A Janus-Wedge DNA Triplex with A-W<sub>1</sub>-T and G-W<sub>2</sub>-C Base Triplets

Han, Caixia; Meena, .; McLaughlin, Larry W.

doi:10.1021/ja804607v

Cited by 48 publications

(39 citation statements)

References 14 publications

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“…Using this information, ligand 1 was designed with a well-known acridine DNA intercalator and a triaminotriazine unit to recognize T-T (U-U) through Janus-wedge (12,13) hydrogen bonding (Fig. 1).…”

Section: Resultsmentioning

confidence: 99%

A simple ligand that selectively targets CUG trinucleotide repeats and inhibits MBNL protein binding

Arambula

Ramisetty

Baranger

et al. 2009

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

207

246

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Section: Resultsmentioning

confidence: 99%

A simple ligand that selectively targets CUG trinucleotide repeats and inhibits MBNL protein binding

Arambula

Ramisetty

Baranger

et al. 2009

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

207

246

View full text Add to dashboard Cite

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“…To maintain the triplex structures during the simulation, N3 of cytosine in the third strand was protonated. For this analysis, the grooves of a pyrimidine motif triplex are defined as the major part of the major groove (ma-major groove), the minor part of the major groove (mi-major groove) and the minor groove (Figure 7) (10). Snapshots of Ts1 after 20-ns MD simulations in the absence and presence of choline ions are shown in Figure 8a and b, respectively.…”

Section: Dna Stability In Ilsmentioning

confidence: 99%

Structure, stability and behaviour of nucleic acids in ionic liquids

Tateishi‐Karimata

2014

Nucleic Acids Res

116

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Nucleic acids have become a powerful tool in nanotechnology because of their conformational polymorphism. However, lack of a medium in which nucleic acid structures exhibit long-term stability has been a bottleneck. Ionic liquids (ILs) are potential solvents in the nanotechnology field. Hydrated ILs, such as choline dihydrogen phosphate (choline dhp) and deep eutectic solvent (DES) prepared from choline chloride and urea, are ‘green’ solvents that ensure long-term stability of biomolecules. An understanding of the behaviour of nucleic acids in hydrated ILs is necessary for developing DNA materials. We here review current knowledge about the structures and stabilities of nucleic acids in choline dhp and DES. Interestingly, in choline dhp, A–T base pairs are more stable than G–C base pairs, the reverse of the situation in buffered NaCl solution. Moreover, DNA triplex formation is markedly stabilized in hydrated ILs compared with aqueous solution. In choline dhp, the stability of Hoogsteen base pairs is comparable to that of Watson–Crick base pairs. Moreover, the parallel form of the G-quadruplex is stabilized in DES compared with aqueous solution. The behaviours of various DNA molecules in ILs detailed here should be useful for designing oligonucleotides for the development of nanomaterials and nanodevices.

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“…For example, in a triple helix, a third strand, called triplex-forming oligonucleotide, binds with sequence specificity to A*T and G*C Hoogsteen base pairs (the asterisk indicates the Hoogsteen base pair) in the major groove of a Watson–Crick base-paired DNA duplex11121314. Although previous studies have hypothesized that Hoogsteen base pairs and triplex structures play an important role in transcription, replication and other cellular processes, Hoogsteen base pairs and triplexes are not considered common structures815.…”

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confidence: 99%

Comparable Stability of Hoogsteen and Watson–Crick Base Pairs in Ionic Liquid Choline Dihydrogen Phosphate

Tateishi‐Karimata

Nakano

Sugimoto

2014

Sci Rep

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The instability of Hoogsteen base pairs relative to Watson–Crick base pairs has limited biological applications of triplex-forming oligonucleotides. Hydrated ionic liquids (ILs) provide favourable environments for a wide range of chemical reactions and are known to impact the stabilities of Watson–Crick base pairs. We found that DNA triplex formation was significantly stabilized in hydrated choline dihydrogen phosphate as compared with an aqueous buffer at neutral pH. Interestingly, the stability of Hoogsteen base pairs was found to be comparable with that of Watson–Crick base pairs in the hydrated IL. Molecular dynamics simulations of a DNA triplex in the presence of choline ions revealed that the DNA triplex was stabilized because of the binding of choline ion around the third strand in the grooves. Our finding will facilitate the development of new DNA materials. Our data also indicate that triplex formation may be stabilized inside cells where choline ions and their derivatives are abundant in vivo.

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A Janus-Wedge DNA Triplex with A-W₁-T and G-W₂-C Base Triplets

Cited by 48 publications

References 14 publications

A simple ligand that selectively targets CUG trinucleotide repeats and inhibits MBNL protein binding

A simple ligand that selectively targets CUG trinucleotide repeats and inhibits MBNL protein binding

Structure, stability and behaviour of nucleic acids in ionic liquids

Comparable Stability of Hoogsteen and Watson–Crick Base Pairs in Ionic Liquid Choline Dihydrogen Phosphate

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A Janus-Wedge DNA Triplex with A-W1-T and G-W2-C Base Triplets

Cited by 48 publications

References 14 publications

A simple ligand that selectively targets CUG trinucleotide repeats and inhibits MBNL protein binding

A simple ligand that selectively targets CUG trinucleotide repeats and inhibits MBNL protein binding

Structure, stability and behaviour of nucleic acids in ionic liquids

Comparable Stability of Hoogsteen and Watson–Crick Base Pairs in Ionic Liquid Choline Dihydrogen Phosphate

Contact Info

Product

Resources

About

A Janus-Wedge DNA Triplex with A-W₁-T and G-W₂-C Base Triplets