Synthesis and Duplex Stabilization of Oligonucleotides Consisting of Isonucleosides

Yang, Zhenjun; Zhang, Huyi; Min, Ji-Mei; Ma, Ling-Tai; Zhang, Lihe

doi:10.1002/(sici)1522-2675(19991110)82:11<2037::aid-hlca2037>3.0.co;2-i

Cited by 17 publications

(24 citation statements)

References 9 publications

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“…Another modification of deoxynucleotides involved the repositioning of the base-sugar connection from the C1- to the C2-position to afford 1,4-anhydro-2-deoxy- d - and - l -arabinitol, dubbed isonucleosides (Figure ). In 14-mer strands with homo-T bases, d -arabinitol formed slightly less stable duplexes with d-A 14 (Δ T m = −5.9 °C) than with d-T 14 , while l -arabinitol was unable to complex with this complement . Addition of a methylhydroxyl moiety to the C1‘-position of the d -arabinitol generates the d -mannitol monomer, and 14-mers of both d - 546 and l -mannitol 545 complexed with d-A 14 showed that the methylhydroxyl promotes stability by Δ T m = +1.2 °C.…”

Section: Backbones With C2‘-base Connectivitiesmentioning

confidence: 99%

“…In 14-mer strands with homo-T bases, D-arabinitol formed slightly less stable duplexes with d-A 14 (∆T m ) -5.9 °C) than with d-T 14 , while L-arabinitol was unable to complex with this complement. 545 Addition of a methylhydroxyl moiety to the C1′-position of the D-arabinitol gener- ates the D-mannitol monomer, and 14-mers of both D-546 and L-mannitol 545 complexed with d-A 14 showed that the methylhydroxyl promotes stability by ∆T m ) +1.2 °C. b. HNAs.…”

Section: Backbones With C2′-base Connectivitiesmentioning

confidence: 99%

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A Field Guide to Foldamers

et al. 2001

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He attended Point Loma Nazarene University in San Diego, CA, where he worked with Professor Victor L. Heasley on the halogenation of unsaturated carbonyl compounds. After receiving his B.A. degree in Chemistry in 1997, he began his graduate career at the University of Illinois with Professor Jeffrey S. Moore. Currently he is in his fifth year investigating solvent effects on the helix−coil transition in oligo(m-phenylene ethynylene) foldamers. Matthew J. Mio (left) was born in Michigan in 1974. He attended the University of Detroit Mercy, where he worked with Professor Kevin. D. Belfield (now at the University of Central Florida) on the synthesis of nonlinear optical chromophores for use in polymeric systems. He graduated with his B.S. degree in Chemistry in 1997. Later that year, he began his graduate career at the University of Illinois at Urbana−Champaign with Professor Jeffrey S. Moore. There, Matt studied the synthesis and solution/ solid-state properties of oligo(m-phenylene ethynylene) foldamers and graduated with his Ph.D. degree in 2001. He then went to the Chemistry Department at Macalester College (St. Paul, MN) as a Mellon Postdoctoral Fellow to study the synthesis of novel CpCo−cyclobutadienyl-bridged cyclophanes with Professor Ronald G. Brisbois. Thomas S. Hughes (right) is currently a postdoctoral fellow in the research group of Professor Jeff Moore at the University of Illinois. He was born in 1970 in Philadelphia, PA, and received his B.S. degree from Temple University in 1991. In 1999 he received his Ph.D. degree from Cornell University, where he worked in the laboratories of Professor Barry Carpenter. He is currently studying the association kinetics of the binding of a helical oligomer to a rodlike guest. He is also investigating the thermodynamics of oligo(phenylene ethynylene) folding using molecular mechanics. Jeffrey S. Moore (second from right) was born in Illinois in 1962. After receiving his B.S. degree in Chemistry from the University of Illinois in 1984, he completed his Ph.D. degree in Materials Science and Engineering, also at the University of Illinois, with Samuel Stupp (1989). He then went to the California Institute of Technology as an NSF postdoctoral fellow to study with Robert Grubbs. In 1990 he joined the chemistry faculty at the University of Michigan in Ann Arbor. He returned to the University of Illinois in 1993, where he is currently a Professor of Chemistry and Materials Science and Engineering. In 1995 he became a part-time faculty member of the Beckman Institute for Advanced Science and Technology, where he now serves as co-chairman of the Molecular and Electronic Nanostructures Main Research Theme. Ryan B. Prince was born in Robbinsdale, MN, in 1972. He graduated from Southeast Missouri State University in 1995 with his B.S. degree in Chemistry, where he worked for Professor Jin K. Gong on the synthesis and characterization of transition-metal complexes that bind and activate carbon dioxide. He then went to the University of Illinois and worked with Professor Jeffrey...

