Interstrand communication between 2′-N-(pyren-1-yl)methyl-2′-amino-LNA monomers in nucleic acid duplexes: directional control and signalling of full complementarity

Hrdlicka, Patrick J.; Babu, B. Ravindra; Sørensen, Mads D.; Wengel, Jesper

doi:10.1039/b404446k

Cited by 94 publications

(90 citation statements)

References 16 publications

(19 reference statements)

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“…These properties have in particular been reported for N-functionalized 2′-amino locked nucleic acids (2′-amino-LNA 26 and isomeric 2′-amino-α-L-LNA 27 (Fig. 1).…”

mentioning

confidence: 86%

“…oxygen, nucleobases), quantum yields of oligonucleotides become very high 26 . Direction of the fluorophore into the groove upon hybridization can also reduce fluorescence quenching 26,44 . The higher quantum yield of single stranded ON6+ON7 relative to ON5 might result from an interaction between the two perylene moieties in the latter case which quenches fluorescence.…”

Section: Synthesis Of Modified Phosphoramidite Reagentmentioning

confidence: 99%

“…Spectra were obtained in a medium salt phosphate buffer at 19°C using an excitation wavelength of 425 nm and 500 nM concentration of the probe a structure shielding the fluorophore from the quenchers (i.e. oxygen, nucleobases), quantum yields of oligonucleotides become very high 26 . Direction of the fluorophore into the groove upon hybridization can also reduce fluorescence quenching 26,44 .…”

Section: Synthesis Of Modified Phosphoramidite Reagentmentioning

confidence: 99%

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Fluorescent oligonucleotides containing a novel perylene 2′-amino-α-L-LNA monomer: Synthesis and analytical potential

Astakhova

Kumar

Wengel

2011

Collect. Czech. Chem. Commun.

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Dedicated to Professor Antonín Holý on the occasion of his 75th birthday in recognition of his outstanding contributions to the area of nucleic acid chemistry.Herein, a novel fluorescent nucleotide analogue, perylene-2′-amino-α-L-LNA, has been prepared and studied within synthetic oligonucleotides of different sequences. The phosphoramidite reagent was synthesized in 85% overall yield starting from 2′-amino-α-L-LNA nucleoside. Incorporation efficiency of the resulting perylene-2′-amino-α-L-LNA monomer (T*) into synthetic oligonucleotides was significantly improved by replacement of the typically used 1H-tetrazole activator with pyridine hydrochloride. Generally, oligonucleotides containing monomer T* showed high binding affinity towards complementary DNA and RNA targets, batochromically shifted excitation/emission wavelengths with respect to the often applied polyaromatic hydrocarbon pyrene, high fluorescent quantum yields and very low target detection limits (5-10 nM). Fluorescence of single stranded LNA/DNA mixmer oligonucleotide having two incorporations of monomers T* was quenched (quantum yield Φ F = 0.21) relative to duplexes of this probe with complementary DNA and RNA (Φ F = 0.42 and 0.35, respectively). On the contrary, a strong fluorescence quenching upon target binding was demonstrated by two short oligonucleotides of analogues sequences containing monomers T* at 5′-and 3′-terminal positions. We explain the hybridization-induced light-up effect observed for double-labeled probe by a reduction of fluorescence quenching due to precise positioning of the fluorophores within the double-stranded complexes. Furthermore, we propose that a covalent link between two T* monomers in the double-labeled probe provides a remarkable degree of rigidity in the double helix which enforces positioning of the bulky perylene moieties in the nonpolar groove resulting in reduced fluorescence quenching.

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“…These properties have in particular been reported for N-functionalized 2′-amino locked nucleic acids (2′-amino-LNA 26 and isomeric 2′-amino-α-L-LNA 27 (Fig. 1).…”

mentioning

confidence: 86%

Section: Synthesis Of Modified Phosphoramidite Reagentmentioning

confidence: 99%

Section: Synthesis Of Modified Phosphoramidite Reagentmentioning

confidence: 99%

See 1 more Smart Citation

Fluorescent oligonucleotides containing a novel perylene 2′-amino-α-L-LNA monomer: Synthesis and analytical potential

Astakhova

Kumar

Wengel

2011

Collect. Czech. Chem. Commun.

