Ribooligonucleotides, r(C-G-C-G) analogs containing 8-substituted guanosine residues, form left-handed duplexes with Z-form-like structure

Uesugi, Seiichi; Ohkubo, Mitsuru; Urata, Hidehito; Ikehara, Morio; Kobayashi, Yuji; Kyōgoku, Yoshimasa

doi:10.1021/ja00324a047

Cited by 30 publications

(16 citation statements)

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“…All of these data and conclusions are consistent with similar results obtained for the DNA B-to-Z transition. Uesugi et al (17) have shown that the ribo-tetramer r(C-Br8G-C-Br8G) adopts a Z-like structure in low salt solution. They also noted that the unsubstituted tetramer rCpGpCpG was unable to adopt a Z-form.…”

Section: Resultsmentioning

confidence: 99%

The tetraribonucleotide_rC_pG_pC_pG forms a left-handed Z-RNA double-helix

Davis¹,

Hall²,

Cruz³

et al. 1986

Nucl Acids Res

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NMR and circular dichroism studies show that the RNA tetranucleotide rCpGpCpG can form a Z-RNA left-handed double-helix. In 1.0 M NaClO4, circular dichroism measurements indicate that the tetramer is in the A-form. In 6.0 M NaClO4, there is a characteristic change in the circular dichroism, indicating that the tetramer adopts a left-handed Z-form. This conformation is verified by phosphorus and proton NMR studies. The 31P spectrum shows a large downfield shift in one of the resonances upon an increase in salt concentration. Proton nuclear Overhauser effect (NOE) experiments indicate that the guanosines are in the syn conformation. These results are consistent with the formation of a Z-form double-helix.

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Section: Resultsmentioning

confidence: 99%

The tetraribonucleotide_rC_pG_pC_pG forms a left-handed Z-RNA double-helix

Davis¹,

Hall²,

Cruz³

et al. 1986

Nucl Acids Res

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“…with salt concentration. Experimentally, however, the transition has been achieved under different conditions, such as chemical modification of the bases ( 122 ); high pressure ( 30 ) or different salt conditions, such as 6.0-M NaClO 4 ( 29 ).…”

Section: Discussionmentioning

confidence: 99%

Ion distributions around left- and right-handed DNA and RNA duplexes: a comparative study

Pan

Roland

Sagui

2014

Nucleic Acids Research

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The ion atmosphere around nucleic acids is an integral part of their solvated structure. However, detailed aspects of the ionic distribution are difficult to probe experimentally, and comparative studies for different structures of the same sequence are almost non-existent. Here, we have used large-scale molecular dynamics simulations to perform a comparative study of the ion distribution around (5′-CGCGCGCGCGCG-3′)2 dodecamers in solution in B-DNA, A-RNA, Z-DNA and Z-RNA forms. The CG sequence is very sensitive to ionic strength and it allows the comparison with the rare but important left-handed forms. The ions investigated include Na+, K+ and Mg2 +, with various concentrations of their chloride salts. Our results quantitatively describe the characteristics of the ionic distributions for different structures at varying ionic strengths, tracing these differences to nucleic acid structure and ion type. Several binding pockets with rather long ion residence times are described, both for the monovalent ions and for the hexahydrated Mg[(H2O)6]2+ ion. The conformations of these binding pockets include direct binding through desolvated ion bridges in the GpC steps in B-DNA and A-RNA; direct binding to backbone oxygens; binding of Mg[(H2O)6]2+ to distant phosphates, resulting in acute bending of A-RNA; tight ‘ion traps’ in Z-RNA between C-O2 and the C-O2′ atoms in GpC steps; and others.

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“…Furthermore, bromination of guanosine has been used to reduce the conformational heterogeneity of RNA [105] and to probe the conformation about glycosidic bonds in unusual nucleic acid structures [106]. Indeed, the presence of a bulky substituent at the C8 position of guanosine could change the usual anti orientation of the base to the syn conformation, or could further stabilize the already existing syn glycosidic conformation [107]. This implication was investigated for a unimolecular antiparallel stranded quadruplex of sequence d(TTTGGTTTGGTTTGGTTTGG), in which the substitution at positions required to be anti, destabilizes the quadruplex [106].…”

Section: Modified Aptamersmentioning

confidence: 99%

Quadruplex-Forming Oligonucleotides as Tools in Anticancer Therapy and Aptamers Design: Energetic Aspects

Petraccone

Barone²,

Giancola³

2005

CMCACA

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Recent investigations on the G-quadruplex motif propose a new strategy for the making of antitumour drugs. Quadruplex-drug complexes have been suggested to inhibit telomerase activity; further, aptamers based on the quadruplex motif have been proved useful as tools aimed at binding and inhibiting particular proteins, thus serving as pharmaceutically active agents. However, the design of new aptamers is difficult because many factors affecting their activity and stability have not still been clarified. The knowledge of the energetics of quadruplex formation is a crucial point in view of their potential therapeutic utilization both as targets as well as therapeutic agents. In this review the energetic aspects of both quadruplex assembly and quadruplex-ligand interactions are discussed together with a summary of recent studies on physico-chemical properties in solution of quadruplex structures obtained from synthetic aptamers, including PNA-DNA chimeras.

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Ribooligonucleotides, r(C-G-C-G) analogs containing 8-substituted guanosine residues, form left-handed duplexes with Z-form-like structure

Cited by 30 publications

References 0 publications

The tetraribonucleotide_rC_pG_pC_pG forms a left-handed Z-RNA double-helix

The tetraribonucleotide_rC_pG_pC_pG forms a left-handed Z-RNA double-helix

Ion distributions around left- and right-handed DNA and RNA duplexes: a comparative study

Quadruplex-Forming Oligonucleotides as Tools in Anticancer Therapy and Aptamers Design: Energetic Aspects

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Ribooligonucleotides, r(C-G-C-G) analogs containing 8-substituted guanosine residues, form left-handed duplexes with Z-form-like structure

Cited by 30 publications

References 0 publications

The tetraribonucleotiderCpGpCpG forms a left-handed Z-RNA double-helix

The tetraribonucleotiderCpGpCpG forms a left-handed Z-RNA double-helix

Ion distributions around left- and right-handed DNA and RNA duplexes: a comparative study

Quadruplex-Forming Oligonucleotides as Tools in Anticancer Therapy and Aptamers Design: Energetic Aspects

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The tetraribonucleotide_rC_pG_pC_pG forms a left-handed Z-RNA double-helix

The tetraribonucleotide_rC_pG_pC_pG forms a left-handed Z-RNA double-helix