DNA with Purine–Purine Base Pairs: Size and Position of Isoguanine and 8-Aza-7-deazaisoguanine Clickable Residues Control the Molecular Recognition of Guanine and 5-Aza-7-deazaguanine

Abstract

Purine–purine base pairs represent an alternative recognition system to the purine-pyrimidine pairing reported by Watson and Crick. Modified purines are the source for non-canonical interactions. To mimic dG–dC interactions, 2′-deoxyisoguanosine (1a) and 8-aza-7-deaza-2′-deoxyisoguanosine (2a) are used to construct base pairs with 2′-deoxyguanosine or 5-aza-7-deaza-2′-deoxyguanosine (dZ). This work reports the chemical functionalization of 1a and its shape mimic 2a in purine–purine base pairs. Clickable rigid ethynyl and more flexible octadiynyl side chain derivatives of 1a and 2a were synthesized. They were protected and converted into phosphoramidites. Building blocks were employed in the synthesis of base-modified 12-mer oligonucleotides with clickable side chains. Pyrene azide was clicked to the linkers. After hybridization, oligonucleotides with purine–purine base pairs were constructed with linkers and pyrene adducts at position-8 of isoguanine and at position-7 of 8-aza-7-deazaisoguanine. Recognition and stability of purine–purine base pairs were explored using T m values, thermodynamic data, and CD-spectroscopic changes. Side chains at position-7 of 8-aza-7-deazaisoguanine–guanine base pairs or with 5-aza-7-deazaguanine are well accommodated in DNA, whereas functionalization at 8-position of isoguanine makes the DNA unstable. Pyrene click adducts verified the observation. In conclusion, position-7 is the place of choice for purine–purine base pair functionalization.

Purine–Purine Base Pairs in Parallel DNA: β-D Anomeric 8-Aza-7-deazaisoguanine and 7-Functionalized Conjugates Form Stable Base Pairs with α-D 5-Aza-7-deaza-2′-deoxyguanosine

“…For comparison, the right column shows data of corresponding duplexes with both strands in β-D configuration and uses data reported recently. 28 From the data of Table 2, the following conclusions can be drawn regarding the impact of the functionalization sites. Functionalization at the 7-position of the 8-aza-7-deazapurine residue has a strong positive impact on the duplex stability (ODN-10•ODN-2).…”

“…For the construction of anomeric DNAs with purine–purine base pairs, two series of oligonucleotides were prepared by solid-phase synthesis using phosphoramidites that have been described by our laboratory: ,,, (i) β-D anomeric oligonucleotides containing isoguanine nucleosides 3a – c or 8-aza-7-deazaisoguanine nucleosides 4a – c with and without side chain functionalization and (ii) α-D oligonucleotides incorporating three α-D 5-aza-7-deaza-2′-deoxyguanosines ( 2 ) together with canonical nucleosides in α-D configuration (ODN- 2 ). All oligonucleotide strands were 12-mers and followed the sequence pattern commonly used in our laboratory.…”

“…The left column displays anomeric duplexes with one strand in α-D and the other in β-D configuration. For comparison, the right column shows data of corresponding duplexes with both strands in β-D configuration and uses data reported recently …”

“…This investigation will give us beneficial information on the new base pairing system of anomeric purine DNA and its functionalization. To this end, 12-mer duplexes were constructed containing runs of anomeric purine base pairs formed by β-D isoguanine 2′-deoxyribonucleosides 3a – c and 4a – c in front of α-D 5-aza-7-deaza-2′-deoxyguanosine ( 2 ) . They are embedded in anomeric DNA with Watson–Crick pairs.…”

The Base Pairs of Isoguanine and 8-Aza-7-deazaisoguanine with 5-Methylisocytosine as Targets for DNA Functionalization

“…Recently, the functionalization of the alkynylated 8-aza-7deaza-2′-deoxyisoguanine nucleosides 1b,c and 2b,c to 1e,f and 2e,f by the copper-catalyzed alkyne−azide Huisgen-Meldal-Sharpless cycloaddition was reported. 36 Now, the tripropargylated 8-aza-7-deazaisoguanine nucleoside 2d was used to functionalize the isoG d -m isoC d base pair with two sensor units. For the purpose, pyrene methyl azide 9 46 widely used as fluorescence probe in biomolecules according to its favorable properties (chemical resistance, long fluorescence lifetime, high quantum yields).…”