A new, but old, nucleoside analog: the first synthesis of 1-deaza-2'-deoxyguanosine and its properties as a nucleoside and as oligodeoxynucleotides

1-Deazaguanosine-Modified RNA: The Missing Piece for Functional RNA Atomic Mutagenesis

Atomic mutagenesis is the key to advance our understanding of RNA recognition and RNA catalysis. To this end, deazanucleosides are utilized to evaluate the participation of specific atoms in these processes. One of the remaining challenges is access to RNA-containing 1-deazaguanosine (c¹G). Here, we present the synthesis of this nucleoside and its phosphoramidite, allowing first time access to c¹G-modified RNA. Thermodynamic analyses revealed the base pairing parameters for c¹G-modified RNA. Furthermore, by NMR spectroscopy, a c¹G-triggered switch of Watson-Crick into Hoogsteen pairing in HIV-2 TAR RNA was identified. Additionally, using X-ray structure analysis, a guanine–phosphate backbone interaction affecting RNA fold stability was characterized, and finally, the critical impact of an active-site guanine in twister ribozyme on the phosphodiester cleavage was revealed. Taken together, our study lays the synthetic basis for c¹G-modified RNA and demonstrates the power of the completed deazanucleoside toolbox for RNA atomic mutagenesis needed to achieve in-depth understanding of RNA recognition and catalysis.

Access to 3-Deazaguanosine Building Blocks for RNA Solid-Phase Synthesis Involving Hartwig-Buchwald C-N Cross-Coupling

3-Deazaguanosine (c³G) and phosphoramidite derivatives thereof that allow incorporation of this modification into RNA are needed for atomic mutagenesis experiments to explore mechanistic aspects of ribozyme catalysis. Here, we report a practical synthesis for c³G phosphoramidites from inexpensive starting materials. The key reaction sequence is a silyl-Hilbert-Johnson nucleosidation followed by Hartwig-Buchwald cross-coupling to achieve the N²-phenoxyacetyl protected c³G nucleoside.

Optimization of an unnatural base pair toward natural-like replication

Predominantly hydrophobic unnatural nucleotides that selectively pair within duplex DNA as well as during polymerase-mediated replication have recently received much attention as the cornerstone of efforts to expand the genetic alphabet. We recently reported the results of a screen and subsequent lead hit optimization that led to identification of the unnatural base pair formed between the nucleotides dMMO2 and d5SICS. This unnatural base pair is replicated by the Klenow fragment of Escherichia coli DNA polymerase I with better efficiency and fidelity than other candidates reported in the literature. However, its replication remains significantly less efficient than a natural base pair, and further optimization is necessary for its practical use. To better understand and optimize the slowest step of replication of the unnatural base pair, the insertion of dMMO2 opposite d5SICS, we synthesized two dMMO2 derivatives, d5FM and dNaM, which differ from the parent nucleobase in terms of shape, hydrophobicity, and polarizability. We find that both derivatives are inserted opposite d5SICS more efficiently than dMMO2 and that overall the corresponding unnatural base pairs are generally replicated with higher efficiency and fidelity than the pair between dMMO2 and d5SICS. In fact, in the case of the dNaM:d5SICS heteropair, the efficiency of each individual step of replication approaches that of a natural base pair, and the minimum overall fidelity ranges from 10(3) to 10(4). In addition, the data allow us to propose a generalized model of unnatural base pair replication, which should aid in further optimization of the unnatural base pair and possibly in the design of additional unnatural base pairs that are replicated with truly natural-like efficiency and fidelity.

Convenient Synthesis of 2-pyridyl thioglycosides

A reported method for preparation of a new class of pyridine thioglycosides via reaction of pyridine-2(1 H)-thiones with 2,3,4-tri- O-acetyl-α-d-xylo- and -β-d-arabinopyranosyl bromides has been studied.

Generation of an abasic site in an oligonucleotide by using acid-labile 1-deaza-2'-deoxyguanosine and its application to postsynthetic modification

We developed a new convenient method for generation of an abasic site at the 3'-terminus of an oligonucleotide. This method uses a 1-deaza-2'-deoxyguanosine residue, which easily undergoes depurination under acidic conditions. The abasic site of the oligonucleotide can be further modified with external functional groups. We report herein the chemical stability of 1-deaza-2'-deoxyguanosine in the oligodeoxynucleotide and the application to the postsynthetic modification of an oligonucleotide by utilizing the chemical property of 1-deaza-2'-deoxyguanosine. [Structure: see text]