Hoogsteen-Based Parallel-Stranded Duplexes of DNA. Effect of 8-Amino-purine Derivatives

Cubero, Elena; Aviñó, Anna; Torre, Beatriz G. de la; Frieden, Miriam; Eritja, Ramón; Luque, F. Javier; González, Carlos; Orozco, Modesto

doi:10.1021/ja011928+

Cited by 39 publications

(53 citation statements)

References 75 publications

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“…At the 3′-end a thiol molecule was added for immobilization onto the gold sensor surface and, depending on the sequence type, it is further modified or not with three 8-aminoadenines (3 A ). They were prepared on an automatic Applied Biosystems 392 DNA synthesizer as described elsewhere (15,16,34,38,39). 5′-5′ Clamps were prepared in three steps.…”

Section: Methodsmentioning

confidence: 99%

Sensitive and label-free biosensing of RNA with predicted secondary structures by a triplex affinity capture method

Carrascosa

Gómez-Montes

Aviñó

et al. 2012

Nucleic Acids Research

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A novel biosensing approach for the label-free detection of nucleic acid sequences of short and large lengths has been implemented, with special emphasis on targeting RNA sequences with secondary structures. The approach is based on selecting 8-aminoadenine-modified parallel-stranded DNA tail-clamps as affinity bioreceptors. These receptors have the ability of creating a stable triplex-stranded helix at neutral pH upon hybridization with the nucleic acid target. A surface plasmon resonance biosensor has been used for the detection. With this strategy, we have detected short DNA sequences (32-mer) and purified RNA (103-mer) at the femtomol level in a few minutes in an easy and level-free way. This approach is particularly suitable for the detection of RNA molecules with predicted secondary structures, reaching a limit of detection of 50 fmol without any label or amplification steps. Our methodology has shown a marked enhancement for the detection (18% for short DNA and 54% for RNA), when compared with the conventional duplex approach, highlighting the large difficulty of the duplex approach to detect nucleic acid sequences, especially those exhibiting stable secondary structures. We believe that our strategy could be of great interest to the RNA field.

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Section: Methodsmentioning

confidence: 99%

Sensitive and label-free biosensing of RNA with predicted secondary structures by a triplex affinity capture method

Carrascosa

Gómez-Montes

Aviñó

et al. 2012

Nucleic Acids Research

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“…To date, the parallel structures have been mostly investigated by X-ray [156] [157], IR [158], and NMR [159] [160] techniques. Molecular-dynamics simulations showed that sequences containing a similar number of d(AÀT) and d(GÀC) pairs (which are non-isomorphous) arranged in a reverse WatsonÀCrick structure are unstable, while stable structures were found when Hoogsteen pairing was assumed [161]. For unmodified oligonucleotides, the thermal stability of parallel duplexes is significantly lower compared to antiparallel WatsonÀCrick duplexes.…”

Section: For Example the Duplex [All-(s P )-Ps]-da 12 /T 12 Is More mentioning

confidence: 99%

Phosphorothioate Nucleotides and Oligonucleotides – Recent Progress in Synthesis and Application

Guga

Koziołkiewicz

2011

Chemistry & Biodiversity

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We dedicate this work to Prof. Fritz Eckstein (MPI, Gçttingen) and Prof. Wojciech J. Stec (CMMS PAS, Łó dź ), who invented the phosphorothioate modification of nucleic acids, envisioned its many important applications, carefully elucidated its biochemical and stereochemical aspects, and fostered PS-Oligos over decades. We are very grateful to have had the honor and pleasure to develop our understanding of PS-Oligos through guidance by their papers and lectures, and through stimulating scientific discussions with these two great scientists.

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“…8-Aminoadenine [20] and 8-aminoguanine [21] stabilize parallel duplexes [22] and triplexes as well as antiparallel triplexes [23]. 8-Aminoadenine may stabilize parallel duplexes and triplexes because the amino group is positioned to form an extra hydrogen bond with the keto group of the Hoogsteen thymidine (Scheme 1).…”

Section: Introductionmentioning

confidence: 99%

Structural Properties of G,T‐Parallel Duplexes

Aviñó

Cubero

Gargallo

et al. 2010

Journal of Nucleic Acids

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The structure of G,T-parallel-stranded duplexes of DNA carrying similar amounts of adenine and guanine residues is studied by means of molecular dynamics (MD) simulations and UV- and CD spectroscopies. In addition the impact of the substitution of adenine by 8-aminoadenine and guanine by 8-aminoguanine is analyzed. The presence of 8-aminoadenine and 8-aminoguanine stabilizes the parallel duplex structure. Binding of these oligonucleotides to their target polypyrimidine sequences to form the corresponding G,T-parallel triplex was not observed. Instead, when unmodified parallel-stranded duplexes were mixed with their polypyrimidine target, an interstrand Watson-Crick duplex was formed. As predicted by theoretical calculations parallel-stranded duplexes carrying 8-aminopurines did not bind to their target. The preference for the parallel-duplex over the Watson-Crick antiparallel duplex is attributed to the strong stabilization of the parallel duplex produced by the 8-aminopurines. Theoretical studies show that the isomorphism of the triads is crucial for the stability of the parallel triplex.

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Hoogsteen-Based Parallel-Stranded Duplexes of DNA. Effect of 8-Amino-purine Derivatives

Cited by 39 publications

References 75 publications

Sensitive and label-free biosensing of RNA with predicted secondary structures by a triplex affinity capture method

Sensitive and label-free biosensing of RNA with predicted secondary structures by a triplex affinity capture method

Phosphorothioate Nucleotides and Oligonucleotides – Recent Progress in Synthesis and Application

Structural Properties of G,T‐Parallel Duplexes

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