude of the charge on the tag is the same as the magnitude of the charge on the remainder of the tagged nucleotide.
15. The tagged nucleotide of claim 13 , wherein the tag has a positive charge.
16. The tagged nucleotide of claim 13 , wherein the tag further comprises lysines or arginines having a positive charge, wherein the positive charge of the lysines or arginines neutralizes the negative charge of the phosphates of the tagged nucleotide.
17. The tagged nucleotide of claim 13 , wherein removal of the tag changes the charge of the tagged nucleotide.