Alternating d(G-A) sequences form a parallel-stranded DNA homoduplex.

Rippe, Karsten; Fritsch, Valérie; Westhof, Éric; Jovin, Thomas M.

doi:10.1002/j.1460-2075.1992.tb05463.x

Cited by 153 publications

(187 citation statements)

References 47 publications

(47 reference statements)

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“…I-') and at 240 nm ( A c = -5 M-' cm-I) suggest that this oligonucleotide assumes a secondary structure. Its CD profile is consistent with that reported for the duplex made by two parallel strands of (GA),, in S mM Mg" whose AE,,,, = 10 M-' cm-' and = 5 M-' cm-' (Rippe et al, 1992). Heating 20AG to 50°C produced a progressive reduction of the intensity of these two ellipticities as a result of duplex denaturation.…”

Section: Resultssupporting

confidence: 86%

“…For instance, telomeric DNA characterised by sequences containing a variety of regular motifs of the type d(TTAGGG),, d(TTGGGG),, d(TTTTGGGG), has been shown to form Gquartet structures (Guschlbauer et al, 1990;Williamson, 1993). Moreover, sequences containing alternating GA repeats can form parallel duplexes stabilized by G:G and A:A base pairs (Rippe et al, 1992). Taking these data into consideration.…”

Section: Discussionmentioning

confidence: 99%

“…G duplex structures (Williamson et al, 1989;Sen and Gilbert, 1990;Laughlan et al, 1994;Henderson et al, 1987). In addition, alternating (GA), sequences have been reported to form parallel and antiparallel duplexes (Rippe et al, 1992;Evertsz et a]., 1994). Aggregation by G-rich oligonucleotides has in some cases been observed also in non-telomeric G-rich sequences (Olivas and Maher, 1995;Cheng and van Dyke, 1993;Milligan et al, 1993;Noonberg et al, 1995).…”

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confidence: 99%

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Guanine‐Rich Oligonucleotides Targeted to a Critical R · Y Site Located in the Ki‐ras Promoter

Alunni-Fabbroni

Manzini

Quadrifoglio

et al. 1996

European Journal of Biochemistry

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The promoter of the murine JS-rus proto-oncogene contains a (C+G)-rich homopurine . homopyrimidine (R . Y) sequence that is essential for transcription activity. We have designed two G-rich oligonucleotides, d(TGGGTGGGTGGTTGGGTGGG) (20GT) and d(AGGGAGGGAGGAAGGGAGGG) (20AG), that have the potential to bind the critical Ki-rus sequence via tripIex-helix formation. Band-shift experiments have shown that 20GT binds the Ki-rus R . Y duplex with a AG value of -40 -t 5 kJ/mol, while 20AG appeared to have a lower affinity under the experimental conditions adopted: 50 mM Tris/HCI, pH 7.4, 50 inM NaC1, 5 mM MgCl,, 25°C. In the absence of Mg2+, 20GT did not bind to the Ki-rus R . Y target, while 20AG exhibited the same affinity observed in the magnesium-containing buffer. To gain insight into the solution properties of 20GT and 20AG, we have performed several experiments including polyacrylamide gel electrophoresis (PAGE), hydroxyapatite chromatography, ultraviolet absorption melting and circular dichroism (CD). We found that 20AG rapidly self-associates into presumably a duplex, even at low concentration (< 1 pM), while 20GT forms aggregates slowly, a process favoured by high oligonucleotide concentrations (> 25 pM). The critical Ki-rus sequence was inserted in Bluescript KS+, downstream from the T7 promoter, to investigate to what extent 20AG and 20GT, which are directed against the R . Y target, are able to inhibit T7 RNA polymerase transcription, under nearphysiological conditions. Transcription experiments conducted in vitro at pH 7.4 have shown that oligonucleotide 20GT produced a remarkable repression of T7 RNA polymerase activity in the concentration range (10-25 pM), whereas 20AG had little effect on transcription. In conclusion, the results of this work together with other data reported in the literature

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Section: Resultssupporting

confidence: 86%

Section: Discussionmentioning

confidence: 99%

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confidence: 99%

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Guanine‐Rich Oligonucleotides Targeted to a Critical R · Y Site Located in the Ki‐ras Promoter

Alunni-Fabbroni

Manzini

Quadrifoglio

et al. 1996

European Journal of Biochemistry

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“…33,34 At physiological salt concentrations at neutral pH, (GA) n generates a homoduplex that is parallel-stranded. 12 However, our data are incompatible with syn glycosidic orientation of the guanine residues, which makes a model containing G(syn)ÁG(syn) base pairs 12 improbable as a correct solution of the (GA) n homoduplex structure. We rather prefer G(anti) residues to be present in the (GA) n homoduplex.…”

Section: Discussionmentioning

confidence: 70%

“…7,8 In the presence of Zn 2+ ions they form hairpins 9 and antiparallel duplexes, 10,11 which probably are the constituent arrangements of the neutral triplex structure. 10 More interestingly, the (GA) n strands associate into parallelstranded homoduplexes at physiological conditions 12 and fold into an ordered single-stranded structure at acid pH values. [13][14][15][16] In addition, an ordered single-stranded structure is also stable at neutral pH in the presence of ethanol, 17 dimethyl sulphoxide, 18 and other organic solvents 18 where adenine is not protonated.…”

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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Parallel-stranded duplex DNA containing dA · dU base pairs

Förtsch¹,

Fritzsche²,

Birch-Hirschfeld³

et al. 1998

Biopolymers

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DNA oligonucleotides with dA and dU residues can form duplexes with trans d(A · U) base pairing and the sugar‐phosphate backbone in a parallel‐stranded orientation, as previously established for oligonucleotides with d(A · T) base pairs. The properties of such parallel‐stranded DNA (ps‐DNA) 25‐mer duplexes have been characterized by absorption (uv), CD, ir, and fluorescence spectroscopy, as well as by nuclease sensitivity. Comparisons were made with duplex molecules containing (a) dT in both strands, (b) dU in one strand and dT in the second, and (c) the same base combinations in reference antiparallel‐stranded (aps) structures. Thermodynamic analysis revealed that total replacement of deoxythymine by deoxyuridine was accompanied by destabilization of the ps‐helix (reduction in Tm by −13°C in 2 mM MgGl2, 10 mM Na‐cacodylate). The U‐containing ps‐helix (U1 · U2) also melted 14°C lower than the corresponding aps‐helix under the same ionic conditions; this difference was very close to that observed between ps and aps duplexes with d(A · T) base pairs. Force field minimized structures of the various ps and aps duplexes with either d(A · T) or d(A · U) base pairs ps/aps and dT/dU combinations are presented. The energy‐minimized helical parameters did not differ significantly between the DNAs containing dT and dU. © 1996 John Wiley & Sons, Inc.

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Alternating d(G-A) sequences form a parallel-stranded DNA homoduplex.

Cited by 153 publications

References 47 publications

Guanine‐Rich Oligonucleotides Targeted to a Critical R · Y Site Located in the Ki‐ras Promoter

Guanine‐Rich Oligonucleotides Targeted to a Critical R · Y Site Located in the Ki‐ras Promoter

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

Parallel-stranded duplex DNA containing dA · dU base pairs

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