Effects of the O2' hydroxyl group on Z-DNA conformation: structure of Z-RNA and (araC)-[Z-DNA]

Teng, M.; Liaw, Yen-Chywan; Marel, Gijs A. van der; Boom, Jacques H. van; Wang, A. H.-J.

doi:10.1021/bi00438a001

Cited by 49 publications

(58 citation statements)

References 20 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The latter finding contradicts the results of earlier computational simulations that suggested a preference for the C2′-endo pucker by arabinose (22). Although the above experimental data are consistent with similar conformational tendencies by FANA and ANA, the conformation of ANA was demonstrated to vary significantly depending on the geometry of the parent duplex (23)(24)(25)(26)(27)(28)(29).…”

contrasting

confidence: 72%

2‘-Fluoroarabino- and Arabinonucleic Acid Show Different Conformations, Resulting in Deviating RNA Affinities and Processing of Their Heteroduplexes with RNA by RNase H^,

Sarkhel

Wilds

et al. 2006

Biochemistry

View full text Add to dashboard Cite

2′-Deoxy-2′-fluoro-arabinonucleic acid (FANA) and arabinonucleic acid (ANA) paired to RNA are substrates of RNase H. The conformation of the natural DNA/RNA hybrid substrates appears to be neither A-form nor B-form. Consistent with this, the conformations of FANA and ANA were found to be intermediate between the A-and B-forms. However, FANA opposite RNA is preferred by RNase H over ANA, and the RNA affinity of FANA considerably exceeds that of ANA. By investigating the conformational boundaries of FANA and ANA residues in crystal structures of A-and B-form DNA duplexes at atomic resolution, we demonstrate that FANA and ANA display subtle conformational differences. The structural data provide insight into the structural requirements at the catalytic site of RNase H. They also allow conclusions with regard to the relative importance of stereoelectronic effects and hydration as modulators of RNA affinity.

show abstract

contrasting

confidence: 72%

2‘-Fluoroarabino- and Arabinonucleic Acid Show Different Conformations, Resulting in Deviating RNA Affinities and Processing of Their Heteroduplexes with RNA by RNase H^,

Sarkhel

Wilds

et al. 2006

Biochemistry

View full text Add to dashboard Cite

show abstract

“…One RNA-DNA hybrid crystal structure determined to date is left-handed and of Z-type, 95 while the remainder are all right-handed. This hybrid consists of alternating purine and pyrimidine bases 97 These structures adopt a B-form structure with two distamycin A molecules lying within the minor groove of the B-form duplex (see below for a further discussion of these two structures).…”

Section: Rna-dna Hybrid Structuresmentioning

confidence: 99%

Crystal structures of nucleic acids and their drug complexes

Neidle¹,

Nunn²

1998

Nat. Prod. Rep.

View full text Add to dashboard Cite

“…Although the low-energy forms of right-handed duplexes of B-DNA and A-RNA are structurally very different, they adopt similar left-handed Z-conformations (14)(15)(16). The Z-DNA conformation, favored by alternating purines and pyrimidines, is stabilized in vitro by high concentrations of salt and other agents that screen repulsion between electronegative phosphate residues, which are closer together in the Z-conformation (17, 18).…”

mentioning

confidence: 99%

The Zα domain of the editing enzyme dsRNA adenosine deaminase binds left-handed Z-RNA as well as Z-DNA

Brown

Lowenhaupt

Wilbert

et al. 2000

Proc. Natl. Acad. Sci. U.S.A.

