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Oligo Chain Terminator Modifications

Bio-Synthesis provides 3' chain terminator or end blocker oligo modifications to block ligation at 5' terminus or preventing polymerase extension from the 3' terminus. These bases can also be used internally to create a 5'-2' phosphate linkage in the oligo. All four bases are available with the deoxyribose sugar blocked at the 3' position, to give 3'-deoxy terminator G, T, C, and A. Cordecypin is an alternative name for the 3'-deoxy A terminator. These modifiers are preferred in place of dideoxy modifications. 2',3'- dideoxy chain terminator are designed to be used with reverse 5' to 3' synthesis and support.

In situations where ligation must be blocked at the 5' terminus, 5'-OMe-dT may be used. 5'-OMe modification of a strand of siRNA using 5'-OMe-T can control guide strand selection and targeting specificity.1 5'-Amino-dT terminates an oligonucleotide with a 5'-amino group which may be used for attaching a peptide or a PNA sequence.

3'-Termination can also be effected using a 3'-3' linkage formed using 5'-supports, other non-nucleoside blocker of 3'-terminus such as 3'-Spacer C3, 3'-Phosphate can also be use as 3' terminator. Ion exchange HPLC or PAGE should be used to purify these dideoxy terminated oligos to ensure that shorter sequences (containing 3'-OH) groups are removed.

contact us Bio-Synthesis for Oligo Chain Termination Modification Services.

End Blocker Oligo Modification

Bio-Synthesis end blocker modification can be incorporate at 5' or 3' end of an oligonucleotide using 5'-5'' or 3'-5' synthesis strategy.

Every oligo synthesized is strictly controlled for quality by using either MALDI-TOF mass spectrometry or polyacrylamide gel electrophoresis (PAGE) analysis. Final yields are determined using UV absorbance at OD260 In addition, we perform QC methods tailored to specific modifications, such as OD ratio measurement where appropriate.

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2', 3' Dideoxyadenosine (2,3ddA) 2,3ddA-5 N N Y

2',3' Dideoxyadenosine (2,3ddA) is a dideoxyribonucleoside that can only be use to block 5' end of the oligo via 5' to 5' synthesis strategy. ddA is added to the 5’-end of an oligo via 5’-to-5’ synthesis, using a 2’,3’-ddA, 5’-phosphoramidite. Purification must be by PAGE or ion-exchange HPLC.

  • Modification Code: ddA-5'
  • 5 Prime: Y
  • Internal: Y
  • 3 Prime: Y
  • Molecular Weight (mw) 297.21
  • Extinction Coeficient (ec) 15.4

2', 3' Dideoxycytosine (2,3ddC) 2,3ddC-5 or 2,3ddC-3 N N Y

2',3' Dideoxycytosine (2,3ddC) is a dideoxyribonucleoside that can only be use to block 5' or 3' end of an oligo and prevent from polymerase extension. ddC 5' end blocker is added to the 5’-terminus of an oligo via 5’-to-5’ synthesis, using a 2’,3’-ddC, 5’-phosphoramidite. Purification must be by PAGE purification or Ion-exchange HPLC.

  • Modification Code: ddC-5', or ddC-3'
  • 5 Prime: Y
  • Internal: N
  • 3 Prime: Y
  • Molecular Weight (mw) 273.18
  • Extinction Coeficient (ec) 7.2


2', 3' Dideoxythymidine (2,3ddT) 2,3ddG-5 N N Y

2',3' Dideoxthymidine (2,3ddT) is a dideoxyribonucleoside that can only be use to block 5' end of the oligo via 5' to 5' synthesis strategy. ddT is added to the 5’-end of an oligo via 5’-to-5’ synthesis, using a 2’,3’-ddT, 5’-phosphoramidite. Purification must be by PAGE or ion-exchange HPLC.

  • Modification Code: ddT-5'
  • 5 Prime: Y
  • Internal: N
  • 3 Prime: N
  • Molecular Weight (mw) 288.19
  • Extinction Coeficient (ec) 8.7

2',3' Dideoxyguanosine (2,3ddG) 2,3ddG-5 N N Y

2',3' Dideoxyguanosine (2,3ddG) is a dideoxyribonucleoside that can only be use to block 5' end of the oligo via 5' to 5' synthesis strategy. ddG is added to the 5’-end of an oligo via 5’-to-5’ synthesis, using a 2’,3’-ddG, 5’-phosphoramidite. Purification must be by PAGE or ion-exchange HPLC.

