<i>Hoogsteen</i>‐Duplex DNA: Synthesis and base pairing of oligonucleotides containing 1‐deaza‐2′‐deoxyadenosine

Seela, Frank; Wenzel, Thomas J.

doi:10.1002/hlca.19940770604

Cited by 23 publications

(19 citation statements)

References 43 publications

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“…However, different base-pairing properties have previously been reported in the absence of Ag + . Whereas 1-deazaadenine forms stable Hoogsteen-type duplexes in the absence of Ag + , [16] 1,3-dideazaadenine does not do so despite an identical sequence. [17] It was therefore highly interesting to study 1,3-dideazaadenine in the context of metal-mediated base pairs and to investigate whether the different base-pairing properties would also be manifested in the presence of Ag + .…”

Section: Introductionmentioning

confidence: 88%

Contiguous Metal‐Mediated Base Pairs Comprising Two Ag^IIons

Megger

Guerra

Hoffmann

et al. 2011

Chemistry A European J

107

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The incorporation of transition-metal ions into nucleic acids by using metal-mediated base pairs has proved to be a promising strategy for the site-specific functionalization of these biomolecules. We report herein the formation of Ag(+)-mediated Hoogsteen-type base pairs comprising 1,3-dideaza-2'-deoxyadenosine and thymidine. By defunctionalizing the Watson-Crick edge of adenine, the formation of regular base pairs is prohibited. The additional substitution of the N3 nitrogen atom of adenine by a methine moiety increases the basicity of the exocyclic amino group. Hence, 1,3-dideazaadenine and thymine are able to incorporate two Ag(+) ions into their Hoogsteen-type base pair (as compared with one Ag(+) ion in base pairs with 1-deazaadenine and thymine). We show by using a combination of experimental techniques (UV and circular dichroism (CD) spectroscopies, dynamic light scattering, and mass spectrometry) that this type of base pair is compatible with different sequence contexts and can be used contiguously in DNA double helices. The most stable duplexes were observed when using a sequence containing alternating purine and pyrimidine nucleosides. Dispersion-corrected density functional theory calculations have been performed to provide insight into the structure, formation and stabilization of the twofold metalated base pair. They revealed that the metal ions within a base pair are separated by an Ag···Ag distance of about 2.88 Å. The Ag-Ag interaction contributes some 16 kcal mol(-1) to the overall stability of the doubly metal-mediated base pair, with the dominant contribution to the Ag-Ag bonding resulting from a donor-acceptor interaction between silver 4d-type and 4s orbitals. These Hoogsteen-type base pairs enable a higher functionalization of nucleic acids with metal ions than previously reported metal-mediated base pairs, thereby increasing the potential of DNA-based nanotechnology.

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Section: Introductionmentioning

confidence: 88%

Contiguous Metal‐Mediated Base Pairs Comprising Two Ag^IIons

Megger

Guerra

Hoffmann

et al. 2011

Chemistry A European J

107

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“…1‐Deazaadenine ( 1D A) represents a slightly modified natural nucleobase. Compared with adenine, the N1 position is replaced by a CH group, hence Watson–Crick pairing is not possible between 1D A and T. Instead, a duplex comprising 1D A:T Hoogsteen‐type base pairs is formed in the absence of metal ions 27. As known from other metal‐mediated base pairs, the substitution of the thymine imino proton by a metal ion leads to a metal‐mediated base pair, too (Scheme ).…”

Section: Metal‐mediated Base Pairs With Natural Nucleosides and Theirmentioning

confidence: 99%

Nucleic Acids With Metal‐Mediated Base Pairs and Their Applications

2012

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Metal‐mediated base pairs represent an elegant way for the site‐specific functionalisation of nucleic acids. In this type of base pair, the hydrogen bonds between complementary nucleobases are replaced formally by coordinative bonds to one or more transition‐metal ions. This Review presents an overview of metal‐mediated base pairs reported so far. It gives an insight into the characterisation of metal‐mediated base pairs and into the structures of the resulting metal‐modified nucleic acids. In addition, a summary of applications exploiting the formation of metal‐mediated base pairs is presented. The applications include, for example, metal‐ion sensors of various types, a protein sensor, and DNA‐based molecular machines. Initial reports on the potential use of metal‐mediated base pairs in the context of charge transfer through nucleic acid double helices are summarised as well.

