METHODS AND COMPOSITIONS FOR ANALYZING NUCLEIC ACID
Technology provided herein relates in part to methods, processes, compositions and apparatuses for analyzing nucleic acid.
1 . A composition comprising four nucleotide species, wherein the nucleotide species have substantially identical separation properties when separated by a mass-sensitive process.
2 . The composition of claim 1 , wherein polynucleotides having an equal total number of the nucleotide species have substantially identical separation properties when separated by a mass-sensitive process.
3 . The composition of claim 1 , wherein at least three of the nucleotide species are mass-modified.
4 . The composition of claim 3 , wherein the nucleotide species have substantially identical mass.
5 . The composition of claim 1 , wherein the nucleotide species each are capable of hybridizing to one of adenine, thymine, cytosine and guanine in a polynucleotide, wherein the adenine, thymine, cytosine and guanine are not mass-modified.
6 . The composition of claim 1 , wherein the nucleotide species are capable of forming phosphodiester bonds when polymerized.
7 . The composition of claim 1 , wherein the nucleotide species are capable of being polymerized by a polymerase on a nucleic acid template.
8 . The composition of claim 3 , wherein each mass-modified nucleotide species comprises one or more mass modifiers.
9 . The composition of claim 3 , wherein each mass-modified nucleotide species comprises one or more isotopes.
10 . The composition of claim 9 , wherein the one or more isotopes are one or more stable isotopes.
11 . The composition of claim 3 , wherein each mass-modified nucleotide species comprises one or more isotopes and one or more other mass modifiers.
12 . The composition of claim 9 , wherein the one or more isotopes comprise a hydrogen isotope.
13 . The composition of claim 12 , wherein the hydrogen isotope is deuterium.
14 . The composition of claim 9 , wherein the one or more isotopes comprise a nitrogen isotope.
15 . The composition of claim 14 , wherein the nitrogen isotope is nitrogen-15.
16 . The composition of claim 9 , wherein the one or more isotopes comprise an oxygen isotope.
17 . The composition of claim 16 , wherein the oxygen isotope is oxygen-17 or oxygen-18.
18 . The composition of claim 9 , wherein the one or more isotopes comprise a carbon isotope.
19 . The composition of claim 18 , wherein the carbon isotope is carbon-13.
20 . A method for determining length of a nucleic acid fragment, comprising:
a) contacting, under annealing conditions, a nucleic acid fragment with a probe, which probe:
(i) comprises at least two nucleotide species which have substantially identical separation properties, and
(ii) is longer than the nucleic acid fragment to which it anneals,
thereby generating a fragment-probe species comprising one or more unhybridized probe portions;
b) removing the one or more unhybridized probe portions from the fragment-probe species, thereby generating a trimmed probe; and
c) determining the length of the trimmed probe, thereby determining the length of the nucleic acid fragment.
21 . A method for determining lengths of nucleic acid fragments in a mixture of nucleic acid fragments having different lengths, comprising:
a) contacting, under annealing conditions, nucleic acid fragments with a plurality of probes, which probes:
(i) comprise at least two nucleotide species which have substantially identical separation properties, and
(ii) are longer than the nucleic acid fragments to which they anneal,
thereby generating fragment-probe species comprising unhybridized probe portions;
b) removing the unhybridized probe portions from the fragment-probe species, thereby generating trimmed probes; and
c) determining lengths of the trimmed probes, thereby determining the lengths of the nucleic acid fragments.
22 - 201 . (canceled)