Conformational and stacking properties of 3′-5′ and 2′-5′ linked oligoribonucleotides studied by CD

Sawai, Hiroaki; Kuroda, Kensei; Seki, Junichi; Ozaki, Hiroaki

doi:10.1002/(sici)1097-0282(199608)39:2<173::aid-bip5>3.0.co;2-m

Cited by 21 publications

(13 citation statements)

References 44 publications

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“…It is now well established that nucleic acids, even with 2¢,5¢ linkages, associate to form Watson and Crick paired duplexes [2][3][4][5]10,11,[32][33][34][35][36][37]. They also selectively associate with DNA and RNA with a varying degree of stability.…”

Section: Discussionmentioning

confidence: 99%

Solution structure of 2′,5′ d(G₄C₄)

Premraj

Raja

Bhavesh

et al. 2004

European Journal of Biochemistry

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The NMR structure of 2¢,5¢ d(GGGGCCCC) was determined to gain insights into the structural differences between 2¢,5¢-and 3¢,5¢-linked DNA duplexes that may be relevant in elucidating nature's choice of sugar-phosphate links to encode genetic information. The oligomer assumes a duplex with extended nucleotide repeats formed out of mostly N-type sugar puckers. With the exception of the 5¢-terminal guanine that assumes the syn glycosyl conformation, all other bases prefer the anti glycosyl conformation. Base pairs in the duplex exhibit slide ()1.96 Å ) and intermediate values for X-displacement ()3.23 Å ), as in ADNA, while their inclination to the helical axis is not prominent. Major and minor grooves display features intermediate to A and BDNA. The duplex structure of iso d(GGGGCCCC) may therefore be best characterized as a hybrid of A and BDNA. Importantly, the results confirm that even 3¢ deoxy 2¢,5¢ DNA supports duplex formation only in the presence of distinct slide ( ‡ )1.6 Å ) and X-displacement ( ‡ )2.5 Å ) for base pairs, and hence does not favor an ideal BDNA topology characterized by their near-zero values. Such restrictions on base pair movements in 2¢,5¢ DNA, which are clearly absent in 3¢,5¢ DNA, are expected to impose constraints on its ability for deformability of the kind observed in DNA during its compaction and interaction with proteins. It is therefore conceivable that selection pressure relating to the optimization of topological features might have been a factor in the rejection of 2¢,5¢ links in preference to 3¢,5¢ links.Keywords: structure of 2¢,5¢ DNA; evolution of 3¢,5¢ vs. 2¢,5¢ links in nucleic acids; AB hybrid structure; restrained base pair movements; topological restrictions in 2¢,5¢ DNA.Nature's selection of 3¢,5¢ linkages (instead of 2¢,5¢ linkages) in nucleic acids, to encode genetic information, is intriguing. The fact that 2¢,5¢ links are formed in abundance and serve as a template in nonenzymatic reactions suggest that they might have been the ancestors of the biotic 3¢,5¢ links, which could have evolved from a pool of 3¢,5¢ and 2¢,5¢ links [1]. Nucleic acids with 2¢,5¢ links satisfy one of the critical features required for the fidelity of replication, namely that they associate to form Watson and Crick base-paired duplex structures [2][3][4][5], although with weaker affinity than 3¢,5¢-linked DNA strands. However, detailed knowledge about stereochemistry, polymorphism and topological properties of 2¢,5¢ DNA duplexes, which may provide insights into the factors that determine nature's choice of sugar-phosphate links from a stereochemical perspective, is sparse [6][7][8][9]. In fact, there are only two reports of NMR structure determination -one on a 2¢,5¢ DNA fragment [10] and one on a 2¢,5¢ RNA fragment [11] -both of which suggest an A-type duplex structure with some stereochemical details that differ from genomic DNA and RNA duplexes. In this context, it is relevant to recognize the results from recent modeling studies on 2¢,5¢ nucleic acids, which suggest that 2¢,5¢ DNA can...

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Section: Discussionmentioning

confidence: 99%

Solution structure of 2′,5′ d(G₄C₄)

Premraj

Raja

Bhavesh

et al. 2004

European Journal of Biochemistry

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“…D-and L-adenosine 5 -phosphorimidazolides were prepared from D-and L-adenosine 5 -phosphate, respectively, with imidazole using dipyridyl disulfide and triphenylphosphine as a condensing agent (Lohrmann and Orgel, 1978;Sawai et al, 1989). Authentic samples of 2 -5 and 3 -5 linked D-oligoadenylates were prepared by the methods described previously (Sawai et al, 1996). Authentic samples of diastereomers of adenylyladenosine, ApA, were prepared by Urata et al (Urata et al, 2002).…”

Section: Methodsmentioning

confidence: 99%

Chiral Selection in Oligoadenylate Formation in the Presence of a Metal ion Catalyst or Poly(U) Template

