Table 1.
Polymerases evolved to accept modified nucleotides.
| Polymerase | Mutations | Activity | References |
|---|---|---|---|
| T7 RNAP (RGFH) | (Y639F) | Incorporates with 2′-F, 2′-amino, 2′-OMe pyrimidines, 2′-deoxy-2′-thio CTP | 1;2 |
| T7 RNAP(RGFA) | (Y639F:H784A) | Synthesizes transcripts containing 2′-OMe pyrimidines, 2′-azidoU or 2′-azidoC | 3;4;5 |
| T7 RNAP (VRS) | (G542V:H784S:H772R) | Incorporates 2′-F-pyrimidines | 5 |
| T7 RNAP (RGVG, E593G, V685A) | (Y639V:H784G:E593G:V685A) | Incorporates 2′-OMe pyrimidines | 5 |
| T7 RNAP (RGLH, A255T) | (Y639L:A255T) | Incorporates 2′-F pyrimidines, 2′-OMe pyrimidines | 5 |
| Taq DNAP | (I614K) | Incorporates rNTPs more efficiently than wild type | 6;7 |
| Taq DNAP | (I614N:L616I) | Incorporates rNTPs more efficiently than wild type | 6;7 |
| Taq DNAP | (A661E) | Incorporates rGTPs more efficiently than wild type | 8;9 |
| Taq DNAP AA40 | (E602V:A608V:I614M:E615G) | RNAP and RT activity. Incorporates rNTP, 2′-azido-NTP and 2′-F-NTP | 10 |
| Sf DNAP R1 | (K531E:A597T:A600T:W604G:A608S:L609V:I614T:E615G) | Incorporates rNTPs more efficiently than wild type | 11 |
| Sf DNAP R2 | (A597T:E615G) | Incorporates rNTP substrates more efficiently than wild type | 11 |
| Sf DNAP R3 | (A597T:W604R:L605Q:I614T:E615G) | Incorporates rNTP substrates more efficiently than wild type | 11 |
| Sf DNAP M19 | (I614E:E615G) | Incorporates 2′-O-methylNTP, rNTP, 2′-amino-NTP, 2′-azido-NTP, 2′-F-NTP | 12;13 |
| Kf DNAP | (I709F) | Incorporates rNTPs more efficiently than wild type | 14 |
| TgoT DNAP C7 | (TgoT:E654Q:E658Q:K659Q:V661A:E664Q:Q665P:D669A:K671Q:T676K:R709K) | Replication of DNA CeNA and LNA | 15 |
| TgoT DNAP D4K | (TgoT:L403P:P657T:E658Q:K659H:Y663H:E664K:D669A:K671N:T676I) | Replication of DNA using ANA, or FANA | 15 |
| TgoT DNAP 6G12 | (TgoT:V589A:E609K:I610M:K659Q:E664Q:Q665P:R668K:D669Q:K671H:K674R:T676R:A681S:L704P:E730G) | Replication of DNA using HNA | 15 |
| TgoT DNAP RT521 | (TgoT:E429G:I521L:K726R) | RT activity for oligonucleotides containing HNA, ANA, and FANA | 15 |
| TgoT DNAP RT521K | (RT521:A385V:F445L:E664K) | RT activity for oligonucleotides containing CeNA and LNA | 15 |
| Taq DNAP M1 | (G84A:D144G:K314R:E520G:F598L:A608V:E742G) | Replicates templates containing abasic sites, cis-syn cyclobutane pyrimidine dimer, or 5-nitroindole. Incorporates 7-deaza-dGTP, Rhodamine-5-dUTP, Biotin-16-dUTP, Fluorescein-12-dATP. | 16 |
| Taq DNAP | (M444V:P527A:D551E:E832V) | Accepts nucleotides with nonstandard hydrogen bond patterns | 17 |
| Taq DNAP | (N580S:L628V:E832V) | Accepts nucleotides with nonstandard hydrogen bond patterns | 17 |
| Tth and Taq DNAP chimera 5D4 | (V62I:Y78H:T88S:P114Q:P264S:E303V:G389V:E424G:E432G:E602G:A608V:I614M:M761T:M775T) | Forms and extends d5NI and d5NIC self-pairs and heteropairs with all four bases. Extends HBA pairs such as Pyrene: abasic site, d5NI: abasic site, and ICS:7AI | 18 |
| Sf DNAP P2 | (F598I:I614F:Q489H) | Forms and extends DNA bearing ICS base pairing. | 19 |
| Pfu DNAP E10 | (Pfu(exo-):V93Q:V337I:E399D:N400D:R407I:Y546H) | Accepts Cy3-dCTP and Cy5-dCTP as substrates. | 20 |
| Taq DNAP M1 | (G84A:D144G:K314R:E520G:F598L:A608V:E742G) | Accepts phophorothioates. Alllows a full substitution of dNTPs with αS dNTPs. | 16 |
| Pfu DNAP | Q484R + split | Incorporates γ-phosphate-O-linker dabcyl derivatives. | 21 |
DNAP, DNA polymerase; RNAP, RNA polymerase; NTP, nucleoside triphosphate; CeNA, cyclohexenyl nucleic acid; LNA, locked nucleic acid; ANA, arabino nucleic acid; FANA, 2′-F-arabino nucleic acid; HNA, 1,5-anhydrohexitol nucleic acid; d5NI, 5-nitroindole; d5NIC, 5-nitroindole-3-carboxamide; ICS, isocarbostyril; 7AI, 7-azaindole. Refrences: 1 (Padilla and Sousa, 1999); 2 (Raines and Gottlieb, 1998); 3 (Padilla and Sousa, 2002); 4 (Burmeister et al., 2006); 5 (Chelliserrykattil and Ellington, 2004); 6 (Patel and Loeb, 2000); 7 (Patel et al., 2001); 8 (Suzuki et al., 1996); 9 (Ogawa et al., 2001); 10 (Ong et al., 2006); 11 (Xia et al., 2002); 12 (Fa et al., 2004); 13 (Schultz et al., 2015); 14 (Shinkai et al., 2001); 15 (Pinheiro et al., 2012); 16 (Ghadessy et al., 2004); 17 (Laos et al., 2013); 18 (Loakes et al., 2009); 19 (Leconte et al., 2005); 20 (Ramsay et al., 2010); 21 (Hansen et al., 2011).