Conformational Polymorphism of d(A-G)n and Related Oligonucleotide Sequences

Dolinnaya, Nina G.; Fresco, Jacques R.

doi:10.1016/s0079-6603(03)75009-0

Cited by 8 publications

(56 citation statements)

References 62 publications

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“…1 They are involved in biological processes 2,3 such as DNA recombination, which is very likely a consequence of their peculiar structural properties. 3,4 They are known to form triplexes consisting of either two purine and one pyrimidine strands 5 in the presence of metal ions or two pyrimidine and one purine strands appearing at acidic pH. 6 Apart from triplexes, the (GA) n strands have long been known to self-associate and generate cooperatively melting structures even in the absence of the complementary pyrimidine strand.…”

Section: Introductionmentioning

confidence: 99%

Towards a better understanding of the unusual conformations of the alternating guanine–adenine repeat strands of DNA

et al. 2006

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Alternating guanine–adenine strands of DNA are known to self‐associate into a parallel‐stranded homoduplex at neutral pH, fold into an ordered single‐stranded structure at acid pH, and adopt yet another ordered single‐stranded conformer in aqueous ethanol. The unusual conformers melt cooperatively and exhibit distinct circular dichroism spectra suggestive of a substantial conformational order, but their molecular structures are not known yet. Here, we have probed the molecular structures using guanine and adenine analogs lacking the N7 atom, and thus unable of Hoogsteen pairing, or those restrained in the less‐frequent syn glycosidic orientation. The studies showed that the syn glycosidic orientation of dA residues promoted the neutral homoduplex, whereas the syn orientation of dG was incompatible with the homoduplex. In addition, Hoogsteen pairing of dA seemed to be a crucial property of the homoduplex whereas dG did not pair in this way. The situation was the same in both single‐stranded conformers with the dG residues. On the other hand, the presence of N7 was important with dA but its syn geometry was not favorable. The present data can be used as restraints to model the unusual molecular structures of the alternating guanine–adenine strands of DNA. © 2006 Wiley Periodicals, Inc. Biopolymers 85: 19–27, 2007.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

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Section: Introductionmentioning

confidence: 99%

Towards a better understanding of the unusual conformations of the alternating guanine–adenine repeat strands of DNA

et al. 2006

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“…Whereas a pair of purines in the anti configuration about the glycosyl bond requires a glycosyl bond separation $2.4 Å longer than a complementary base pair, a pair with one base oriented syn and the other anti maintains the standard separation distance for a complementary pair, although there may be some distortion of the dihedral angles of the glycosyl bonds (Topal and Fresco 1976b;Patel et al 1984;Hunter et al 1986b;Dolinnaya et al 1997;Nissen et al 2001;Battle and Doudna 2002;Dolinnaya and Fresco 2003). The cost of forming such a base pair with a syn-oriented purine residue is hardly more than a kcal/mol (Topal and Fresco 1976b).…”

Section: Purineápurine Combinationsmentioning

confidence: 99%

Are stop codons recognized by base triplets in the large ribosomal RNA subunit?

Liang¹,

Landweber

Fresco

2005

RNA

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The precise mechanism of stop codon recognition in translation termination is still unclear. A previously published study by Ivanov and colleagues proposed a new model for stop codon recognition in which 3-nucleotide Ter-anticodons within the loops of hairpin helices 69 (domain IV) and 89 (domain V) in large ribosomal subunit (LSU) rRNA recognize stop codons to terminate protein translation in eubacteria and certain organelles. We evaluated this model by extensive bioinformatic analysis of stop codons and their putative corresponding Ter-anticodons across a much wider range of species, and found many cases for which it cannot explain the stop codon usage without requiring the involvement of one or more of the eight possible noncomplementary base pairs. Involvement of such base pairs may not be structurally or thermodynamically damaging to the model. However, if, according to the model, Ter-anticodon interaction with stop codons occurs within the ribosomal A-site, the structural stringency which that site imposes on sense codonÁtRNA anticodon interaction should also extend to stop codonÁTer-anticodon interactions. Moreover, with Ter-tRNA in place of an aminoacyl-tRNA, for each of the various Ter-anticodons there is a sense codon that can interact with it preferentially by complementary and wobble base-pairing. Both these considerations considerably weaken the arguments put forth previously.

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“…To find more about the primary structure specificity of these structures, we performed parallel comparative studies of related tetranucleotide repeats (GAGC) 5 , (GAGT) 5 , and (GACA) 5 . The general conclusion following from these comparative studies is that the primary structure specificity is fairly high, indicating that not only guanines but also adenines play a significant role in the stabilization of these unusual structures.…”

Section: Introductionmentioning

confidence: 99%

“…4 and 5). Our laboratory focused mainly on (GAGA) 5 and the related 20-mers. [6][7][8][9][10][11][12][13][14] In contrast to the early studies, these molecules were shown not to form guanine quadruplexes unless guanine dominates over adenine in the molecule, but instead these molecules were shown to generate various unusual conformers depending on the solution conditions.…”

mentioning

confidence: 99%

“…15 The homoduplex is parallel-stranded, in contrast to the Watson-Crick duplex, which is antiparallel. Second, at acid pH and low salt, (GAGA) 5 adopts an ordered single-stranded structure where adenine is protonated. [16][17][18][19][20] However, circular dichroism (CD) spectra indicate that this structure contains strong guanine-guanine stacking like in the homoduplex.…”

mentioning

confidence: 99%

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Conformations of DNA strands containing GAGT, GACA, or GAGC tetranucleotide repeats

Kypr¹,

Kejnovská²,

Vorlı́čková³

2007

Biopolymers

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The (GA)(n) microsatellite has been known from previous studies to adopt unusual, ordered, cooperatively melting secondary structures in neutral aqueous solutions containing physiological concentrations of salts, at acid pH values or in aqueous ethanol solutions. To find more about the primary structure specificity of these structures, we performed parallel comparative studies of related tetranucleotide repeats (GAGC)(5), (GAGT)(5), and (GACA)(5). The general conclusion following from these comparative studies is that the primary structure specificity is fairly high, indicating that not only guanines but also adenines play a significant role in the stabilization of these unusual structures. (GAGC)(5) is a hairpin or a duplex depending on DNA concentration. Neither acid pH nor ionic strength or the presence of ethanol changed the secondary structure of (GAGC)(5) in a significant way. (GACA)(5) forms a weakly stable hairpin in neutral aqueous solutions but forms a duplex at acid pH where cytosine is protonated. (GAGT)(5) behaves most similar to (GAGA)(5). Salt induces its hairpin to duplex transition at neutral pH and an isomerization into another, probably parallel stranded, duplex takes place at acid pH. (GAGT)(5) is the only of the three present 20-mers that responds to ethanol like (GAGA)(5).

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Conformational Polymorphism of d(A-G)n and Related Oligonucleotide Sequences

Cited by 8 publications

References 62 publications

Towards a better understanding of the unusual conformations of the alternating guanine–adenine repeat strands of DNA

Towards a better understanding of the unusual conformations of the alternating guanine–adenine repeat strands of DNA

Are stop codons recognized by base triplets in the large ribosomal RNA subunit?

Conformations of DNA strands containing GAGT, GACA, or GAGC tetranucleotide repeats

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