Ethidium Probing of the Parallel Double- and Four-Stranded Structures Formed by the Telomeric DNA Sequences dG(GT)4G and d(GT)5. a Beschetnova, I., Kaluzhny, D. N, a Livshits, M., Shchyolkina, A. K, & Borisova, O. F July 2003. abstract bibtex Oligonucleotides 3'-d(GT)(5)-(CH(2)CH(2)O)(3)-d(GT)(5)-3' (parGT), containing GT repeats present in the telomeric DNA from Saccharomyces cerevisiae, had been demonstrated to form bimolecular structure, GT-quadruplex (qGT) [O. F. Borisova et al. FEBS Letters 306, 140-142 (1992)]. Four d(GT)(5) strands of the GT-quadruplex are parallel and form five G-quartets while thymines are bulged out. The four GT repeats when flanked by guanines, 3'-dG(TG)(4)G-(CH(2)CH(2)O)(3)-dG(GT)(4)G-3' (hp-GT), had been shown to form a novel parallel-stranded (ps) double helix with G.G and T.T base pairs (hp-GT ps-DNA) [A. K. Shchyolkina et al. J. Biomol. Struct. Dyn. 18, 493-503 (2001)]. In the present study the intercalator ethidium bromide (Et) was used for probing the two structures. The mode of Et binding and its effect on thermostability of qGT and hp-GT were compared. The quantum yield (q) and the fluorescence lifetime (tau) of Et:qGT (q = 0.15 +/- 0.01 and tau = 24 +/- 1 ns) and Et:hp-GT (q = 0.10 +/- 0.01 and tau = 16.5 +/- 1 ns) indicative of intercalation mode of Et binding were determined. Et binding to qGT was found to be cooperative with corresponding coefficient omega = 3.9 +/- 0.1 and the binding constant Kappa = (6.4 +/- 0.1).10(4) M(-1). The maximum number of Et molecules intercalating into GT-quadruplex is as high as twice the number of innerspaces between G-quartets (eight in our case). The data conform to the model of Et association with GT-quadruplex suggested earlier [O. F. Borisova et al. Mol. Biol. (Russ) 35, 732-739 (2001)]. The anticooperative type of Et binding was observed in case of hp-GT ps-DNA, with the maximum number of bound Et molecules, N = 4 / 5, and the association constant Kappa = (1.5 +/- 0.1).10(5) M(-1). Thermodynamic parameters of formation of Et:qGT and EtBr:hp-GT complexes were calculated from UV thermal denaturation profiles.
@generic{Beschetnova2003,
title = {Ethidium Probing of the Parallel Double- and Four-Stranded Structures Formed by the Telomeric {{DNA}} Sequences {{dG}}({{GT}}){{4G}} and d({{GT}})5.},
author = {a Beschetnova, Irina and Kaluzhny, Dmitry N and a Livshits, Mikhail and Shchyolkina, Anna K and Borisova, Olga F},
year = {2003},
month = jul,
journal = {Journal of biomolecular structure \& dynamics},
volume = {20},
number = {6},
eprint = {12744708},
eprinttype = {pubmed},
pages = {789--99},
issn = {0739-1102},
abstract = {Oligonucleotides 3'-d(GT)(5)-(CH(2)CH(2)O)(3)-d(GT)(5)-3' (parGT), containing GT repeats present in the telomeric DNA from Saccharomyces cerevisiae, had been demonstrated to form bimolecular structure, GT-quadruplex (qGT) [O. F. Borisova et al. FEBS Letters 306, 140-142 (1992)]. Four d(GT)(5) strands of the GT-quadruplex are parallel and form five G-quartets while thymines are bulged out. The four GT repeats when flanked by guanines, 3'-dG(TG)(4)G-(CH(2)CH(2)O)(3)-dG(GT)(4)G-3' (hp-GT), had been shown to form a novel parallel-stranded (ps) double helix with G.G and T.T base pairs (hp-GT ps-DNA) [A. K. Shchyolkina et al. J. Biomol. Struct. Dyn. 18, 493-503 (2001)]. In the present study the intercalator ethidium bromide (Et) was used for probing the two structures. The mode of Et binding and its effect on thermostability of qGT and hp-GT were compared. The quantum yield (q) and the fluorescence lifetime (tau) of Et:qGT (q = 0.15 +/- 0.01 and tau = 24 +/- 1 ns) and Et:hp-GT (q = 0.10 +/- 0.01 and tau = 16.5 +/- 1 ns) indicative of intercalation mode of Et binding were determined. Et binding to qGT was found to be cooperative with corresponding coefficient omega = 3.9 +/- 0.1 and the binding constant Kappa = (6.4 +/- 0.1).10(4) M(-1). The maximum number of Et molecules intercalating into GT-quadruplex is as high as twice the number of innerspaces between G-quartets (eight in our case). The data conform to the model of Et association with GT-quadruplex suggested earlier [O. F. Borisova et al. Mol. Biol. (Russ) 35, 732-739 (2001)]. The anticooperative type of Et binding was observed in case of hp-GT ps-DNA, with the maximum number of bound Et molecules, N = 4 / 5, and the association constant Kappa = (1.5 +/- 0.1).10(5) M(-1). Thermodynamic parameters of formation of Et:qGT and EtBr:hp-GT complexes were calculated from UV thermal denaturation profiles.},
pmid = {12744708},