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“…Duplexes formed in the absence of metal ions between an ssLNA that contained a 2PA ligand and an ssDNA had a thermal stability higher than that of nonmodified duplexes (121). This effect is opposite to that observed for ligand-modified DNA duplexes, which are typically less stable than their nonmodified counterparts, but is similar to the effect previously observed for LNA.DNA duplexes containing N-functionalized 2 0 -aminoÀ ÀLNAs (138).…”

Section: [3þ1] Coordinationmentioning

confidence: 36%

Metal‐Containing Nucleic Acid Structures Based on Synergetic Hydrogen and Coordination Bonding

He¹,

Franzini²,

Achim³

2007

Progress in Inorganic Chemistry

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“…This has been successfully exploited for the helical organization of various classes of p conjugated chromophores, which can provide an efficient medium for the migration of excitation energy for the development of photoactive and functional nanomaterials. [6][7][8][9][10][11][12][13] Herein, we demonstrate how to use the DNA backbone for the combination of a donor and an acceptor in such a way that a white-light-emitting DNA is formed upon hybridization. We synthesized DNA1 bearing the blue-green emitter, ethynyl pyrene (400-600 nm) and DNA2 bearing the red emitter, ethynyl nile red (600-750 nm).…”

mentioning

confidence: 99%

White‐Light‐Emitting DNA (WED)

Varghese

Wagenknecht

2009

Chemistry A European J

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White-light-emitting organic molecules have received great attention for potential applications in full-colour light emitting diodes (LEDs) and lighting purposes.[1] A common and efficient approach to obtain these organic materials is based on the partial energy transfer (dET) between donors and suitable acceptors. The acceptor is either doped in the donor scaffold or covalently attached to the donor and the system simultaneously emits over the whole visible range (l = 400-750 nm). This approach has been successfully applied in polymers blended with luminescent dyes and other systems. [2,3] Moreover, white-light-emitting ensembles have been developed by making use of supramolecular recognition of specific non-covalent interactions encoded in the donor and acceptor molecules. [4,5] Notably, in all these cases, an efficient interaction and close proximity (Fçrster distance, < 10 nm) of the donor and acceptor are essential for the fluorescence resonance energy transfer (FRET).The characteristic structural features of DNA like its inherent double helical conformation and the typical stacking distance of % 3.4 between the bases offers a unique structural scaffold for the helical organization of covalently attached chromophores with very efficient electronic interactions between them. This has been successfully exploited for the helical organization of various classes of p conjugated chromophores, which can provide an efficient medium for the migration of excitation energy for the development of photoactive and functional nanomaterials. [6][7][8][9][10][11][12][13] Herein, we demonstrate how to use the DNA backbone for the combination of a donor and an acceptor in such a way that a white-light-emitting DNA is formed upon hybridization. We synthesized DNA1 bearing the blue-green emitter, ethynyl pyrene (400-600 nm) and DNA2 bearing the red emitter, ethynyl nile red (600-750 nm). Both chromophores were conjugated to the 5-position of 2'-deoxyuridine to maintain the canonical dU:A base pairing. In DNA3-6 both chromophores were combined as an energy donor-acceptor couple and placed adjacent to each other in order to obtain an efficient electronic interaction between them (Figure 1). The phosphoramidite of 5-(1-pyrenylethynyl)-2'-deoxyuridine was commercially available. The corresponding phosphoramidite of 2'-deoxyuridine modified with ethynyl nile red was synthesized by palladium catalysed Sonogashira coupling of ethynyl nile red (which was synthesized according to the methodology in a recent literature report) [14] and 5'-O-(4,4'-dimethoxytrityl)-5-iodo-2'-deoxyuridine followed by the phosphoramidite reaction under standard conditions.[15] Using both DNA building blocks, the modified oligonucleotides DNA1-6 were synthesized by [a]

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Interstrand communication between 2′-N-(pyren-1-yl)methyl-2′-amino-LNA monomers in nucleic acid duplexes: directional control and signalling of full complementarity

Abstract: Very efficient interstrand communication systems in nucleic acid duplexes, based on pyrene excimer formation between 2'-N-(pyren-1-yl)methyl-2'-amino-LNA monomers, demonstrate the versatility of functionalized 2'-amino-LNA monomers for Angstrom-scale chemical engineering.

Cited by 94 publications

References 16 publications

Fluorescent oligonucleotides containing a novel perylene 2′-amino-α-L-LNA monomer: Synthesis and analytical potential

Fluorescent oligonucleotides containing a novel perylene 2′-amino-α-L-LNA monomer: Synthesis and analytical potential

Metal‐Containing Nucleic Acid Structures Based on Synergetic Hydrogen and Coordination Bonding

White‐Light‐Emitting DNA (WED)

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