Duplex stability and, therefore, melting temperature can be raised using the modified bases. For replacement of dC with 5-Me-dC, duplex melting temperature is increased by 1.3 º. Improved stacking in this case is believed to be brought about by elimination of water molecules from the duplex. The additional hydrogen bond formed by substituting dA with 2-amino-dA leads to a melting temperature increase of 3º.P> The design of primers is frequently complicated by the degeneracy of the genetic code. Three strategies are now available to confront this problem. In the first, a mixed base addition (N) is used to form the degenerate site. This approach is best if the number of degenerate sites is small. A second option is the use of 2'-deoxyInosine or 2'-deoxyNebularine, which exhibit low, but unequal, hydrogen bonding to the other four bases. The third option is the use of a universal nucleoside. In this strategy, the base analog does not hybridize significantly to the other four bases and makes up some of the duplex destabilization by acting as an intercalating agent. 3-Nitropyrrole 2'-deoxynucleoside (M) is the first example of a set of universal bases. Subsequently, 5-nitroindole was determined to be an effective universal base and to be superior to 3-nitropyrrole, based on duplex melting experiments.
The modified bases designated P and K show considerable promise as degenerate bases. The pyrimidine derivative P, when introduced into oligonucleotides, base pairs with either A or G, while the purine derivative K base pairs with either C or T. A dP+dK mix also can serve as a mixed base with much less degeneracy than dA+dC+dG+dT (N).
A standard Watson and Crick base pair is formed between iso-C and iso-G, but the hydrogen bonding pattern is quite different from the natural base pairs A-T and C-G (The 5-methyl analogue was chosen as the synthetic target due to the reported instability of 2'-deoxyisocytidine caused by deamination during oligonucleotide synthesis or deprotection).
| Product | Code | Catalog No. | 50 nmol scale (XX=05) | 200 nmol scale (XX=02) | 1 umol scale (XX=01) | 2 umol scale (XX=03) | 5 umol scale (XX=06) | 10 umol scale (XX=10) | 15 umol scale (XX=15) |
| 3'-rA (2'-5' linked) | [3rA2-5] | 26-6682 | $410.00 | $410.00 | $575.00 | $748.00 | $558.00 | $3,987.00 | $4,984.00 |
| 3'-rC (2'-5' linked) | [3rC2-5] | 26-6911 | $410.00 | $410.00 | $575.00 | $748.00 | $558.00 | $3,987.00 | $4,984.00 |
| 3'-rG (2'-5' linked) | [3rG2-5] | 26-6912 | $410.00 | $410.00 | $575.00 | $748.00 | $558.00 | $3,987.00 | $1,241.00 |
| 3'-rU (2'-5' linked) | [3rU2-5] | 26-6913 | $410.00 | $410.00 | $575.00 | $748.00 | $558.00 | $3,987.00 | $1,241.00 |
| 4-Thio-Uridine (s4U) | [s4U] | 27-6445 | $536.00 | $636.00 | $676.00 | $823.00 | $2,713.50 | $3,616.00 | $6,026.00 |
| 5-bromo dC (5-Br dC) | [5-Br-dC] | 26-6411 | $84.00 | $84.00 | $110.00 | $164.00 | $495.00 | $876.00 | $1,095.00 |