117

123

View full text Add to dashboard Cite

The Z␣ domain of human double-stranded RNA adenosine deaminase 1 binds specifically to left-handed Z-DNA and stabilizes the Z-conformation. Here we report spectroscopic and analytical results that demonstrate that Z␣ can also stabilize the left-handed Z-conformation in double-stranded RNA. Z␣ induces a slow transition from the right-handed A-conformation to the Z-form in duplex r(CG) 6, with an activation energy of 38 kcal mol ؊1 . We conclude that Z-RNA as well as Z-DNA can be accommodated in the tailored binding site of Z␣. The specific binding of Z-RNA by Z␣ may be involved in targeting double-stranded RNA adenosine deaminase 1 for a role in hypermutation of RNA viruses. D ouble-stranded RNA (dsRNA) adenosine deaminase (ADAR1) is an enzyme that modifies the genetic message by deaminating adenosine in pre-mRNAs; the resulting inosine acts like guanosine in translation. ADAR1 requires a dsRNA substrate, which often is provided by the pairing of exons with introns (1); therefore, editing must take place before the removal of introns from pre-mRNAs. In addition to a deaminase domain and three dsRNA binding domains, ADAR1 contains a Z-DNA binding domain, Zab, at its N terminus (2, 3). The Z␣ subdomain of Zab has been isolated and binds left-handed Z-DNA with a low nanomolar dissociation constant (4, 5). Recently, Z␣ has been crystallized with a segment of left-handed Z-DNA, and the resulting structure reveals the tailored fitting of the Z␣ domain to a number of specific geometrical and electrostatic features of the left-handed nucleic acid conformation (6). Z-DNA is stabilized in vivo by negative supercoiling of DNA, which occurs upstream of a moving RNA polymerase (7). This stabilization by supercoiling has given rise to the suggestion that the Z-DNA binding domain of ADAR1 may target the enzyme to actively transcribing genes, thereby ensuring that editing can precede splicing (8).When an RNA virus such as measles infects a cell, the antiviral interferon response leads to increased activity of interferoninducible genes, including the ADAR1 gene, which is strongly up-regulated and produces the full-length protein, including the Z␣ domain (9). In addition, the distribution of ADAR1 changes from primarily nuclear localization to both nuclear and cytoplasmic localization. The measles virus replicates in the cytoplasm (as do most RNA viruses), and late in infection it has been observed that the viral RNA has been subjected to hypermutation in which a significant fraction of adenines have been changed to guanines, and uracil residues to cytosines (10). Such mutations are the expected result of the action of ADAR1 on the viral RNA replication system and may be an attempt on the part of the host cell to disable the virus. Hypermutation similar to that found in the measles virus has also been found in the RNA of vesicular stomatitis virus, respiratory syncytial virus, and parainfluenza virus 3 (11, 12).RNA viruses generally use a double-stranded intermediate during some period of their life cycle (13). Little is known abo...

show abstract

Effects of the O2' hydroxyl group on Z-DNA conformation: structure of Z-RNA and (araC)-[Z-DNA]

Cited by 49 publications

References 20 publications

2‘-Fluoroarabino- and Arabinonucleic Acid Show Different Conformations, Resulting in Deviating RNA Affinities and Processing of Their Heteroduplexes with RNA by RNase H^,

2‘-Fluoroarabino- and Arabinonucleic Acid Show Different Conformations, Resulting in Deviating RNA Affinities and Processing of Their Heteroduplexes with RNA by RNase H^,

Crystal structures of nucleic acids and their drug complexes

The Zα domain of the editing enzyme dsRNA adenosine deaminase binds left-handed Z-RNA as well as Z-DNA

Contact Info

Product

Resources

About

Effects of the O2' hydroxyl group on Z-DNA conformation: structure of Z-RNA and (araC)-[Z-DNA]

Cited by 49 publications

References 20 publications

2‘-Fluoroarabino- and Arabinonucleic Acid Show Different Conformations, Resulting in Deviating RNA Affinities and Processing of Their Heteroduplexes with RNA by RNase H,

2‘-Fluoroarabino- and Arabinonucleic Acid Show Different Conformations, Resulting in Deviating RNA Affinities and Processing of Their Heteroduplexes with RNA by RNase H,

Crystal structures of nucleic acids and their drug complexes

The Zα domain of the editing enzyme dsRNA adenosine deaminase binds left-handed Z-RNA as well as Z-DNA

Contact Info

Product

Resources

About

2‘-Fluoroarabino- and Arabinonucleic Acid Show Different Conformations, Resulting in Deviating RNA Affinities and Processing of Their Heteroduplexes with RNA by RNase H^,

2‘-Fluoroarabino- and Arabinonucleic Acid Show Different Conformations, Resulting in Deviating RNA Affinities and Processing of Their Heteroduplexes with RNA by RNase H^,