Sequence-specific recognition of double helical nucleic acids by proteins.

Seeman, Nadrian C.; Rosenberg, John M.; Rich, Alexander

doi:10.1073/pnas.73.3.804

Cited by 1,092 publications

(718 citation statements)

References 19 publications

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“…Several recent papers have tentatively proposed models for the recognition process involving protein interactions in the small groove of DNA?6a, 31 33 These models postulate structural complementary between protein backbones in an antiparallel B-sheet conformation folded around the small groove. Other models have been proposed [34][35][36] which consider the large groove as the site of interaction . The proposed recognition in either case can only occur between the base atoms exposed in the DNA groove and amino-acid side chains.…”

Section: Resultsmentioning

confidence: 99%

Form of DNA and the nature of interactions with proteins in chromatin

Goodwin¹,

Brahms²

1978

Nucl Acids Res

113

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Studies of native chromatins and of isolated nucleosomes (from calf thymus) show that the DNA is in the B form or modified B form. This was determined by Raman spectroscopy of chromatins, of nucleosomes (from calf thymus) and of DNA fibres and directly correlated with X-ray diffraction studies. The Raman spectra of three forms of DNA (A, B and C) have been characteri zed i n fi bres btt by X-ray di ffracti on and Raman spectroscopy on the same sample. In particular, the Raman spectrum of the C form of DNA is characterized by a band of about 870 cma1. For the first time,, chromatins of different origins with increasing content of non-histone proteins have been investigated by Raman spectroscopy. The site of interaction of the non-histone proteins appears to involve the N7 position of guanine while the histone core does not interact at this site. It is proposed that the mechanism of specific recognition in chromatin involves the large groove.

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Section: Resultsmentioning

confidence: 99%

Form of DNA and the nature of interactions with proteins in chromatin

Goodwin¹,

Brahms²

1978

Nucl Acids Res

113

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“…DdRps primarily interact with their respective templates via sequence-specific contacts (17). For example, the Escherichia coli RNA polymerase holoenzyme recognizes the identities of nucleotides at the Ϫ10 and Ϫ35 regions relative to the transcriptional start site (18).…”

Section: Discussionmentioning

confidence: 99%

Sequence-specific recognition of a subgenomic RNA promoter by a viral RNA polymerase

Siegel

Adkins

Kao

1997

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

109

129

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RNA templates of 33 nucleotides containing the brome mosaic virus (BMV) core subgenomic promoter were used to determine the promoter elements recognized by the BMV RNA-dependent RNA polymerase (RdRp) to initiate RNA synthesis. Nucleotides at positions ؊17, ؊14, ؊13, and ؊11 relative to the subgenomic initiation site must be maintained for interaction with the RdRp. Changes to every other nucleotide at these four positions allow predictions for the base-specific functional groups required for RdRp recognition. RdRp contact of the nucleotide at position ؊17 was suggested with a template competition assay. Comparison of the BMV subgenomic promoter to those from other plant and animal alphaviruses shows a remarkable degree of conservation of the nucleotides required for BMV subgenomic RNA synthesis. We show that the RdRp of the plant-infecting BMV is capable of accurately, albeit inefficiently, initiating RNA synthesis from the subgenomic promoter of the animalinfecting Semliki Forest virus. The sequence-specific recognition of RNA by the BMV RdRp is analogous to the recognition of DNA promoters by DNA-dependent RNA polymerases.Viral RNA replication, a process fundamental to pathogenicity, requires specific recognition of RNA features by proteins. RNA-dependent RNA polymerase (RdRp) is a complex composed of viral and cellular proteins that directs viral RNA synthesis from infecting RNA templates (1). Many viral RdRp proteins have been sequenced and analyzed (2); however, a comprehensive mechanism describing RNA synthesis is lacking. Consequently, general knowledge of RdRps is significantly less than that of other RNA and DNA polymerases.To investigate the mechanism of RNA-directed RNA synthesis, we study brome mosaic virus (BMV), type member of the bromovirus group of plant viruses in the alphavirus-like superfamily of (ϩ)-strand RNA viruses (3). The BMV genome is comprised of three RNAs designated 1, 2, and 3, and a subgenomic RNA4 which is initiated from (Ϫ)-strand RNA3. Enriched BMV RdRp preparations from infected barley can, in a highly specific manner, synthesize (Ϫ)-strand RNA from (ϩ)-strand templates and subgenomic (ϩ)-strand products from (Ϫ)-strand templates (4-6).We have developed a system to study BMV subgenomic RNA initiation from minimal templates, designated proscripts, because they contain the promoter and template for (ϩ)-strand RNA synthesis. We have shown that the 20 nt 3Ј of the subgenomic initiation nucleotide, recognized as the subgenomic core promoter (7,8), are sufficient to direct (ϩ)-strand RNA synthesis (6), permitting the design of proscripts focusing only on the core promoter.In this paper, we have used a functional assay to determine that nucleotides Ϫ17, Ϫ14, Ϫ13, and Ϫ11 relative to the subgenomic initiation site are required for RNA synthesis from the subgenomic core promoter. Moreover, at least one of these nucleotides, Ϫ17, was found likely to be contacted by the BMV RdRp. The resolution achieved in this study allows us to predict the base moieties contacted by RdRp and dem...

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“…As the differential free energy change for forming such a hydrogen bond may be small (as both groups may be hydrated in the free state), one contribution to specificity may be that in non-specific complexes many of the hydrogen bonds cannot be formed at all. The reason for concentrating on hydrogen bonding patterns derives from the considerations of Seeman et al (1976), who showed that discrimination of base pairs by hydrogen bonding is possible in the major groove. Fig.…”

Section: Beta Proteinsmentioning

confidence: 99%