  • Modification Code: ddG-5'
  • 5 Prime: Y
  • Internal: N
  • 3 Prime: Y
  • Molecular Weight (mw) 313.2
  • Extinction Coeficient (ec) 11.5

3' Phosphate 3P1los N N Y

Phosphate group can be incorporate at 5' or 3' end of an oligonucleotide. 3' phosphate modifiation, a phosphate ester, or using an inverted 3'-3' linkage is a simple and economic non-nucleosidic 3' blocker to prevent polymerase extension.

  • Modification Code: 5Phos or 3Phos
  • 5 Prime: Y
  • Internal: N
  • 3 Prime: Y
  • Molecular Weight (mw) 288.19
  • Extinction Coeficient (ec) 8.7

3'-Deoxycytidine(3'-dA) 3dA(2'-5') N N Y

3'-dA (2'-5' Linked) 3'-deoxyadenosine (3’-dA)–(2'-5' linked) is deoxy at the 3’-position of the ribose, instead of at the usual 2’-position. 3'-deoxynucleoside at the 3' end can effectively blocks polymerase extension. Modification Code: 3dA(2-5) 5 Prime: Y Internal: Y 3 Prime: Y Molecular Weight (mw) 313.21 Extinction Coeficient (ec) 15.4

  • Modification Code: 3dA(2-5)
  • potentially better results of measurements in e.g. Fluorescence Correlation Spectroscopy (FCS) than with conventional fluorophores
  • 5 Prime: Y
  • Internal: Y
  • Molecular Weight (mw) 313.21
  • Extinction Coeficient (ec) 15.4

3'-Deoxycytidine(3'-dC) 3dC(2'-5' N N Y

3'-deoxycytidine (3’-dC)–(2'-5' linked) is deoxy at the 3’-position of the ribose, instead of at the usual 2’-position. 3'-deoxynucleoside at the 3' end can effectively blocks polymerase extension.

  • Modification Code: 3dC(2-5)
  • 5 Prime: Y
  • Internal: Y
  • 3 Prime: Y
  • Molecular Weight (mw) 289.18
  • Extinction Coeficient (ec) 7.4

3'-deoxyGuanosine(3'-dG) 3dG(2'-5') N N Y

3'-deoxyguanosine (3’-dG)–(2'-5' linked) is deoxy at the 3’-position of the ribose, instead of at the usual 2’-position. 3'-deoxynucleoside at the 3' end can effectively blocks polymerase extension.

  • Modification Code: 3dG(2-5)
  • 5 Prime: Y
  • Internal: Y
  • 3 Prime: Y
  • Molecular Weight (mw) 329.21
  • Extinction Coeficient (ec) 7.4

3'-Deoxycytidine(3'dT) 3dT(2'-5') N N Y

3'-deoxythymidine (3’-dG)–(2'-5' linked) is deoxy at the 3’-position of the ribose, instead of at the usual 2’-position. 3'-deoxynucleoside at the 3' end can effectively blocks polymerase extension.

  • Modification Code: 3dT(2-5)
  • 5 Prime: Y
  • Internal: Y
  • 3 Prime: Y
  • Molecular Weight (mw) 304.2
  • Extinction Coeficient (ec) 8.7

3'-Spacer C3 3SpacerC3 N N Y

Spacer C3 is a three-carbon spacer that is used to incorporate a short spacer arm into an oligonucleotide. Spacer C3 can be incorporated in consecutive additions if a longer spacer is required. Oligo C3 spacer modification have been used in a number of different application. When incorporate Spacer C3 incorporated at the 3’-end of an oligo functions as an effective blocking agent against polymerase extension at that end in PCR reactions

  • Modification Code: ddT-5'
  • 5 Prime: Y
  • Internal: N
  • 3 Prime: Y
  • Molecular Weight (mw) 288.19
  • Extinction Coeficient (ec) 8.7

1,2-Dihydro-(3H)-pyrrolo[3,2-e]indole-7-carboxylate tripeptide CDPI3 Y N Y

1,2-Dihydro-(3H)-pyrrolo[3,2-e]indole-7-carboxylate tripeptide (CDPI3), a minor groove binder (MGB) can be covalently attached to oligonucleotide and use as antigene agents to inhibit primer extension attribute to DNA polymerase's inability to display the 5' end of the duplex super-stabilized with the CDPI3 group1. CDPI3 modified oligo can be used as PCR blockers to prevent amplification of selected DNA sequences.

  • Modification Code: CDPI3
  • 5' Prime: Y
  • Internal: N
  • 3' Prime: Y
  • Molecular Weight (mw)
  • Extinction Coeficient (ec)
  • Ref: I. Afonina, I. Kutyavin, E. Lukhtanov, R.B.Meyer, and H.Gamper. Proc. Natl. Acad. Sci USA, 1996, 93, 3199-3204.

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