Methods and compositions for determining the sequence of nucleic acid molecules

A compound of the formula:

• Tms—L—X
• wherein,
• Tms is an organic group detectable by mass spectrometry, comprising carbon, at least one of hydrogen and fluoride, and optional atoms selected from oxygen, nitrogen, sulfur, phosphorus and iodine;
• L is an organic group which allows a unique Tms-containing moiety to be cleaved from the remainder of the compound, wherein the Tms-containing moiety comprises a functional group which supports a single ionized charge state when the compound is subjected to mass spectrometry and is selected from tertiary amine, quaternary amine and organic acid;
• X is a nucleic acid fragment attached to L at other than the 3′ end of the nucleic acid fragment;
• with the provisos that the compound is not bonded to a solid support nor has a mass of less than 250 daltons.

A composition comprising a plurality of compounds of the formula:

• TMS—L—MOI
• wherein,
• Tms is an organic group detectable by mass spectrometry, comprising carbon, at least one of hydrogen and fluoride, and optional atoms selected from oxygen, nitrogen, sulfur, phosphorus and iodine;
• L is an organic group which allows a Tms-containing moiety to be cleaved from the remainder of the compound, wherein the Tms-containing moiety comprises a functional group which supports a single ionized charge state when the compound is subjected to mass spectrometry and is selected from tertiary amine, quaternary amine and organic acid;
• MOI is a nucleic acid fragment wherein L is conjugated to the MOI at a location other than the 3′ end of the MOI;
• and
• wherein no two compounds have either the same Tms or the same MOI.

A composition comprising a plurality of sets of compounds, each set of compounds having the formula:

• Tms—L—MOI
• wherein,
• Tms is an organic group detectable by mass spectrometry, comprising carbon, at least one of hydrogen and fluoride, and optional atoms selected from oxygen, nitrogen, sulfur, phosphorus and iodine;
• L is an organic group which allows a Tms-containing moiety to be cleaved from the remainder of the compound, wherein the Tms-containing moiety comprises a functional group which supports a single ionized charge state when the compound is subjected to mass spectrometry and is selected from tertiary amine, quaternary amine and organic acid;
• MOI is a nucleic acid fragment wherein L is conjugated to the MOI at a location other than the 3′ end of the MOI;
• wherein within a set, all members have the same Tms group, and the MOI fragments have variable lengths that terminate with the same dideoxynucleotide selected from ddAMP, ddGMP, ddCMP and ddTMP;
• and
• wherein between sets, the Tms groups differ by at least 2 amu.

A kit for DNA sequencing analysis comprising a plurality of container sets, each container set comprising at least five containers, wherein a first container contains a vector, a second, third, fourth and fifth containers contain compounds of the formula:

• Tms—L—MOI
• wherein,
• Tms is an organic group detectable by mass spectrometry, comprising carbon, at least one of hydrogen and fluoride, and optional atoms selected from oxygen, nitrogen, sulfur, phosphorus and iodine;
• L is an organic group which allows a Tms-containing moiety to be cleaved from the remainder of the compound, wherein the Tms-containing moiety comprises a functional group which supports a single ionized charge state when the compound is subjected to mass spectrometry and is selected from tertiary amine, quaternary amine and organic acid;
• and
• MOI is a nucleic acid fragment wherein L is conjugated to the MOI at a location other than the 3′ end of the MOI;
• such that
• the MOI for the second, third, fourth and fifth containers is identical and complementary to a portion of the vector within the set of containers, and the Tms group within each container is different from the other Tms groups in the kit.