An indole-linked C8-deoxyguanosine nucleoside acts as a fluorescent reporter of Watson–Crick versus Hoogsteen base pairing

Schlitt, Katherine M.; Millen, Andrea L.; Wetmore, Stacey D.; Manderville, Richard A.

doi:10.1039/c0ob00883d

Cited by 19 publications

(45 citation statements)

References 52 publications

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“…In contrast, the indole-linked derivative (IndG) extends the Hoogsteen H-bonding face by an H-bonding donor, and exhibits emission at 395 nm ( Φ fl = 0.78 in H 2 O, λ ex = 321 nm) that is sensitive to WC (quenched emission) versus Hoogsteen H-bonding (enhanced emission intensity). 75 The para -substituted phenolic nucleoside (pPhOHG) exhibits pH-sensitive fluorescent properties. 76 The neutral adduct displays emission at 390 nm ( Φ fl = 0.47 in H 2 O) that is quenched upon phenolate formation (p K a ∼ 8.9).…”

Section: Nucleoside Synthesis Structure and Propertiesmentioning

confidence: 99%

C-Linked 8-aryl guanine nucleobase adducts: biological outcomes and utility as fluorescent probes

Manderville

Wetmore

2016

Chem. Sci.

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Section: Nucleoside Synthesis Structure and Propertiesmentioning

confidence: 99%

C-Linked 8-aryl guanine nucleobase adducts: biological outcomes and utility as fluorescent probes

Manderville

Wetmore

2016

Chem. Sci.

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“…[21][22][23][24] In addition to backbone alterations, nucleobase moieties have been modified, [25][26][27] which has led to the synthesis and subsequent incorporation of modified nucleotides into DNA helices. [28][29][30][31] Unlike natural nucleobases, many of the altered bases are fluorescent, [31][32][33][34][35][36][37][38] and therefore have promising applications in the study of nucleic acid structure 39 and dynamics, [39][40][41] as well as interactions between nucleic acids and proteins. 42 Of particular interest is base expansion, which has been attempted using several different ring spacers.…”

Section: Introductionmentioning

confidence: 99%

yDNA versus yyDNA pyrimidines: computational analysis of the effects of unidirectional ring expansion on the preferred sugar–base orientation, hydrogen-bonding interactions and stacking abilities

Sharma

Lait

Wetmore

2013

Phys. Chem. Chem. Phys.

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The properties of natural, y- and yy-pyrimidines are compared using computational (B3LYP, MP2) methods. Ring expansion upon incorporation of benzene or naphthalene into the natural pyrimidines affects the preferred orientation of the base about the glycosidic bond in the corresponding nucleoside to a similar extent. Specifically, although the natural pyrimidines preferentially adopt the anti orientation with respect to the 2'-deoxyribose moiety, the expanded analogues will likely display (anti/syn) conformational heterogeneity, which may lead to alternate hydrogen-bonding modes in double-stranded duplexes. Nevertheless, the A:T Watson-Crick hydrogen-bond strengths do not significantly change upon base expansion, while the G:C interaction energy is slightly strengthened upon incorporation of either expanded pyrimidine. The largest effect of base expansion occurs in the stacking energies. Specifically, the maximum (most negative) stacking energies in isolated dimers formed by aligning the nucleobase centers of mass can be increased up to 45% by inclusion of a single y-pyrimidine and up to 55% by consideration of a yy-pyrimidine. Similar increases in the stacking interactions are found when a simplified duplex model composed of two stacked (hydrogen-bonded) base pairs is considered, where both the intrastrand and interstrand stacking interactions can be increased and the effects are more pronounced for the yy-pyrimidines. Moreover, the total stability (sum of all hydrogen-bonding and stacking interactions) is greater for duplexes containing expanded yy-pyrimidines compared to y-pyrimidines, which is mainly due to enhanced stacking interactions. Thus, our calculations suggest that multiple unidirectional increases in the size of the nucleobase spacer can continuously enhance the stability of expanded duplexes.

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“…Similarly, when the furan group is appended at the 8 position of adenine, its emission wavelength increases to 374 nm, whereas phenol or indole groups redshift the guanine emission to 390 nm (Fig. 3e, 8-Furan-A, 8-Phenol-G and 8-Indole-G) 47–49 . Evidence (primarily environmental sensitivity) suggests that the internal charge transfer mechanism functions to provide enhanced quantum yields and redshifts in these cases.…”

Section: Purine Architecture Modificationsmentioning

confidence: 97%

Fluorescent nucleobases as tools for studying DNA and RNA

2017

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Understanding the diversity of dynamic structures and functions of DNA and RNA in biology requires tools that can selectively and intimately probe these biomolecules. Synthetic fluorescent nucleobases that can be incorporated into nucleic acids alongside their natural counterparts have emerged as a powerful class of molecular reporters of location and environment. They are enabling new basic insights into DNA and RNA, and are facilitating a broad range of new technologies with chemical, biological and biomedical applications. In this Review, we will present a brief history of the development of fluorescent nucleobases and explore their utility as tools for addressing questions in biophysics, biochemistry and biology of nucleic acids. We provide chemical insights into the two main classes of these compounds: canonical and non-canonical nucleobases. A point-by-point discussion of the advantages and disadvantages of both types of fluorescent nucleobases is made, along with a perspective into the future challenges and outlook for this burgeoning field.

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An indole-linked C8-deoxyguanosine nucleoside acts as a fluorescent reporter of Watson–Crick versus Hoogsteen base pairing

Cited by 19 publications

References 52 publications

C-Linked 8-aryl guanine nucleobase adducts: biological outcomes and utility as fluorescent probes

C-Linked 8-aryl guanine nucleobase adducts: biological outcomes and utility as fluorescent probes

yDNA versus yyDNA pyrimidines: computational analysis of the effects of unidirectional ring expansion on the preferred sugar–base orientation, hydrogen-bonding interactions and stacking abilities

Fluorescent nucleobases as tools for studying DNA and RNA

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