Structure and Activity Studies

Bio-synthesis offers a wide range of modified oligonucleotides which are useful for structural/activity studies. These modified oligonucleotides allow investigating the effect of key structural elements on the activity of an oligonucleotide by using a variety of modifications. Oligonucleotides containing 7-deaza-dA and 7-deaza-dG lack functional groups critical for hydrogen bonding.

7-Deaza-8-aza-dA and 7-deaza-8-aza-dG (PPG) modified nucleic acid bases are isomers of A and G but have similar electron density. Their presence in oligonucleotides slightly stabilizes the oligonucleotides relative to A and G. Unlike G, PPG does not lead to aggregation and G-rich oligos can be easily prepared and isolated. This stability enhancement has led to interest in the use of PPG in diagnostic probe applications since 5'-Fluorescein oligos with PPG at the 5'-terminus are much less quenched than the equivalent G oligos.

Enzymes that interact with DNA, such as polymerases, reverse transcriptases, restriction enzymes, etc., may use a hydrogen bond donating group to contact the hydrogen bond acceptor in the minor groove. The 3-Deaza-2'-deoxyadenosine (3-deaza-dA) base has the ability for regular Watson-Crick hydrogen bonding to T but is lacking the electron pair at the 3-position normally provided at nitrogen of N3. 3-deaza-2’-dA modified oligonucleotide can be used to probe minor groove interactions of duplex DNA.

2'-deoxypseudouridine form stable C:pseudoU-A triplets. 2-Aminopurine lacks groups critical for hydrogen bonding and is a mildly fluorescent base. Sulfur containing 6-Thio-dG, 4-Thio-dT and 4-thio-dU are sulfur modified bases primary used for photo cross-linking and photoaffinity applications. 2-Thio-dT act as photosensitizing probe to study protein-DNA interactions. The thiocarbonyl group in the 2-Thio-dT can react with compounds associating with the minor group of DNA. 2-Amino-A form stable base pairing with T containing three hydrogen bonds but less stable with 2-Thio-dT due to steric hindrance between the 2-thio group. Oligonucleotides containing 2-amino-dA and 2-Thio-dT exhibit high affinity for natural oligonucleotides.

8-Amino-dA and 8-amino-dG are useful in triplex formation due to the presence of the additional amino groups. 2'-DeoxyXanthosine (dX) is a naturally occurring nucleoside that may be derived from oxidative deamination of 2'-deoxyGuanosine (dG). dX base pairs with all four natural bases and has been considered as a potential universal base. dX has also interested researchers in the field of DNA damage and repair since it is a product of nitric oxide-induced mutagenesis.

contact us for structure and activity study modified base

Product Modification Code 5 Prime Internal 3 Prime
2-Aminopurine-2'-deoxyriboside [2APdR] Y Y Y
8-Bromo-2'-deoxyadenosine [8-Bromo-dA] Y Y Y
8-Bromo-2'-deoxyguanosine [8-Bromo-dG] Y Y Y
7-Deaza-2'-deoxyadenosine [7-Deaza-dA] Y Y Y
7-Deaza-2'-deoxyguanosine [7-Deaza-dG] Y Y Y
7-Deaza-8-aza-deoxyadenosine [7-Deaza-8-aza-dA] Y Y Y
7-Deaza-8-aza-deoxyguanosine [7-Deaza-8-aza-dG] Y Y Y
3-Deaza-deoxyadenosine [3-Deaza-dA] Y Y Y
2'-Deoxypseudouridine [Pseudo-dU] Y Y Y
2-Aminopurine-riboside Y Y Y
6-Thio-dG Y Y Y
4-Thio-dT Y Y Y
4-Thio-dU Y Y Y
2-Thio-dT Y Y Y
8-Amino-dA Y Y Y
8-Amino-dG Y Y Y
2'-DeoxyXanthosine [dX] Y Y Y
Etheno-2'-deoxyadenosine [Etheno-dA] Y Y Y
O6-Phenyl-2'deoxyinosine [O6-Phenyl-dI ] Y Y Y
8-Oxo-2'-deoxyadenosine [8-Oxo-dA] Y Y Y
8-Oxo-2'-deoxyguanosine [8-Oxo-dG] Y Y Y
5.6-Dihydrothymidine Y Y Y
5,6-Dihydro-2'-deoxyuridine Y Y Y
5-Hydroxymethyl-2'-deoxyuridine Y Y Y
6-O-(TMP)-5-F-2'-deoxyuridine Y Y Y
C4-(1,2,4-Triazol-1-yl)-2'-deoxyuridine Y Y Y
Aracytidine [Ara-C] Y Y Y
5-Methyluridine [5-Methyl-U] Y Y Y
2-Aminopurine-2'-O-methylriboside Y Y Y
5-Fluoro-2'-O-Methyluridine Y Y Y
5-Fluoro-4-O-TMP-2'-O-Methyluridine Y Y Y
5-Methyl-2'-O-Methylthymidine Y Y Y
5-Hydroxy-2'-deoxycytidine Y Y Y
Pyrrolo-2'-deoxycytidine Y Y Y
Pyrrolocytidine Y Y Y