Oligonucleotides Incorporating 7-(Aminoalkynyl)-7-deaza-2‘-deoxyguanosines:  Duplex Stability and Phosphodiester Hydrolysis by Exonucleases

Abstract

Oligonucleotides containing 7-(omega-aminoalkyn-1-yl)-7-deaza-2'-deoxyguanosines (1a-c) were investigated regarding their thermal stability (T(m) values) as well as their phosphodiester hydrolysis catalyzed by exonucleases. Those derivatives are suitable for the labeling of nucleic acid constituents as well as for the postlabeling of DNA. For this, the phosphoramidites 7a,c (obtained from the nucleoside 1a,b), protected by an isobutyryl group at the 2-amino group and a phthaloyl residue at the side-chain amino function, were synthesized. Using compounds 7a,c together with the phosphoramidite of 1c in solid-phase synthesis, a series of self-complementary and non-self-complementary oligonucleotides were prepared and characterized by MALDI-TOF mass spectrometry. A comparison of the T(m) values of the modified oligomers shows that the thermal stability of the duplexes decreases with the length of the nucleobase 7-(omega-aminoalkyn-1-yl) side chain. Exonucleolytic cleavage of oligonucleotide single strands incorporating either the 7-(3-aminopropyn-1-yl)- or the 7-(4-aminobutyn-1-yl)-substituted nucleosides 1a or 1b, respectively, reveals that 3' --> 5' specific snake venom phosphodiesterase liberates 1a 5'-monophosphate but not the methylene-extended 1b 5'-monophosphate. On the contrary, the 5' --> 3' specific bovine spleen exonuclease is able to cleave off single 1a and 1b 3'-monophosphate residues; its action is, however, terminated in the case of oligonucleotides containing two consecutive 1a or 1b nucleotide units.

Stability of Hoogsteen‐Type Triplexes – Electrostatic Attraction between Duplex Backbone and Triplex‐Forming Oligonucleotide (TFO) Using an Intercalating Conjugate

“…To avoid the complication of quadruplex formation of G-rich TFOs, we consider it possible to optimize the 7-deaza-2'-deoxyguanosine approach by using our compatible intercalator approach in a proper combination [17]. In this context, it could also be interesting to use 7-(aminoalkynyl)-7-deaza-2'-deoxyguanosine to take advantage of a possible ion-pair stabilization [18].…”

Advances in the Synthesis of 7-Deazapurine - Pyrrolo[2,3-d]pyrimidine 2-Deoxyribonucleosides Including D- and L-Enantiomers, Fluoro Derivatives and 2,3-Dideoxyribonucleosides

“…Fluorinated 7-deazapurine nucleosides, such as 2'-deoxy-2'-fluoroarabinosangivamycin (97c) and 2-amino-2'-deoxy-2'-fluoroarabinotubercidin (98a), can act as antiviral agents [108][109][110]. Selected 7-deazapurine fluoroarabinonucleosides (97)(98)(99)(100)(101) are shown in Scheme 37. These nucleosides have been synthesized by a convergent route using the nucleobase anion glycosylation.…”

“…Furthermore, oligonucleotides become resistant against enzymatic degradation [97]. Oligonucleotides with aminoalkynyl chains are used for the functionalization with reporter groups applied to nucleic acid sequencing or as tool in DNA or RNA diagnostics.…”

Hoogsteen vs. Watson–Crick Base Pairing: Incorporation of 2‐Substituted Adenine‐ and 7‐Deazaadenine 2′‐Deoxy‐β‐D‐ribonucleosides into Oligonucleotides

“…Quantification of the resulting nucleosides was achieved on the basis of the peak areas which were divided by the extinction coefficients of the nucleoside constituents at l 260 nm: dA, 15400; dC, 7300; dG, 11700; dT, 8800; Cl . MALDI-TOF-MS were recorded by Mrs. Stephanie Hahner, University of Münster, on a home-built device or on a Biflex III instrument (Bruker Daltronik GmbH, D-Leipzig) in the reflector mode; for details see [62]. Melting Experiments.…”