A Highly Fluorescent DNA Base Analogue that Forms Watson−Crick Base Pairs with Guanine

Wilhelmsson, Marcus; Holmén, and Anders; Lincoln, Per; Nielson, P. E.; Nordén, Bengt

doi:10.1021/ja0025797

Cited by 108 publications

(104 citation statements)

References 15 publications

Supporting

Mentioning

102

Contrasting

Unclassified

Order By: Relevance

“…Notably, Matteucci's examples of phenothiazine and phenoxazine derviatives 41 which were later described as highly emissive and environmentally insensitive fluorophores useful for fluorescence resonance energy transfer (FRET) based studies. 42,43 Saito's group has reported fluorescently responsive cytidine analogs based on the pyridopyrimidine scaffold which can discriminate between the different environments presented by an opposing nucleoside in the context of hybridized oligonucleotides and has potential use in single-nucleotide polymorphism detection. 44,45 A structurally related example has been reported by Sekine for which geometrically locking a 4-N-carbamoyldeoxycytidine transformed the nonfluorescent precursor into a fluorescent analog that experienced quenching when paired to guanosine, but not adenosine, in the context of oligomers.…”

Section: Fluorescence Propertiesmentioning

confidence: 99%

Synthesis and spectral characterization of environmentally responsive fluorescent deoxycytidine analogs

Elmehriki

Suchý

Chicas

et al. 2014

Artificial DNA: PNA & XNA

View full text Add to dashboard Cite

Section: Fluorescence Propertiesmentioning

confidence: 99%

Synthesis and spectral characterization of environmentally responsive fluorescent deoxycytidine analogs

Elmehriki

Suchý

Chicas

et al. 2014

Artificial DNA: PNA & XNA

View full text Add to dashboard Cite

“…33 Thus, the less polar environment that comes as a result of incorporating tC into oligonucleotides, or when changing from water to less polar solvents, affects the fluorescence quantum yield in different ways. Instead we suggest that hydrogen bonding to tC might play an important role in lowering the quantum yield.…”

Section: Absorptive and Emissive Properties At Neutral Phmentioning

confidence: 99%

“…We have shown that, the fluorescence quantum yield of tC is high (20%) and essentially the same whether incorporated into a PNA single strand (22%) or a PNA-DNA-duplex (21%). 33 Like the fluorescent base analogues mentioned Figure 1. Structure of G-tC base pair on the left, tC nucleoside on the right, and derivatives of tC used in the measurements in the middle (R = H, CH 3 , and K in 1,3-diaza-2-oxophenothiazin-3-yl acetic acid (AtC), its methyl ester (MtC), and its potassium salt (KtC), respectively).…”

Section: Introductionmentioning

confidence: 97%

“…33 Previously it had been shown that this tricyclic cytosine analogue discriminates well between G and A targets 34 and also increases the base stacking, thus increasing the melting temperature of DNA-RNA-, 34 DNA-peptide nucleic acid (PNA)-, 35 and PNA-PNA-duplexes 35 . We have shown that, the fluorescence quantum yield of tC is high (20%) and essentially the same whether incorporated into a PNA single strand (22%) or a PNA-DNA-duplex (21%).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Photophysical Characterization of Fluorescent DNA Base Analogue, tC

et al. 2003

Self Cite

View full text Add to dashboard Cite

The neutral, base-pairing form of tC, having a fluorescence quantum yield of 0.2, is found to be the totally predominant species in a wide pH interval, 4-12. We show that the absorption band of tC at lowest energy, centred at 26700 cm -1 and well separated from the nucleobase absorption, is due to a single electronic transition polarized approximately at 35 from the long-axis of the molecule. The 2-deoxyribonucleoside of 1,3-diaza-2-oxophenothiazine, synthesized for further incorporation into DNA was found to display a fluorescence quantum yield nearly the same as in the form of tC that was incorporated into PNA, confirming the notion of the tC nucleoside being a probe with very promising fluorescence properties essentially invariant of environment, also upon incorporation into a DNA strand and upon hybridization.2

show abstract

“…It specifically Watson-Crick base-pairs with thymine or uracil and has proven its utility as a probe to monitor local conformational changes in nucleic acid structure, for example, in catalytic RNA and upon formation of nucleic acid-protein complexes (Millar 1996;O'Neill and Barton 2002;Walter et al 2002;Patel and Bandwar 2003;Roy 2003;Bradrick and Marino 2004;Clerte and Hall 2004). Several fluorescent pyrimidine analogs also have been developed, although they have not yet reached a similar level of popularity (Inoue et al 1985;Wu et al 1990;Godde et al 1998;Wilhelmsson et al 2001).…”

Section: Introductionmentioning

confidence: 99%

Pyrrolo-C as a fluorescent probe for monitoring RNA secondary structure formation

Tinsley¹,

Walter²

2006

RNA

View full text Add to dashboard Cite

Pyrrolo-C (PC), or 3-[b-D-2-ribofuranosyl]-6-methylpyrrolo [2,3-d]pyrimidin-2(3H)-one, is a fluorescent analog of the nucleoside cytidine that retains its Watson-Crick base-pairing capacity with G. Due to its red-shifted absorbance, it can be selectively excited in the presence of natural nucleosides, making it a potential site-specific probe for RNA structure and dynamics. Similar to 2-aminopurine nucleoside, which base-pairs with uridine (or thymidine), PC's fluorescence becomes reversibly quenched upon base-pairing, most likely due to stacking interactions with neighboring bases. To test its utility as an RNA probe, we examined PC's fluorescent properties over a wide range of ionic strengths, pH, organic cosolvents, and temperatures. Incorporation of PC into a single-stranded RNA results in an $60% reduction of fluorescence intensity, while duplex formation reduces the fluorescence by $75% relative to the free ribonucleoside. We find that the fluorescence intensity of PC is only moderately affected by ionic strength, pH, and temperature, while it is slightly enhanced by organic cosolvents, making it a versatile probe for a broad range of buffer conditions. We demonstrate two applications for PC: fluorescent measurements of the kinetics of formation and dissociation of an RNA/DNA complex, and fluorescent monitoring of the thermal denaturation of the central segment of an RNA duplex. Taken together, our data showcase the potential of pyrrolo-C as an effective fluorescent probe to study RNA structure, dynamics, and function, complementary to the popular 2-aminopurine ribonucleoside.

show abstract

A Highly Fluorescent DNA Base Analogue that Forms Watson−Crick Base Pairs with Guanine

Cited by 108 publications

References 15 publications

Synthesis and spectral characterization of environmentally responsive fluorescent deoxycytidine analogs

Synthesis and spectral characterization of environmentally responsive fluorescent deoxycytidine analogs

Photophysical Characterization of Fluorescent DNA Base Analogue, tC

Pyrrolo-C as a fluorescent probe for monitoring RNA secondary structure formation

Contact Info

Product

Resources

About