| 5-bromo dU (5-Br-dU) | [5-Br-dU] | 26-6412 | $84.00 | $84.00 | $110.00 | $164.00 | $495.00 | $876.00 | $1,095.00 |
| 5-hydroxy deoxyuridine (OH dU) | [5-OH-dU] | 26-6695 | $267.00 | $267.00 | $347.00 | $521.00 | $1,561.50 | $2,780.00 | $3,475.00 |
| 5-Iodo deoxycytosine dC | [5-I dC] | 26-6414 | $175.00 | $300.00 | $227.00 | $341.00 | $1,021.50 | $1,820.00 | $2,274.00 |
| 5-iodo deoxyuridine dU | [5-I-dU] | 26-6415 | $84.00 | $144.00 | $110.00 | $164.00 | $495.00 | $876.00 | $1,095.00 |
| 5-methyl isodeoxycytosine (Me iso dC) | [5-Me-isodC] | 26-6513 | $140.00 | $140.00 | $183.00 | $274.00 | $823.50 | $1,460.00 | $1,825.00 |
| 5-Methyl-Uridine (m5U) | [m5U] | 27-6557 | $267.00 | $267.00 | $347.00 | $520.00 | $1,561.50 | $2,774.00 | $3,468.00 |
| 8-bromo dA (8-Br dA) | [8-Br-dA] | 26-6527 | $127.00 | $127.00 | $153.00 | $227.00 | $688.50 | $958.00 | $1,524.00 |
| 8-bromo dG (8-Br dG) | [8-Br-dG] | 26-6528 | $127.00 | $127.00 | $191.00 | $227.00 | $859.50 | $958.00 | $1,524.00 |
| 8-Oxo deoxyguanosine (8-Oxo dG) | [8-Oxo-dG] | 26-6434 | $383.00 | $383.00 | $498.00 | $748.00 | $2,241.00 | $3,987.00 | $4,984.00 |
| Amino C6 U (RNA) | [AmC6U] | 27-6422 | $875.00 | $875.00 | $910.00 | $2,110.00 | $2,844.00 | $4,421.00 | $6,336.00 |
| Amino dC N4 PEG3 amino linker | [Am-dC-C6] | 26-6670 | $267.00 | $267.00 | $298.00 | $344.00 | $1,341.00 | $1,717.00 | $2,404.00 |
| Amino deoxyadenosine dA C6 | [Am-dA-C6] | 26-6666 | $267.00 | $267.00 | $298.00 | $344.00 | $1,228.50 | $1,717.00 | $2,404.00 |
| Amino deoxyguanosine dG C6 | [Am-dG-C6] | 26-6669 | $518.00 | $518.00 | $551.00 | $594.00 | $2,479.50 | $2,538.00 | $3,408.00 |
| Amino deoxythymidine dT C6 | [Am-dT-C6] | 26-6438 | $199.00 | $199.00 | $228.00 | $297.00 | $1,026.00 | $1,485.00 | $1,782.00 |
| Carboxy-dT | [CO-dT] | 26-6697 | $341.00 | $341.00 | $411.00 | $524.00 | $1,849.50 | $2,426.00 | $3,033.00 |
| Convertible dG (2-Fluoro deoxy inosine) | [2-FdI] | 26-6671 | $489.00 | $489.00 | $676.00 | $758.00 | $2,272.50 | $4,044.00 | $5,054.00 |
| deaza dG (7 deaza dG) | [deaza-7-dG] | 26-6656 | $383.00 | $383.00 | $498.00 | $748.00 | $2,241.00 | $2,048.00 | $2,555.00 |
| deaza dG (PPG) 7 deaza 8 aza dG | [deaza-PPG-dG] | 26-6654 | $427.00 | $427.00 | $555.00 | $832.00 | $2,497.50 | $4,437.00 | $5,546.00 |
| deaza rG (7 deaza rG) | [deaza-7-rG] | 27-6656 | $491.00 | $491.00 | $551.00 | $659.00 | $2,479.50 | Inquire | Inquire |
| dihydro dC (5-6 DHC) | [5aza 5-6 DHC] | 26-6893 | $389.00 | $389.00 | $505.00 | $758.00 | $2,272.50 | $4,044.00 | $5,054.00 |
| dihydro dT (5-6 DHT) | [5-6-DHT] | 26-6890 | $253.00 | $253.00 | $329.00 | $493.00 | $1,480.50 | $2,628.00 | $3,285.00 |
| dihydro dUracil (5-6 DHdU) | [5-6-DHdU] | 26-6683 | $253.00 | $253.00 | $329.00 | $493.00 | $1,480.50 | $2,628.00 | $3,285.00 |
| dihydro rUracil (5-6 DH rU) | [5-6-DHrU] | 27-6683 | $335.00 | $335.00 | $603.00 | $723.00 | $2,713.50 | $3,616.00 | $6,026.00 |