Osawa

Urata

Sawai

2005

Orig Life Evol Biosph

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The lead ion-catalyzed oligomerization of 5'-phosphorimidazolides of D-, L- or racemic DL-adenosine (D-ImpA, L-ImpA and DL-ImpA) gave oligoadenylates up to a pentamer. The oligomers resulting from racemic ImpA were comparable in yields and length to those from chiral D- or L-ImpA. A complex mixture of homochiral and heterochiral oligomers was formed in the reaction from racemic ImpA. Total dimer product from racemic ImpA by the lead ion catalyst showed homochiral selectivity. The reaction catalyzed by uranyl ion yielded oligoadenylates up to 15mer from chiral D- or L-ImpA in over 95% yield. A complex mixture of isomeric oligoadenylates was formed from racemic DL-ImpA in the presence of uranyl ion catalyst in comparable yields to those from D- or L-ImpA. The analysis of the dimer product from DL-ImpA showed that the homochiral 2' -5' linked dimer was selectively formed. D-ImpA polymerized effectively on a poly(U) template, which is exclusively composed of D-uridine, yielding oligoadenylates up to a pentamer. In contrast, L-ImpA or racemic DL-ImpA polymerized far less efficiently on the poly(U) template, demonstrating that chiral selection takes place in the poly(U) template-directed oligoadenylate formation.

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“…The CD bands of 2Ј,5Ј phosphorothioate oligoadenylates decreased with increasing temperature as did those of the corresponding 2Ј,5Ј phosphodiester oligoadenylates. 27 The temperature-dependent change in the CD of these compounds is ascribed to a shifting of the stackedunstacked two-state equilibrium, because isoelliptic points were observed in the CD spectra. The equilibrium constant is expressed by and [] u values at 270 nm in Table I.…”

Section: Spectroscopymentioning

confidence: 99%

Conformational properties of 2′,5′ linked Rp‐ and Sp‐phosphorothioate oligoadenylates studied by circular dichroism and NMR

et al. 2002

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2Ј,5Ј-Linked oligoadenylates (2-5A) are involved in the antiviral action of interferon. The 2-5A binds and activates 2-5A dependent RNase (RNase L), which degrades viral mRNA, resulting in the inhibition of protein synthesis. 2Ј,5Ј-Linked phosphorothioate oligoadenylates with an Rp configuration bind to and activate the RNase L. On the other hand, 2Ј,5Ј phosphorothioate oligoadenylate with an Sp configuration weakly binds to the RNase L and is devoid of the RNase L activation ability. Comparative circular dichroism (CD) and NMR studies are carried out to characterize the difference in properties between the two configurations of the 2Ј,5Ј phosphorothioate oligoadenylates. 2Ј,5Ј Rp-Phosphorothioate oligoadenylates showed CD spectra similar to those of the corresponding native 2Ј,5Ј oligoadenylates, while the 2Ј,5Ј Sp-phosphorothioate oligoadenylates exhibited a weaker CD band compared to the former two, indicating the weaker base-stacking interaction of the 2Ј,5Ј Sp-phosphorothioate oligoadenylates. The temperature-dependent change in the CD revealed that 2Ј,5Ј phosphorothioate oligoadenylates showed larger ⌬H°and ⌬S°values for the thermal transition of the conformation than the corresponding native 2Ј,5Ј oligoadenylates. The NMR spectral assignment was accomplished by several NMR measuring techniques. The 2Ј-H of the ribose ring linked to the 2Ј,5Ј Sp-phosphorothioate showed a higher field chemical shift of the proton NMR than that linked to the corresponding 2Ј,5Ј Rp-phosphorothioate. 2Ј,5Ј Rp-and Sp-phosphorothioate oligoadenylates possess a sugar conformation similar to that of the corresponding native 2Ј,5Ј oligoadenylates.

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Conformational and stacking properties of 3′-5′ and 2′-5′ linked oligoribonucleotides studied by CD

Cited by 21 publications

References 44 publications

Solution structure of 2′,5′ d(G₄C₄)

Solution structure of 2′,5′ d(G₄C₄)

Chiral Selection in Oligoadenylate Formation in the Presence of a Metal ion Catalyst or Poly(U) Template

Conformational properties of 2′,5′ linked Rp‐ and Sp‐phosphorothioate oligoadenylates studied by circular dichroism and NMR

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Conformational and stacking properties of 3′-5′ and 2′-5′ linked oligoribonucleotides studied by CD

Cited by 21 publications

References 44 publications

Solution structure of 2′,5′ d(G4C4)

Solution structure of 2′,5′ d(G4C4)

Chiral Selection in Oligoadenylate Formation in the Presence of a Metal ion Catalyst or Poly(U) Template

Conformational properties of 2′,5′ linked Rp‐ and Sp‐phosphorothioate oligoadenylates studied by circular dichroism and NMR

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Solution structure of 2′,5′ d(G₄C₄)

Solution structure of 2′,5′ d(G₄C₄)