Ein stabiler DNA-Duplex mit einem nichtwasserstoffverbrückenden, nichtformkomplementären Basenpaar: Interstrang-Stapelwechselwirkungen als stabilitätsbestimmender Faktor

Brotschi, Christine; Häberli, Adrian; Leumann, Christian J.

doi:10.1002/1521-3757(20010817)113:16<3101::aid-ange3101>3.0.co;2-y

Cited by 40 publications

(29 citation statements)

References 31 publications

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“…[30] More recently, the effects of the number and position of fluorine atoms within fluorinated DNA bases on duplex stability were evaluated in the "dangling end" motif. [33][34][35] The model is supported by the results of molecular dynamics simulations and by preliminary 1 H NMR data. For a duplex containing an internal aromatic, hydrophobic pair, duplex stability is always higher for fluorinated base surrogates than for the parent nonfluorinated analogues.…”

Section: Introductionmentioning

confidence: 65%

“…Although a high resolution structure of this zipper motif has not yet been characterized, experimental evidence for it has been obtained from the results of molecular modeling, [33] 1 H NMR analysis, and from T m and CD data in various sequence contexts. [35] Therefore, the data described in this paper are relevant to the discussion of the general contribution of energy to stacking in an aqueous environment, and in particular, to fluorinated versus nonfluorinated aromatic hydrocarbons.…”

Section: Discussionmentioning

confidence: 99%

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Pentafluorophenyl–Phenyl Interactions in Biphenyl‐DNA

Zahn

Brotschi

Leumann

2005

Chemistry A European J

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102

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We prepared and investigated oligonucleotide duplexes of the sequence d(GATGAC(X)nGCTAG).d(CTAGC(Y)nGTCATC), in which X and Y designate biphenyl- (bph) and pentafluorobiphenyl- ((5F)bph) C-nucleotides, respectively, and n varies from 0-4. These hydrophobic base substitutes are expected to adopt a zipperlike, interstrand stacking motif, in which not only bph/bph or (5F)bph/(5F)bph homo pairs, but also (5F)bph/bph mixed pairs can be formed. By performing UV-melting curve analysis we found that incorporation of a single (5F)bph/(5F)bph pair leads to a duplex that is essentially as stable as the unmodified duplex (n=0), and 2.4 K more stable than the duplex with the nonfluorinated bph/bph pair. The T(m) of the mixed bph/(5F)bph pair was in between the T(m) values of the respective homo pairs. Additional, unnatural aromatic pairs increased the T(m) by +3.0-4.4 K/couple, irrespective of the nature of the aromatic residue. A thermodynamic analysis using isothermal titration calorimetry (ITC) of a series of duplexes with n=3 revealed lower (less negative) duplex formation enthalpies (DeltaH) in the (5F)bph/(5F)bph case than in the bph/bph case, and confirmed the higher thermodynamic stability (DeltaG) of the fluorinated duplex, suggesting it to be of entropic origin. Our data are compatible with a model in which the stacking of (5F)bph versus bph is dominated by dehydration of the aromatic units upon duplex formation. They do not support a model in which van der Waals dispersive forces (induced dipoles) or electrostatic (quadrupole) interactions play a dominant role.

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Section: Introductionmentioning

confidence: 65%

Section: Discussionmentioning

confidence: 99%

Pentafluorophenyl–Phenyl Interactions in Biphenyl‐DNA

Zahn

Brotschi

Leumann

2005

Chemistry A European J

Self Cite

102

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“…One of the first examples of an artificial nucleoside comprising two coordination sites was based on the 2,2′‐bipyridine moiety (Scheme ). However, whereas the (metal‐free) Bipy:Bipy base pair shows a stability similar to that of the G:C base pair, it does not form stable metal‐mediated base pairs, as only a decrease in thermal stability has been reported 44. 45 It is assumed that the direct attachment of the Bipy ligand to the sugar moiety does not provide enough structural flexibility to allow the formation of a metal‐mediated base pair.…”

Section: Metal‐mediated Base Pairs With Artificial Nucleosidesmentioning

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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“…[26][27][28] A recent NMR structure confirmed the interstrand stacking motif for a system with one biphenyl pair. [29] In addition we could show that the remote biphenyl rings can be equipped with acceptor or donor substituents without alteration of the overall duplex architecture.…”

Section: Introductionmentioning

confidence: 99%

2‐Phenanthrenyl–DNA: Synthesis, Pairing, and Fluorescence Properties

Grigorenko

Leumann

2008

Chemistry A European J

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Three 2′‐phenanthrenyl‐C‐deoxyribonucleosides with donor (phenNH2), acceptor (phenNO2), or no (phenH) substitution on the phenanthrenyl core were synthesized and incorporated into oligodeoxyribonucleotides. Duplexes containing either one or three consecutive phenR residues, which were located opposite each other, were formed. Within these residues, the phenR residues are expected to recognize each other through interstrand stacking interactions, in much the same way as described previously for biphenyl DNA. The thermal, thermodynamic, and fluorescence properties of such duplexes were determined by UV melting analysis and fluorescence spectroscopy. Depending on the nature of the substituent, the thermal stability of single‐modified duplexes can vary between −2.7 to +11.3 °C in Tm and that of triple‐modified duplexes from +7.8 to +11.1 °C. Van′t Hoff analysis suggested that the observed higher thermodynamic stability in phenH‐ and phenNO2‐containing duplexes is of enthalpic origin. A single phenH or phenNO2 residue in a bulge position also stabilizes a corresponding duplex. If a phenNO2 residue is placed in a bulge position next to a base mismatch this can lead, in a sequence‐dependent manner, to duplex destabilization. The phenNO2 residue was found to be a highly efficient (10–100‐fold) quencher of phenH and phenNH2 fluorescence if placed in the opposite position to the fluorophores. When phenH and phenNH2 residues were placed opposite each other, efficient quenching of phenH and enhancement of phenNH2 fluorescence was found, which is an indicator for electron‐ or energy‐transfer processes between the aromatic units.

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Ein stabiler DNA-Duplex mit einem nichtwasserstoffverbrückenden, nichtformkomplementären Basenpaar: Interstrang-Stapelwechselwirkungen als stabilitätsbestimmender Faktor

Cited by 40 publications

References 31 publications

Pentafluorophenyl–Phenyl Interactions in Biphenyl‐DNA

Pentafluorophenyl–Phenyl Interactions in Biphenyl‐DNA

Nucleic Acids With Metal‐Mediated Base Pairs and Their Applications

2‐Phenanthrenyl–DNA: Synthesis, Pairing, and Fluorescence Properties

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