| EDTA-C2-dT | [EDTA-C2-dT] | 26-6703 | $378.00 | $378.00 | $491.00 | $737.00 | $2,209.50 | $3,931.00 | $4,914.00 |
| etheno dexoyadenosine dA | [Eth dA] | 26-6506 | $255.00 | $255.00 | $352.00 | $632.00 | $1,584.00 | $2,814.00 | $3,518.00 |
| Inverted 2'O methyl A (reverse linkage) | [Inv-mA] | 27-6447A | $202.00 | $202.00 | $448.00 | $741.00 | Inquire | $3,586.00 | $4,482.00 |
| Inverted 2'O methyl C (reverse linkage) | [Inv-mC] | 27-6447C | $202.00 | $202.00 | $448.00 | $741.00 | Inquire | $3,586.00 | $4,482.00 |
| Inverted 2'O methyl G (reverse linkage) | [Inv-mG] | 27-6447G | $202.00 | $202.00 | $448.00 | $741.00 | Inquire | $3,586.00 | $4,482.00 |
| Inverted 2'O methyl mixed bases (reverse linkage) | [Inv-mN] | 27-6447N | $202.00 | $202.00 | $448.00 | $741.00 | Inquire | $3,586.00 | $4,482.00 |
| Inverted 2'O methyl U (reverse linkage) | [Inv-mU] | 27-6447U | $202.00 | $202.00 | $448.00 | $741.00 | Inquire | $3,586.00 | $4,482.00 |
| Inverted dA (reverse linkage) | [Inv-dA] | 26-6551 | $45.00 | $45.00 | $59.00 | $88.00 | $265.50 | $472.00 | $590.00 |
| Inverted dC (reverse linkage) | [Inv-dC] | 26-6552 | $45.00 | $45.00 | $59.00 | $88.00 | $265.50 | $472.00 | $590.00 |
| Inverted dG (reverse linkage) | [Inv-dG] | 26-6553 | $45.00 | $45.00 | $59.00 | $88.00 | $265.50 | $472.00 | $590.00 |
| Inverted dT (reverse linkage) | [Inv-dT] | 26-6554 | $45.00 | $45.00 | $59.00 | $88.00 | $265.50 | $472.00 | $590.00 |
| Inverted rA (reverse linkage) | [Inv-rA] | 27-6441 | $202.00 | $202.00 | $448.00 | $741.00 | $2,016.00 | $3,586.00 | $4,482.00 |
| Inverted rC (reverse linkage) | [Inv-rC] | 27-6442 | $202.00 | $202.00 | $448.00 | $741.00 | $2,016.00 | $3,586.00 | $4,482.00 |
| Inverted rG (reverse linkage) | [Inv-rG] | 27-6443 | $202.00 | $202.00 | $448.00 | $741.00 | $2,016.00 | $3,586.00 | $4,482.00 |
| Inverted rU (reverse linkage) | [Inv-rU] | 27-6444 | $202.00 | $202.00 | $448.00 | $741.00 | $2,016.00 | $3,586.00 | $4,482.00 |
| Iodo-dT-5' | [I-dT] | 26-6926 | $138.00 | $138.00 | $179.00 | $269.00 | $805.50 | $1,432.00 | $1,790.00 |
| iso deoxyguanosine dG (iso dG) | [iso dG] | 26-6514 | $286.00 | $286.00 | $351.00 | $459.00 | $1,579.50 | $2,808.00 | $3,510.00 |
| O6 Methyl dG | [O6-Me-dG] | 26-6409 | $416.00 | $416.00 | $551.00 | $416.00 | $2,479.50 | $1,769.00 | $2,211.00 |
| pseudoiso dC (pidC) (2'deoxypseudocytidine) | [pidC] | 26-6605 | $659.00 | $659.00 | $891.00 | $1,336.00 | $4,009.50 | $7,128.00 | $8,910.00 |
| pseudoUridine-2'deoxy (psi-dU) | [psi-dU] | 26-6531 | $551.00 | $551.00 | $664.00 | $902.00 | $2,988.00 | $5,346.00 | $6,642.00 |
| Thymidine Glycol | [Tg-Thy-Glycol] | 26-6487 | $465.00 | $465.00 | $543.00 | $664.00 | $1,993.50 | $3,542.00 | $4,428.00 |
| Thymidine Ribo | [rT] | 27-6946 | $282.00 | $282.00 | $376.00 | $586.00 | $1,062.00 | $2,016.00 | $2,464.00 |
Oligo Purification