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Section: Backbones With C2‘-base Connectivitiesmentioning

confidence: 99%

Section: Backbones With C2′-base Connectivitiesmentioning

confidence: 99%

A Field Guide to Foldamers

et al. 2001

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“…Previous studies showed that homo-oligoisonucleotides antagonized the hydrolysis of snake venom phosphodiesterase. Furthermore, some kinds of homo-oligoisonucleotides also showed strong binding abilities to their complementary sequences though they were a little weaker than the native counterpart (Figure a , b , c ) ( − ). The results suggested that antisense oligonucleotide constructed from isonucleotide could antagonize the hydrolysis of nuclease and give acceptable binding ability.…”

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confidence: 99%

Properties of Isonucleotide-Incorporated Oligodeoxynucleotides and Inhibition of the Expression of Spike Protein of SARS-CoV

et al. 2005

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Antisense oligonucleotides are recognized to be very efficient tools for the inhibition of gene expression in a sequence specific way. For the discovery of a novel efficient way to modify oligonucleotides, a series of single isonucleotide-incorporated antisense oligodeoxynucleotides have been synthesized, in which an isonucleotide was introduced at different positions of the sequences. The binding behaviors of modified oligodeoxynucleotides to the complementary sequence were studied by UV, CD, and molecular dynamics simulation. The results showed that although the incorporated isonucleotides at certain positions of the sequence interfere with the binding ability to a different extent, B-form duplexes were maintained and the binding abilities of the 3'-end-modified duplexes were better than the corresponding mismatched duplexes. The digestion of modified oligodeoxynucleotides by snake venom phosphodiesterase showed that an isonucleotide strongly antagonizes hydrolysis. The DNA/RNA hybrid formed by a modified oligodeoxynucleotide and its target RNA could activate RNase H. The 3'-end-modified antisense oligodeoxynucelotides inhibited S-glycoprotein expression of SARS-CoV at the mRNA levels in insect Sf9 cells. This study indicated the possibility of designing a novel and effective antisense oligodeoxynucleotide by incorporating an isonucleotide at the 3'-end of the sequence.

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“…1) [9] [10]. Oligonucleotides bearing the isonucleosides 1 or 2 show increased stability towards snakevenom phosphodiesterase (SVPDE), but only oligonucleotides built up from the isonucleoside 2 retained their hybridization property [11]. To investigate whether extension of the phosphodiester linkage formed could improve the hybridization properties, we synthesized 1',4'-anhydro-2',5'-dideoxy-2'-nucleobase-d-altritol 3 in which an additional methylene group is introduced at the 5'-position of compound 2 [12].…”

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confidence: 99%

“…The hyperchromicity value for this duplex was much less than for the control duplex dT 14 ¥ dA 14 , reflecting poor base stacking within the duplex [11]. Oligomer 7 has an extended phosphodiester linkage, and the backbone is more flexible compared to the oligomer consisting of isonucleoside 2.…”

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Synthesis and Hybridization Properties of an Oligonucleotide Consisting of 1′,4′-Anhydro-2′,5′-dideoxy-2′-(thymin-1-yl)-D-altritol

Zhu

Tian

Zhang

et al. 2002

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The novel oligonucleotide analogue 7, consisting of 1',4'-anhydro-2',5'-dideoxy-2'-(thymin-1-yl)-d-altritol (4), residues was synthesized by the phosphoramidite approach on an automated DNA synthesizer. The phosphoramidite building block 6 was obtained by phosphitylation of the corresponding isonucleoside 5. Oligoisonucleotide 7 contains an extended phosphodiester linkage with a higher flexibility. Oligoisonucleotide 7 was studied with respect to hybridization properties, enzymatic stability, and CD spectra. It exhibits a high stability towards snake-venom phosphodiesterase and an acceptable hybridization to complementary singlestranded DNA and RNA.

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Synthesis and Duplex Stabilization of Oligonucleotides Consisting of Isonucleosides

Cited by 17 publications

References 9 publications

A Field Guide to Foldamers

A Field Guide to Foldamers

Properties of Isonucleotide-Incorporated Oligodeoxynucleotides and Inhibition of the Expression of Spike Protein of SARS-CoV

Synthesis and Hybridization Properties of an Oligonucleotide Consisting of 1′,4′-Anhydro-2′,5′-dideoxy-2′-(thymin-1-yl)-D-altritol

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