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“…The incorporation of the synthesized 1-deaza-2Ј-deoxyadenosine was checked by HPLC analysis of the nucleoside composition after enzymatic hydrolysis of the oligomers. [20,21] The duplex oligonucleotides (2 µ) were incubated at 37°C for 165 minutes. Aliquots were withdrawn at regular time intervals and analyzed by polyacrylamide gel electrophoresis under denaturing conditions.…”

Section: Resultsmentioning

confidence: 99%

The Human Telomeric Sequence (T₂AG₃)_n is Efficiently Cross‐Linked by AN1 Binding to the Platinum of a trans‐Pt(NH₃)₂ Chelate of an Antisense Oligo‐2′‐O‐Methylribonucleotide

et al. 2003

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In order to irreversibly cross‐link an antisense oligonucleotide to the human telomeric sequence (T2AG3)n, the inter‐strand bridging rearrangement described by Leng et al. was investigated on (21‐mer antisense) (20‐mer target) duplexes: (G*NG*)(TA) ⇄ (G*NG)(TA*), G*NG* being a trans‐[Pt(NH3)2{1,3‐(GNG)‐N7‐G,N7‐G}] chelate with N = U or T. Three different duplexes were studied, confirming first that for a DNA target strand the rearrangement was faster with a platinated oligo‐2′‐O‐methylribonucleotide than with a deoxy oligonucleotide as antisense strand. Second, a telomeric DNA target strand was cross‐linked faster than an all‐purine oligonucleotide containing a single TA doublet. Accordingly, the half time of formation of the cross‐linked hybrid duplex [2′‐OMe‐r(CCCUAACCCG*UGACCCUAACCC)]·[d(T2AG3)2(TTA*G3)(T2AG3)] is one minute, compared with the nine days required for the complete formation of the bridged d(CTCCTG*TGTCTC)·d(GAGATA*AGGAG) duplex. The NMR analysis of the latter showed that the platinum cross‐link involves the A*N1 moiety as ligand. The timescale difference between the two reactions raised the question of an eventual kinetic cross‐link which might isomerize to the final one observed. This question was addressed using 1‐deazaadenine in the TA doublet of the three target strands of this work. No cross‐linking reaction was observed, proving that AN1 is the bridging atom in all the cases studied so far. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003)

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Hoogsteen‐Duplex DNA: Synthesis and base pairing of oligonucleotides containing 1‐deaza‐2′‐deoxyadenosine

Cited by 23 publications

References 43 publications

Contiguous Metal‐Mediated Base Pairs Comprising Two Ag^IIons

Contiguous Metal‐Mediated Base Pairs Comprising Two Ag^IIons

Nucleic Acids With Metal‐Mediated Base Pairs and Their Applications

The Human Telomeric Sequence (T₂AG₃)_n is Efficiently Cross‐Linked by AN1 Binding to the Platinum of a trans‐Pt(NH₃)₂ Chelate of an Antisense Oligo‐2′‐O‐Methylribonucleotide

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Hoogsteen‐Duplex DNA: Synthesis and base pairing of oligonucleotides containing 1‐deaza‐2′‐deoxyadenosine

Cited by 23 publications

References 43 publications

Contiguous Metal‐Mediated Base Pairs Comprising Two AgIIons

Contiguous Metal‐Mediated Base Pairs Comprising Two AgIIons

Nucleic Acids With Metal‐Mediated Base Pairs and Their Applications

The Human Telomeric Sequence (T2AG3)n is Efficiently Cross‐Linked by AN1 Binding to the Platinum of a trans‐Pt(NH3)2 Chelate of an Antisense Oligo‐2′‐O‐Methylribonucleotide

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Contiguous Metal‐Mediated Base Pairs Comprising Two Ag^IIons

Contiguous Metal‐Mediated Base Pairs Comprising Two Ag^IIons

The Human Telomeric Sequence (T₂AG₃)_n is Efficiently Cross‐Linked by AN1 Binding to the Platinum of a trans‐Pt(NH₃)₂ Chelate of an Antisense Oligo‐2′‐O‐Methylribonucleotide