Reagents and methods for replication, transcription, and translation in semi-synthetic organisms
Disclosed herein are compositions, methods, cells, engineered microorganisms, and kits for increasing the production of proteins or polypeptides comprising one or more unnatural amino acids. Further provided are compositions, cells, engineered microorganisms, and kits for increasing the retention of unnatural nucleic acids encoding the unnatural amino acids in an engineered cell, or semi-synthetic organism.
1. A nucleobase of the structure:
wherein:
each X is independently carbon or nitrogen;
R 2 is present when X is carbon and is independently hydrogen, alkyl, alkenyl, alkynyl, methoxy, methanethiol, methaneseleno, halogen, cyano, or azide group;
Y is sulfur, oxygen, or selenium; and
E is sulfur;
wherein the wavy line indicates a point of bonding to a ribosyl, deoxyribosyl, or dideoxyribosyl moiety, wherein the ribosyl, deoxyribosyl, or dideoxyribosyl moiety is optionally modified at the 2′ position, at the 3′ position, or at the 5′ position, wherein the ribosyl, deoxyribosyl, or dideoxyribosyl moiety is in free form, is connected to a mono-phosphate, diphosphate, triphosphate, α-thiotriphosphate, β-thiotriphosphate, or γ-thiotriphosphate group, or is included in a polynucleotide, optionally wherein the polynucleotide is an RNA, DNA, bicyclic nucleic acid, linked nucleic acid, peptide nucleic acid (PNA), locked nucleic acid (LNA), or a phosphorothioate-containing nucleic acid.
2. The nucleobase of claim 1 , wherein X is carbon and/or Y is sulfur.
3. The nucleobase of claim 1 , which has the structure
4. The nucleobase of claim 1 , which is bound to a complementary base-pairing nucleobase to form an unnatural base pair (UBP), wherein the complementary base-pairing nucleobase is selected from:
5. A double stranded oligonucleotide duplex wherein a first oligonucleotide strand comprises the nucleobase of claim 1 , and a second complementary oligonucleotide strand comprises a complementary base-pairing nucleobase in a complementary base-pairing site thereof.
6. The double stranded oligonucleotide duplex of claim 5 , wherein the first oligonucleotide strand comprises
and the second strand comprises a complementary base pairing nucleobase selected from:
in a complementary base-pairing site thereof.
7. A DNA comprising a nucleobase having the structure
and a complementary base-pairing nucleobase having the structure
or a nucleobase having the structure
and a complementary base-pairing nucleobase having the structure