On the Effect of Covalently Appended Quinolones on Termini of DNA Duplexes

Tuma, Jennifer; Connors, William H.; Stitelman, D.H.; Richert, Clemens

doi:10.1021/ja0125117

Cited by 80 publications

(91 citation statements)

References 44 publications

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“…Nevertheless, optimized cap ogOA does feature a phosphodiester linker, a five-membered ring, and amide linkages, much like the composite T*OA cap identified for DNA:DNA duplexes, in which T* stands for a 5'-amino-5'-deoxythymidine residue with an amide link to oxolinic acid (OA). [40] Our results emphasize the importance of the linker. Although the strong propensity of quinolones to stack on nucleobases appears to be a driving force, unless the linker allows it to do so without disrupting weak base pairs (and contributes some binding affinity itself), no increase in sequence selectivity is imposed upon hybridization probes.…”

Section: Discussionsupporting

confidence: 51%

“…[40] UV melting experiments: Melting curve experiments used sodium phosphate buffer (10 mm) at pH 7 with NaCl concentrations of 150 mm or 1 m and strand concentrations of 1.0 mm for duplexes of 1 and 2 or 1.5 mm (each strand) for duplexes of 15-18. For each sample, at least four curves from 5 to 80 8C were measured at a heating or cooling rate of 1 8C min À1 .…”

Section: Methodsmentioning

confidence: 99%

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A 5′‐Cap for DNA Probes Binding RNA Target Strands

Egetenmeyer

Richert

2011

Chemistry A European J

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Detecting short RNA strands with high fidelity at any of the bases of their sequence, including the termini, can be challenging, since fraying, wobbling, and refolding all compete with canonical base pairing. We performed a search for 5'-substituents of oligodeoxynucleotides that increase base pairing fidelity at the terminus of duplexes with RNA target strands. From a total of over 70 caps, differing in stacking moiety and linker, a phosphodiester-linked sequence of the residues of L-prolinol, glycine, and oxolinic acid, dubbed ogOA, was identified as a 5'-cap that stabilizes any of the four canonical base pairs, with ΔT(m) values of up to +13.1 °C for an octamer. At the same time, the cap increases discrimination against any of the 12 possible terminal mismatches, including mismatches that are more stable than their perfectly matched counterparts in the control duplex, such as A:A. A probe with the cap also showed increased selectivity in the detection of two closely related microRNAs, let7c and let7a, with a ΔT(m) value of 9.2 °C. Melting curves also yielded thermodynamic data that shed light on the uniformity of molecular recognition in the sequence space of DNA:DNA and DNA:RNA duplexes. Hybridization probes with fidelity-enhancing caps should find applications in the individual and parallel detection of biologically active RNA species.

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Section: Discussionsupporting

confidence: 51%

Section: Methodsmentioning

confidence: 99%

A 5′‐Cap for DNA Probes Binding RNA Target Strands

Egetenmeyer

Richert

2011

Chemistry A European J

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“…It has also been shown that by appropriately attaching multiring fused systems [4-desmethylwyosine (39), quinolones (38), phenazinium (51,52), pyrene and phenanthrene (42), phenylurea and naphthylurea (41), cholic acid (53, 54) and a 5′-acylamido FIGURE 2: Definition of the distances used to calculate the hydrogen bond screening value. The schematic view of the X-Y plane of a G-C closing basepair (black) and a G dangling end (blue) shows the distances 1a, 1b, 2a, 2b, 3a, and 3c used to define the extent of screening.…”

