Syntheses and Base-Pairing Properties of Locked Nucleic Acid Nucleotides Containing Hypoxanthine, 2,6-Diaminopurine, and 2-Aminopurine Nucleobases

Abstract

Second generation 2'-O,4'-C-methylene-linked nucleotides 1-3 containing hypoxanthine, 2,6-diaminopurine, and 2-aminopurine nucleobases were synthesized and incorporated into locked nucleic acid (LNA) oligonucleotides by means of the automated phosphoramidite method. The required phosphoramidite monomeric units were efficiently prepared via convergent synthesis. The glycosyl donor 4 was stereoselectively coupled with hypoxanthine and 6-chloro-2-aminopurine to give the 4'-C-branched nucleosides 5 and 17. The methods for conversion of 5 and 17 into phosphoramidites 11, 25, and 29 were developed and described in full details for the first time. Hybridization properties of LNA octamers containing the new LNA nucleotides were assessed against perfect and singly mismatched DNA. The binding studies revealed that all LNA octamers hybridize very efficiently to DNA following Watson-Crick base-pairing rules with increased binding affinity compared to the DNA analogues. The unique properties of the nucleotides 1-3 make them very useful for further strengthening of the LNA technology.

Unrestricted accessibility of short oligonucleotides to RNA

“…Relative to the unmodified target, suppression of the U-T mismatch was much improved for all four modified transcripts, an effect attributable to substitution with sU or cG. In contrast, presence of nA in the RNA strand reduced specificity by accommodating an nA-C mismatch, as has been observed in other LNA-containing hybrids (Koshkin 2004;Rosenbohm et al 2004). Importantly, while substitution with hX decreased the specificity of hybrid formation (panel 5), as expected due to the degeneracy of hX in base-pairing (Martin et al 1985;Case-Green and Southern 1994), introduction of cG retained the specificity (panels 2 and 4), allowing only the cG-C base-pairing.…”

A Versatile Total Synthesis of Trachycladines A and B and Their Analogues

“…Initial runs were carried out with 15 using 2‐chloroadenine ( 17 ) or hypoxanthine ( 18 ) as coupling partners in TMSOTf‐promoted (TMS = trimethylsilyl) glycosylation protocols using N , O ‐bis(trimethylsilyl)acetamide (BSA) as the nucleobase silylating agent in the presence or absence of DBU (1,8‐diazabicyclo[5.4.0]undec‐7‐ene; Scheme and Table 1). 10,16–18 However, the results were highly discouraging. Thus, for the reactions of 17 , protected trachycladine A derivative 19 was formed only in trace amounts (<2 %).…”

“…Initial runs were carried out with 15 using 2-chloroadenine (17) Table 1). [10,[16][17][18] However, the results were highly discouraging. Thus, for the reactions of 17, protected trachycladine A derivative 19 was formed only in trace amounts (Ͻ2 %).…”

“…Therefore, 16a and 16b were used as a mixture in the optimization runs. The pilot couplings were carried out with 2-chloroadenine (17) or hypoxanthine (18) in TMSOTf-promoted glycosylation protocols using BSA, as described in Scheme 3. [16,17] To our delight, these reactions gave the corresponding protected nucleosides (i.e., 23 and 24) in much better yields ( Table 2, entries 1-2 and 3-5, respectively).…”

Directed Evolution of Dunaliella salina Ds-26-16 and Salt-Tolerant Response in Escherichia coli

“…Due to the short open reading frame (159 bp), it is not easy to create enough random mutations using traditional error prone PCR, such as increasing concentrations of Mg 2+ and Mn 2+ . Therefore, dITP, a deoxyribonucleic analogue that could pair with C, T or A [25], was supplied here to mediate the reaction. The effect was demonstrated in our study as seven variants were screened from the library.…”