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

Abstract

The isoguanine-isocytosine base pair (isoG-isoC) represents an important expansion of the DNA coding system. The base pair is more stable than the canonical adenine-thymine or guanine-cytosine pairs. However, nothing is known on the functionalization of the noncanonical isoG-isoC pair at the isoguanine site. In this work, functionalization of the isoG-isoC and the isosteric base pair that contains 8-aza-7-deazaisoguanine in place of isoguanine is studied. Short ethynyl, more space demanding octadiynyl, and dendritic tripropargylamine residues attached to the isoG-isoC base pairs were introduced to oligonucleotides. 12-mer duplexes were formed by hybridization with single base pair modification. The use of the two modified nucleobases gave us the freedom to shift nucleobase substituents within the major groove of double helical DNA. Clickable side chains at position-7 stabilize the base pair, whereas 8-substituents reduce its stability strongly. The weak isoguanine-thymine or 8-aza-7-deazaisoguanine-thymine base pairs show a similar sensitivity to the position of nucleobase functionalization as base pair matches formed with 5-methylisocytosine. CD spectra of all modified duplexes display the typical shape of a B-DNA with only marginal changes. Fluorescent pyrene labeled DNA with long, short, and branched linkers was generated using click chemistry. Pyrene click adducts with long linkers are essential to maintain or to increase base pair stability. Labeled duplexes are more fluorescent than corresponding single strands. For the dendritic linker excimer emission was observed for single strands but only monomer emission in duplexes.

7-Deaza-2′-deoxyisoguanosine, a Noncanonical Nucleoside for Nucleic Acid Code Expansion and New DNA Constructs: Nucleobase Functionalization of Inverse Watson–Crick and Purine–Purine Base Pairs

“…28% aq NH 3 at rt for 24 h. Then, the oligonucleotide solutions were applied to OPC columns. 47 Detritylation was performed with 3% trifluoroacetic acid on the column (for details, see the Experimental Procedures section). Purity of all oligonucleotides was proven by RP-18 HPLC analysis (Figure S3, SI).…”

“…28% aq NH 3 at rt for 24 h. Then, the oligonucleotide solutions were applied to OPC columns. 47 Detritylation was performed with 3% trifluoroacetic acid on the column. When necessary, an additional HPLC purification step was performed (for more details see ref 47).…”

Nucleobase-Functionalized 7-Deazaisoguanine and 7-Deazapurin-2,6-diamine Nucleosides: Halogenation, Cross-Coupling, and Cycloaddition

“…[2,3-d]pyrimidin-2,4-diamine (4h). 17 Compound 4h was prepared according to the literature and obtained as a colorless solid. TLC (silica gel, CH 2 Cl 2 /MeOH, 5:1) R f 0.5.…”

“…Analytical data were identical to those described in the literature. 17 [2,3-d]pyrimidin-2,4-diamine (4i). Compound 4k (170 mg, 0.47 mmol) was dissolved in methanol (6 mL) and treated with K 2 CO 3 (130 mg, 0.94 mmol) for 2 h at rt.…”

Purine DNA Constructs Designed to Expand the Genetic Code: Functionalization, Impact of Ionic Forms, and Molecular Recognition of 7-Deazaxanthine–7-Deazapurine-2,6-diamine Base Pairs and Their Purine Counterparts

“…To this end, modified nucleosides were incorporated into DNA in place of canonical building blocks . The dG–dC base pair was replaced by the isoG d –isoC d pair, − and also entirely new base pair motifs were developed with or without hydrogen bonding . Systems with parallel strand orientation formed by heterochiral strands containing anomeric nucleosides were constructed. − One of the more recent developments for code expansion is the construction of purine DNA. − In purine DNA, two purine nucleobases form the base pair instead of a purine and a pyrimidine base as in Watson–Crick DNA.…”