Synthesis and Hybridization Property of Oligonucleotides Containing Carbocyclic Oxetanocins

Honzawa, Shinobu; Ohwada, Satoshi; Mori­shita, Yohei; Sato, Katsutoshi; Katagiri, Nobuya; Yamaguchi, Masahiko

doi:10.1016/s0040-4020(00)00162-9

Cited by 11 publications

(8 citation statements)

References 11 publications

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“…Previous studies on DNA analogues have shown that the number of bonds in the repetitive DNA backbone can be varied to five12, 36 or seven7 without breakdown of complementary recognition of RNA and DNA. Bicyclo[3.2.1]amide‐DNA is the first analogue to demonstrate that the distance between the base and the backbone can also be extended from three to four bonds without breakdown of complementary Watson–Crick base‐pairing.…”

Section: Discussionmentioning

confidence: 99%

“…As a note of caution we add that intra-and inter-residue hydrogen-bond formation in PNA, involving the base-linker amide function, has been proposed on the basis of molecular modeling, [32,33] but has never been observed in high-resolution structures of PNA duplexes and triplexes. [34,35] Previous studies on DNA analogues have shown that the number of bonds in the repetitive DNA backbone can be varied to five [12,36] or seven [7] without breakdown of complementary recognition of RNA and DNA. Bicyclo[3.2.1]amide-DNA is the first analogue to demonstrate that the distance between the base and the backbone can also be extended from three to four bonds without breakdown of complementary Watson ± Crick base-pairing.…”

Section: Discussionmentioning

confidence: 99%

“…Major changes in the association behavior of oligonucleotides arise, as expected, from variation of the ribofuranose substructure in DNA and RNA. In this context, six‐membered ring versions (e.g, homo‐DNA,2 HNA,3 CeNA,4 CNA,5 p‐RNA6) and four‐membered ring versions (e.g, carbocyclic oxetanocine‐DNA7 and cyclobutane‐DNA8), as well as ring‐deficient analogues (such as seco ‐DNA9, 10 and glycerol ‐ DNA11) have been evaluated. Besides this, analogues of increased (seven bonds)7 or decreased (five bonds)12 length in the repetitive backbone unit have been evaluated.…”

Section: Introductionmentioning

confidence: 99%

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Bicyclo[3.2.1]amide-DNA: A Chiral, Nonchiroselective Base-Pairing System

et al. 2002

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Bicyclo[3.2.1]amide-DNA: A Chiral, Nonchiroselective Base-Pairing System

et al. 2002

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“…This observation has its precedent in the field of artificial nucleic acids. Carbocyclic 5′‐ nor oligonucleotides (five bonds)7 and carbocyclic oxetanocin oligonucleotides (seven bonds)8 both hybridize with RNA.…”

Section: Methodsmentioning

confidence: 99%

TNA as a Potential Alternative to Natural Nucleic Acids

Herdewijn

2001

Angew. Chem. Int. Ed.

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“…A systematic study was undertaken by Yamaguchi et al to understand the binding properties of both the enantiomeric carbocyclic analogues of oxetanocin (cox) (( Fig. (15), III) coxA) in ONs [90]. Cox-A homooligomer selectively formed highly stable complexes preferably with complementary RNA.…”

Section: Oxetanocins (Ox A) and Carbocyclic Oxetano-cins (Cox A) Nuclmentioning

confidence: 99%

Structure-Editing of Nucleic Acids for Selective Targeting of RNA

Kumar¹,

Ganesh

2007

CTMC

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The synthesis of backbone-modified nucleic acids has been an area of very intense research over the last two decades. The main reason for this research activity is the instability of nucleic acid based drugs in the intracellular conditions. Changes in the sugar-phosphate backbone invariably bring about the changes in the complementation properties of the nucleic acids. The naturally occurring deoxyribose- (DNA) and ribose (RNA) sugar-phosphate backbones are endowed with considerable differences in their binding affinities towards themselves. This occurs because of the different sugar conformations prevalent in DNA and RNA and the subtle structural changes accruing from these in hydrogen bonding, base-stacking interactions and hydration of major/minor grooves. The six-atom phosphodiester linkages and pentose-sugars give immense opportunities for chemical modifications that lead to several backbone-modified nucleic acid structures. This article is focused on such modifications that impart RNA-selective binding properties to the modified nucleic acid mimics and the rationale behind the said selectivity. It is found that the six-atom sugar-phosphate backbone could be replaced by either one-atom extended or one-atom edited repeating units, leading to the folded or extended geometries to maintain the internucleoside distance-complementarity. Other important contributions come from electronegativity of the substituent groups, hydration in the major/minor groove, base stacking etc.

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Synthesis and Hybridization Property of Oligonucleotides Containing Carbocyclic Oxetanocins

Cited by 11 publications

References 11 publications

Bicyclo[3.2.1]amide-DNA: A Chiral, Nonchiroselective Base-Pairing System

Bicyclo[3.2.1]amide-DNA: A Chiral, Nonchiroselective Base-Pairing System

TNA as a Potential Alternative to Natural Nucleic Acids

Structure-Editing of Nucleic Acids for Selective Targeting of RNA

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