Catalog Number: 20-2060-xx
(20-2160-xx)
Description: 5-Me-dC-CPG
5'-Dimethoxytrityl-N-benzoyl-5-methyl-2'-deoxyCytidine,
2'-succinoyl- long chain alkylamino-CPG |
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F.W.: 303.21 |
Diluent: Not Applicable |
| Coupling: This support should be used in a manner identical to normal protected nucleoside support since it contains the DMT group. |
| Deprotection: Deprotect using the protocol required by the nucleobases. |
| Storage: Controlled room temperature or lower, dry |
| Stability in Solution: Not Applicable |
bases affecting duplex stability
C-5 methyl pyrimidine nucleosides are known to stabilize duplexes relative to the non-methylated bases. Therefore, enhanced binding can be achieved using 5-methyl-dC in place of dC, duplex melting temperature being increased by 1.3°. Improved stacking in this case is believed to be brought about by elimination of water molecules from the duplex. 2,6-Diaminopurine 2'-deoxyriboside (2-amino-dA) forms an additional hydrogen bond with Thymidine, thereby leading to duplex stabilization with a melting temperature increase of 3°. Our 2-amino-dA monomer exhibits fast and effective deprotection in ammonium hydroxide and it is stabilized to depurination during synthesis. Sequences with high GC content may contain mismatches and still hybridize because of the high stability of the G-C base pair. The N4-ethyl analogue of dC (N4-Et-dC) hybridizes specifically to natural dG but the stability of the base pair is reduced to about the level of an AT base pair.
AP-dC (G-clamp) enhances oligo hybridization since the AP-C....G base pair contains 4 hydrogen bonds, which makes the interaction much stronger than the regular C....G base pair with its 3 hydrogen bonds.
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