Molecular recognition systems with pyrimidine analog pairing
OwnerShuichi Hoshika, Nicole A Leal +1inventors
InventorsShuichi Hoshika, Nicole A Leal, Steven A Benner
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Abstract
This invention covers a new molecular recognition system, where duplexes of DNA-like molecules comprise segments built from nucleotides that carry only a small pyrimidine-like analog, and where the segments pair by pyrimidine analog:pyrimidine analog “skinny” pairing. This pairing retains hydrogen bonding complementarity. Further, this invention relates to processes for preparing those duplexes, and processes that use such duplexes as primer:template complexes for reactions catalyzed by DNA polymerases.
Claims10
A composition, wherein said composition comprises a first oligonucleotide and a second oligonucleotide, wherein said first oligonucleotide comprises a segment composed entirely of nucleotides carrying heterocycles selected independently from the group consisting of
- and wherein said second oligonucleotide comprises a segment composed entirely of nucleotides comprising heterocycles selected from the group consisting of
- wherein Su indicates the point of attachment of said heterocycle to a sugar of said first or second oligonucleotide, R′ is CH3, alkyl, alkenyl, alkynyl, or alkyl, alkenyl, or alkynyl carrying a functional group, wherein R is H, CH3, alkyl, alkenyl, or alkynyl, or functionalized alkyl, alkenyl, or alkynyl, and X is N or C—NO2, wherein said segments form a duplex region in which said segments are joined by hydrogen-bonding between complementary heterocycles forming skinny pairs, wherein
- and wherein said duplex region comprises at least three such pairs.
A process for forming a molecular complex, said process comprising contacting a first oligonucleotide with a second oligonucleotide in aqueous solution, wherein said first oligonucleotide comprises a segment comprising entirely nucleotides carrying heterocycles selected independently from the group consisting of
- wherein said second oligonucleotide comprises a segment comprising entirely nucleotides carrying heterocycles selected independently from the group consisting of
- wherein Su indicates the point of attachment of said heterocycle to a sugar of said first or second oligonucleotide, R′ is CH3, alkyl, alkenyl, alkynyl, or alkyl, alkenyl, or alkynyl carrying a functional group, wherein R is H, CH3, alkyl, alkenyl, or alkynyl, or alkyl, alkenyl, or alkynyl carrying a functional group, and X is N or C—NO2, wherein said segments form one or more duplex regions, wherein said segments within said duplex region(s) is (are) joined by hydrogen-bonding between complementary heterocycles forming skinny pairs, wherein
- wherein said duplex region comprises at least three such pairs.
A process for extending a primer using a polymerase, said process comprising contacting a polymerase with a duplex comprising a template oligonucleotide and a primer oligonucleotide,
- wherein the template oligonucleotide comprises at least two segments, including a first segment at or near its 3′-end consisting of nucleotides carrying heterocycles selected independently from the group consisting of
- and a second segment positioned 5′-distal to the first segment and comprising any nucleotides,
- and wherein the primer oligonucleotide is complementary to part or all of the 3′ first segment of the template oligonucleotide, and the 3′-end of the primer oligonucleotide comprises a segment consisting of nucleotides carrying heterocycles selected independently from the group consisting of
- wherein Su indicates the point of attachment of said heterocycle to a sugar of said template oligonucleotide or said primer oligonucleotide, wherein R′ is CH3, alkyl, alkenyl, alkynyl, or alkyl, alkenyl or alkynyl carrying a functional group, wherein R is H, CH3, alkyl, alkenyl, alkynyl, or functionalized alkyl, alkenyl or alkynyl, and X is N or C—NO2,
- wherein the 3′ template segment and the 3′ primer segment form one or more duplex regions, wherein segments within said duplex region(s) are joined by hydrogen-bonding between complementary heterocycles to form skinny pairs, wherein each said skinny pair is independently selected from the group consisting of
- wherein at least one said duplex region comprises at least three skinny pairs.
Dependencies are inferred from the claim text.