Section: Resultsmentioning

confidence: 99%

A Uniform Mechanism Correlating Dangling-End Stabilization and Stacking Geometry

Isaksson

Chattopadhyaya

2005

Biochemistry

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The geometry of the dangling base in 105 published structures (from X-ray/NMR) containing single-stranded overhangs has been analyzed and correlated to the thermodynamic stabilization found (UV) for the corresponding dangling base/closing basepair combination in short oligonucleotides. The study considers most combinations of closing basepairs, sequence and dangling base residue type, attached in both the 3′-and 5′-ends of both DNA and RNA. Linear regression analysis showed a straightforward correlation (R ) 0.873) between the degree of screening for the hydrogen bonds of the closing basepair provided by the dangling base and the resulting thermodynamic stabilization in both DNA and RNA series with dangling ends either at the 3′-or at the 5′-terminus. Regression analysis of only the datasets from RNA gives an improved correlation, R ) 0.934, showing that dangling ends on RNA are more ordered than the dangling ends on DNA, R ) 0.376. This study highlights the gain in the free energy of stabilization owing to the favorable stacking between the dangling nucleobase and the neighboring basepair and the resulting strengthening of the hydrogen bond of the closing basepair. By acting as a hydrophobic cap on the terminal of the DNA or RNA duplex, the dangling-end residue restricts the bulk water access to the terminal basepair, thereby providing it with a microenvironment devoid of water, which consequently enhances its thermodynamic stability, making it energetically comparable to the corresponding internal basepair. Thus, one single structural model consisting of the interplay of the above electrostatic interactions can be used to explain the molecular basis of the observed thermodynamic effects for dangling-end attachment to the 3′-and 5′-ends of both DNA and RNA duplexes, which is a key step toward accurate dangling-end effect prediction.Unpaired terminal nucleotides naturally occur in various biologically important RNA structures: The acceptor stem in tRNA (1-3) has a characteristic 3′-NCCA nucleobase overhang that determines its structure, stability, and function. The dangling ends neighboring the codon-anticodon pair have also been found to stabilize the interaction between tRNA and mRNA (4, 5) for protein synthesis in the ribosomal machinery. The efficiency of down regulation of gene expression by RNA interference (RNAi) has been shown to be dependent on a two to three nucleotide overhang (6-9). Similarly, the structures of pseudoknots (10) are stabilized by a complicated interplay between single-stranded and double-stranded motifs. A multitude of literature on the stabilizing interactions of native single-stranded oligonucleotides is available (9,(11)(12)(13)(14).Accurate prediction of nucleic acid secondary structure and stability from its primary sequence is a key interest for probe binding optimization in biotechnological applications such as microarrays (15) and molecular beacons (16). To develop an accurate algorithm (14,(17)(18)(19)(20)(21)(22)(23)(24) for predicting the thermodynamics of hybridi...

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“…The "wobble hypothesis" [4] has helped to explain the degeneracy of the genetic code, but does not allow for more than qualitative predictions outside the ribosome, and the fidelity of base pairing, particularly at the termini, remains difficult-to-predict. [5] Ligands that enhance stability and base-pairing fidelity at the termini when covalently attached to one of the duplex-forming strands have been identified, but the structural diversity among these ligands, ranging from steroids [6] to aromatic systems like quinolones, [7,8] and stilbenes, [9,10] has made it difficult to draw general conclusions.…”

Section: Introductionmentioning

confidence: 99%

Pyrenylmethyldeoxyadenosine: A 3′‐Cap for Universal DNA Hybridization Probes

Printz

Richert

2009

Chemistry A European J

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A ligand that stabilizes a three-dimensional structure can be expected to have a positive effect on the specificity with which this structure is formed. Here we report on a ligand covalently linked to an oligonucleotide that increases duplex stability, but decreases base-pairing selectivity at the terminus. The ligand consists of a dangling 2'-deoxyadenosine residue with a pyrenylmethyl substituent at the N6-position, that is, a deoxynucleoside with a covalently linked polycyclic aromatic hydrocarbon (PAH). In the presence of the pyrene-bearing nucleosides the UV melting point (DeltaT(m)) of duplexes increases by up to 29.1 degrees C. The modified residue lowers the base-pairing fidelity at the terminal and penultimate position of duplexes with a depression in DeltaDeltaT(m) observable in 20 out of 24 sequence contexts tested. The effect can be rationalized based on a modeled three-dimensional structure. The results are significant for the understanding of base-pairing fidelity in DNA duplexes as modulated by the presence of a polycyclic aromatic hydrocarbon. The fidelity-decreasing effect may be useful for universal hybridization probes that bind to a broader range of sequences than conventional oligonucleotides.

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On the Effect of Covalently Appended Quinolones on Termini of DNA Duplexes

Cited by 80 publications

References 44 publications

A 5′‐Cap for DNA Probes Binding RNA Target Strands

A 5′‐Cap for DNA Probes Binding RNA Target Strands

A Uniform Mechanism Correlating Dangling-End Stabilization and Stacking Geometry

Pyrenylmethyldeoxyadenosine: A 3′‐Cap for Universal DNA Hybridization Probes

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