Increasing the Stability of DNA:RNA Duplexes by Introducing Stacking Phenyl-Substituted Pyrazole, Furan, and Triazole Moieties in the Major Groove.
Consecutive incorporations of our previously published thymidine analogue, 5-(1-phenyl-1H-1,2,3-triazol-4-yl)-2'-deoxyuridine monomer W in oligonucleotides, has demonstrated significant duplex-stabilizing properties due to its efficient staking properties in the major groove of DNA:RNA duplexes. The corresponding 2'-deoxycytidine analogue is not as well-accommodated in duplexes, however, due to its clear preference for the ring-flipped coplanar conformation. In our present work, we have used ab initio calculations to design two new building blocks, 5-(5-phenylfuran-2-yl)-2'-deoxycytidine monomer Y and 5-(1-phenyl-1H-pyrazol-3-yl)-2'-deoxycytidine monomer Z, that emulate the conformation of W. These monomers were synthesized by Suzuki-Miyaura couplings, and the pyrazole moiety was obtained in a cycloaddition from N-phenylsydnone. We show that the novel analogues Y and Z engage in efficient stacking either with themselves or with W due to a better overlap of the aromatic moieties. Importantly, we demonstrate that this translates into very thermally stable DNA:RNA duplexes, thus making Y and especially Z good candidates for improving the binding affinities of oligonucleotide-based therapeutics. Since we now have both efficiently stacking T and C analogues in hand, any purine rich stretch can be effectively targeted using these simple analogues. Notably, we show that the introduction of the aromatic rings in the major groove does not significantly change the helical geometry.
Nucleic Acid Center, Department of Physics, Chemistry & Pharmacy, University of Southern Denmark , Campusvej 55, DK-5230 Odense, Denmark.
Mick
M
Hornum
Nucleic Acid Center, Department of Physics, Chemistry & Pharmacy, University of Southern Denmark , Campusvej 55, DK-5230 Odense, Denmark.
Pawan
P
Kumar
Nucleic Acid Center, Department of Physics, Chemistry & Pharmacy, University of Southern Denmark , Campusvej 55, DK-5230 Odense, Denmark.
Patricia
P
Podsiadly
Nucleic Acid Center, Department of Physics, Chemistry & Pharmacy, University of Southern Denmark , Campusvej 55, DK-5230 Odense, Denmark.
Poul
P
Nielsen
D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry*; D003857:Deoxyuridine / Q000031:analogs & derivatives* / Q000737:chemistry*; D005663:Furans / Q000737:chemistry; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry*; D011720:Pyrazoles / Q000737:chemistry; D012313:RNA / Q000737:chemistry*; D014230:Triazoles / Q000737:chemistry
C000605849:5-(1-phenyl-1H-1,2,3-triazol-4-yl)-2'-deoxyuridine; C000605850:5-(1-phenyl-1H-pyrazol-3-yl)-2'-deoxycytidine; D005663:Furans; D009841:Oligonucleotides; D011720:Pyrazoles; D014230:Triazoles; C031280:pyrazole; D012313:RNA; D004247:DNA; C039281:furan; D003857:Deoxyuridine