Metal‐Ion‐Mediated Base Pairs in Nucleic Acids

Müller, Jens

doi:10.1002/ejic.200800301

Cited by 159 publications

(77 citation statements)

References 140 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…One recently established method for the site-specific functionalization of nucleic acids with metal ions is based on the use of metal-mediated base pairs. [2][3][4][5] Such base pairs comprise natural or artificial nucleobases and rely on coordinative bonds to a central metal ion instead of (or in addition to) hydrogen bonds. Depending on the choice of nucleosides, metal ions, and oligonucleotide sequence, a plethora of metal-modified double helices can be generated.…”

mentioning

confidence: 99%

Solution structure of a DNA double helix with consecutive metal-mediated base pairs

et al. 2010

Self Cite

View full text Add to dashboard Cite

Metal-mediated base pairs represent a powerful tool for the site-specific functionlization of nucleic acids with metal ions. The development of applications of the metal-modified nucleic acids will depend on the availability of structural information on these double helices. We present here the NMR solution structure of a self-complementary DNA oligonucleotide with three consecutive imidazole nucleotides in its centre. In the absence of transition-metal ions, a hairpin structure is adopted with the artifical nucleotides forming the loop. In the presence of Ag(I) ions, a duplex comprising three imidazoleAg+-imidazole base pairs is formed. Direct proof for the formation of metal-mediated base pairs was obtained from (1) AbstractMetal-mediated base pairs represent a powerful tool for the site-specific functionalization of nucleic acids with metal ions. The development of applications of the metal-modified nucleic acids will depend on the availability of structural information on these double helices. We present here the NMR solution structure of a self-complementary DNA oligonucleotide with three consecutive imidazole nucleotides in its centre: In the absence of transition metal ions, a hairpin structure is adopted with the artificial nucleotides forming the loop. In the presence of silver(I) ions, a duplex comprising three imidazole-Ag + -imidazole base pairs is formed.Direct proof for the formation of metal-mediated base pairs was obtained from 1 J( 15 N, 107/109 Ag) couplings upon incorporation of 15 N-labelled imidazole. The duplex adopts a B-type conformation with only minor deviations in the region of the artificial base pairs. This structure represents the first example of a metal-modified nucleic acid with a continuous stretch of metal-mediated base pairs.3 Nucleic acids such as DNA are becoming increasingly popular as versatile building blocks in nanobiotechnology as a result of their superb, predictable self-assembling properties and the high rigidity of their double helices on the nanoscale. 1 Their applicability can be extended even further by the introduction of functional groups such as metal ions. One recently established method for the site-specific functionalization of nucleic acids with metal ions is based on the use of metal-mediated base pairs. 2-5 Such base pairs comprise natural or artificial nucleobases and rely on coordinative bonds to a central metal ion instead of (or in addition to) hydrogen bonds. Depending on the choice of nucleosides, metal ions, and oligonucleotide sequence, a plethora of metal-modified double helices can be generated. Even if focussing only on the use of artificial nucleosides, examples exist for DNA duplexes containing one or two metal-mediated base pairs interspersed between natural ones, 6-8 DNA double helices with continuous stretches of metalated base pairs, 9-11 and DNA duplexes with different metalmediated base pairs at pre-defined positions. 12 When including also metal-mediated base pairs from natural nucleosides, 13-15 even more combinations can ...

show abstract

mentioning

confidence: 99%

Solution structure of a DNA double helix with consecutive metal-mediated base pairs

et al. 2010

Self Cite

View full text Add to dashboard Cite

show abstract

“…Examples are Cu 2+ -hydroxypyridone base pairs [122] and salen metal base pairs (Cu 2+ , Mn 2+/3+ , Fe 3+ , Ni 2+ , and VO 2+ ) [123,124]. In a few cases artificial metal ion binding nucleotides have also been incorporated in polynucleotides with modified backbones like PNA (peptide nucleic acid; see also Chapter 12) and GNA (glycol nucleic acid) (see [125] and references therein). For a more detailed discussion on artificial base pairs we refer the reader to Chapters 10 and 11 of this volume and recent reviews by Müller and Clever and Shionoya [125,126].…”

Section: Metallated Nucleic Acids For Nanotechnologymentioning

confidence: 99%

Characterization of Metal Ion-Nucleic Acid Interactions in Solution

Pechlaner

Sigel

2011

Metal Ions in Life Sciences

View full text Add to dashboard Cite

Metal ions are inextricably involved with nucleic acids due to their polyanionic nature. In order to understand the structure and function of RNAs and DNAs, one needs to have detailed pictures on the structural, thermodynamic, and kinetic properties of metal ion interactions with these biomacromolecules. In this review we first compile the physicochemical properties of metal ions found and used in combination with nucleic acids in solution. The main part then describes the various methods developed over the past decades to investigate metal ion binding by nucleic acids in solution. This includes for example hydrolytic and radical cleavage experiments, mutational approaches, as well as kinetic isotope effects. In addition, spectroscopic techniques like EPR, lanthanide(III) luminescence, IR and Raman as well as various NMR methods are summarized. Aside from gaining knowledge about the thermodynamic properties on the metal ion-nucleic acid interactions, especially NMR can be used to extract information on the kinetics of ligand exchange rates of the metal ions applied. The final section deals with the influence of anions, buffers, and the solvent permittivity on the binding equilibria between metal ions and nucleic acids. Little is known on some of these aspects, but it is clear that these three factors have a large influence on the interaction between metal ions and nucleic acids.

show abstract

“…In addition to base-base interactions, base-sugar and base-phosphate interactions also contribute to the stability of nucleobase pairs in RNA ). Several of the base-pair interactions are also known to be mediated by water or ions (Brandl et al 2000;Müller 2008). …”

Section: Some General Observationsmentioning

confidence: 99%

On the role of Hoogsteen:Hoogsteen interactions in RNA: Ab initio investigations of structures and energies

Sharma

Chawla²,

Sharma³

et al. 2010

RNA

View full text Add to dashboard Cite

We use a combination of database analysis and quantum chemical studies to investigate the role of cis and trans Hoogsteen:Hoogsteen (H:H) base pairs and associated higher-order structures in RNA. We add three new examples to the list of previously identified base-pair combinations belonging to these families and, in addition to contextual classification and characterization of their structural and energetic features, we compare their interbase interaction energies and propensities toward participation in triplets and quartets. We find that some base pairs, which are nonplanar in their isolated minimum energy geometries, attain planarity and stability upon triplet formation. A:A H:H trans is the most frequent H:H combination in RNA structures. This base pair occurs at many distinct positions in known rRNA structures, where it helps in the interaction of ribosomal domains in the 50S subunit. It is also present as a part of tertiary interaction in tRNA structures. Although quantum chemical studies suggest an intrinsically nonplanar geometry for this base pair in isolated form, it has the tendency to attain planar geometry in RNA crystal structures by forming higher-order tertiary interactions or in the presence of additional basephosphate interactions. The tendency of this base pair to form such additional interactions may be helpful in bringing together different segments of RNA, thus making it suitable for the role of facilitator for RNA folding. This also explains the high occurrence frequency of this base pair among all H:H interactions.

show abstract

Metal‐Ion‐Mediated Base Pairs in Nucleic Acids

Cited by 159 publications

References 140 publications

Solution structure of a DNA double helix with consecutive metal-mediated base pairs

Solution structure of a DNA double helix with consecutive metal-mediated base pairs

Characterization of Metal Ion-Nucleic Acid Interactions in Solution

On the role of Hoogsteen:Hoogsteen interactions in RNA: Ab initio investigations of structures and energies

Contact Info

Product

Resources

About