Modulation of Pyrene Fluorescence in DNA Probes Depends upon the Nature of the Conformationally Restricted Nucleotide

Abstract

The DNA probes (ODNs) containing a 2'-N-(pyren-1-yl)-group on the conformationally locked nucleosides [2'-N-(pyren-1-yl)carbonyl-azetidine thymidine, Aze-pyr (X), and 2'-N-(pyren-1-yl)carbonyl-aza-ENA thymidine, Aza-ENA-pyr (Y)], show that they can bind to complementary RNA more strongly than to the DNA. The Aze-pyr (X) containing ODNs with the complementary DNA and RNA duplexes showed an increase in the fluorescence intensity (measured at lambda em approximately 376 nm) depending upon the nearest neighbor at the 3'-end to X [dA ( approximately 12-20-fold) > dG ( approximately 9-20-fold) > dT ( approximately 2.5-20-fold) > dC ( approximately 6-13-fold)]. They give high fluorescence quantum yields (Phi F = 0.13-0.89) as compared to those of the single-stranded ODNs. The Aza-ENA-pyr (Y)-modified ODNs, on the other hand, showed an enhancement of the fluorescence intensity only with the complementary DNA (1.4-3.9-fold, Phi F = 0.16-0.47); a very small increase in fluorescence is also observed with the complementary RNA (1.1-1.7-fold, Phi F = 0.17-0.22), depending both upon the site of the Y modification introduced as well as on the chemical nature of the nucleobase adjacent to the modification site into the ODN. The fluorescence properties, thermal denaturation experiments, absorption, and circular dichroism (CD) studies with the X- and Y-modified ODNs in the form of matched homo- and heteroduplexes consistently suggested (i) that the orientation of the pyrene moiety is outside the helix of the nucleic acid duplexes containing a dT-d/rA base pair at the 3'-end of the modification site for both X and Y types of modifications, and (ii) that the microenvironment around the pyrene moiety in the ODN/DNA and ODN/RNA duplexes is dictated by the chemical nature of the conformational constraint in the sugar moiety, as well as by the nature of neighboring nucleobases. The pyrene fluorescence emission in both X and Y types of the conformationally restricted nucleotides is found to be sensitive to a mismatched base present in the target RNA: (i) The X-modified ODN showed a decrease ( approximately 37-fold) in the fluorescence intensity (measured at lambda em approximately 376 nm) upon duplex formation with RNA containing a G nucleobase mismatch (dT-rG pair instead of dT-rA) opposite to the modification site. (ii) In contrast, the Y-modified ODN in the heteroduplex resulted in a approximately 3-fold increase in the fluorescence intensity upon dT-rG mismatch, instead of matched dT-rA pair, in the RNA strand. Our data corroborate that the pyrene moiety is intercalated in the X-modified mismatched ODN/RNA (G mismatch) heteroduplex as compared to that of the Y-modified ODN/RNA (G mismatch) heteroduplex, in which it is located outside the helix.

2‐(1‐Ethynylpyrene)‐Adenosine as a Folding Probe for RNA—Pyrene in or out

“…They have proven useful in the context of recognition and as molecular probes, [6][7][8][9][10][11][12][13] electron injection, [14,15] bioengineering, [16,17] structure stabilisation [18] and structure determination [19][20][21][22][23] as well as nucleobase photophysics. [24,25] Their relatively high quantum efficiency, sensitivity to environmental factors [26,27] and capability to form excimers have opened many possibilities in the field of DNA and RNA hybridisation studies.…”

Electrosynthesis of blue-light-emitting oligo(1-bromopyrene) with favorable solubility

“…For OBrP, the absence of the proton chemical shift at 8.38 and 8.14 ppm (Fig. 5B) indicated that BrP mainly electropolymerized through the coupling at C (3) , C (6) , and C (8) of the BrP. Although the spectrum of OBrP cannot provide distinct and lucid information about the structure of the oligomer, it confirmed the occurrence of the electrochemical polymerization among the monomers.…”

“…For more information on the structure of polymers and the polymerization mechanism, we calculated the atomic electron-density population ( Table 1) and proportion of the frontier orbitals (Scheme 2) of the BrP monomers using the B3LYP/6-31G(d,p) level of Gaussian 03 software. In Table 1, the results of the main atomic electron-density populations revealed negative electric charges at the C (3) , C (4) , C (5) , C (6) , C (8) , C (9) , and C (10) positions in aromatic biphenyl, which implied that these atoms may donate electrons during electrochemical polymerization through radical cation intermediates. But the C (3) , C (6) , and C (8) positions have the more negative electric charges than C (4) , C (5) , C (9) , and C (10) positions.…”

“…Oztekin et al used glucose oxidase and poly-1,10-phenanthroline (PPMH) gained via electrochemical deposition to get the PPMH-modified GC electrode [3]. A pyrene label covalently attached to the sugar part of nucleosides has been used for the detection of nucleic acid hybridization [4][5][6][7][8][9]. Moreover, pyrene is a blue-emitting chromophore and has been proposed as a fluorescent temperature indicator.…”

Highly Efficient Multi-Functional Material for Organic Light-Emitting Diodes; Hole Transporting Material, Blue and White Light Emitter

“…2 Recently, pyrene has been used in various fields involving photo-catalysts, 3 semiconductors, 4 charge-transfer, 5 crystals, 6 carbon nanotubes, 7 DNA probes, 8 and dendrimers. 9 In particular, blue fluorescent emitters based on pyrene units have attracted considerable attention for organic light-emitting diodes (OLEDs), owing to the advantages of pyrene.…”