keywords = {\#nosource,Animals,Base Sequence,DNA,DNA: chemistry,DNA: metabolism,Ethidium,Ethidium: metabolism,Fluorescent Dyes,Fluorescent Dyes: metabolism,G-Quadruplexes,Guanine,Guanine: chemistry,Molecular Sequence Data,Oligonucleotides,Oligonucleotides: metabolism,Spectrophotometry,Telomere,Telomere: chemistry,Temperature,Thermodynamics,Thymine,Thymine: chemistry,Ultraviolet}
}
Downloads: 0
{"_id":"JRdBQ7KqxQX9um8bb","bibbaseid":"abeschetnova-kaluzhny-alivshits-shchyolkina-borisova-ethidiumprobingoftheparalleldoubleandfourstrandedstructuresformedbythetelomericdnasequencesdggt4ganddgt5-2003","author_short":["a Beschetnova, I.","Kaluzhny, D. N","a Livshits, M.","Shchyolkina, A. K","Borisova, O. F"],"bibdata":{"bibtype":"generic","type":"generic","title":"Ethidium Probing of the Parallel Double- and Four-Stranded Structures Formed by the Telomeric DNA Sequences dG(GT)4G and d(GT)5.","author":[{"propositions":["a"],"lastnames":["Beschetnova"],"firstnames":["Irina"],"suffixes":[]},{"propositions":[],"lastnames":["Kaluzhny"],"firstnames":["Dmitry","N"],"suffixes":[]},{"propositions":["a"],"lastnames":["Livshits"],"firstnames":["Mikhail"],"suffixes":[]},{"propositions":[],"lastnames":["Shchyolkina"],"firstnames":["Anna","K"],"suffixes":[]},{"propositions":[],"lastnames":["Borisova"],"firstnames":["Olga","F"],"suffixes":[]}],"year":"2003","month":"July","journal":"Journal of biomolecular structure & dynamics","volume":"20","number":"6","eprint":"12744708","eprinttype":"pubmed","pages":"789–99","issn":"0739-1102","abstract":"Oligonucleotides 3'-d(GT)(5)-(CH(2)CH(2)O)(3)-d(GT)(5)-3' (parGT), containing GT repeats present in the telomeric DNA from Saccharomyces cerevisiae, had been demonstrated to form bimolecular structure, GT-quadruplex (qGT) [O. F. Borisova et al. FEBS Letters 306, 140-142 (1992)]. Four d(GT)(5) strands of the GT-quadruplex are parallel and form five G-quartets while thymines are bulged out. The four GT repeats when flanked by guanines, 3'-dG(TG)(4)G-(CH(2)CH(2)O)(3)-dG(GT)(4)G-3' (hp-GT), had been shown to form a novel parallel-stranded (ps) double helix with G.G and T.T base pairs (hp-GT ps-DNA) [A. K. Shchyolkina et al. J. Biomol. Struct. Dyn. 18, 493-503 (2001)]. In the present study the intercalator ethidium bromide (Et) was used for probing the two structures. The mode of Et binding and its effect on thermostability of qGT and hp-GT were compared. The quantum yield (q) and the fluorescence lifetime (tau) of Et:qGT (q = 0.15 +/- 0.01 and tau = 24 +/- 1 ns) and Et:hp-GT (q = 0.10 +/- 0.01 and tau = 16.5 +/- 1 ns) indicative of intercalation mode of Et binding were determined. Et binding to qGT was found to be cooperative with corresponding coefficient omega = 3.9 +/- 0.1 and the binding constant Kappa = (6.4 +/- 0.1).10(4) M(-1). The maximum number of Et molecules intercalating into GT-quadruplex is as high as twice the number of innerspaces between G-quartets (eight in our case). The data conform to the model of Et association with GT-quadruplex suggested earlier [O. F. Borisova et al. Mol. Biol. (Russ) 35, 732-739 (2001)]. The anticooperative type of Et binding was observed in case of hp-GT ps-DNA, with the maximum number of bound Et molecules, N = 4 / 5, and the association constant Kappa = (1.5 +/- 0.1).10(5) M(-1). Thermodynamic parameters of formation of Et:qGT and EtBr:hp-GT complexes were calculated from UV thermal denaturation profiles.","pmid":"12744708","keywords":"#nosource,Animals,Base Sequence,DNA,DNA: chemistry,DNA: metabolism,Ethidium,Ethidium: metabolism,Fluorescent Dyes,Fluorescent Dyes: metabolism,G-Quadruplexes,Guanine,Guanine: chemistry,Molecular Sequence Data,Oligonucleotides,Oligonucleotides: metabolism,Spectrophotometry,Telomere,Telomere: chemistry,Temperature,Thermodynamics,Thymine,Thymine: chemistry,Ultraviolet","bibtex":"@generic{Beschetnova2003,\n title = {Ethidium Probing of the Parallel Double- and Four-Stranded Structures Formed by the Telomeric {{DNA}} Sequences {{dG}}({{GT}}){{4G}} and d({{GT}})5.},\n author = {a Beschetnova, Irina and Kaluzhny, Dmitry N and a Livshits, Mikhail and Shchyolkina, Anna K and Borisova, Olga F},\n year = {2003},\n month = jul,\n journal = {Journal of biomolecular structure \\& dynamics},\n volume = {20},\n number = {6},\n eprint = {12744708},\n eprinttype = {pubmed},\n pages = {789--99},\n issn = {0739-1102},\n abstract = {Oligonucleotides 3'-d(GT)(5)-(CH(2)CH(2)O)(3)-d(GT)(5)-3' (parGT), containing GT repeats present in the telomeric DNA from Saccharomyces cerevisiae, had been demonstrated to form bimolecular structure, GT-quadruplex (qGT) [O. F. Borisova et al. FEBS Letters 306, 140-142 (1992)]. Four d(GT)(5) strands of the GT-quadruplex are parallel and form five G-quartets while thymines are bulged out. The four GT repeats when flanked by guanines, 3'-dG(TG)(4)G-(CH(2)CH(2)O)(3)-dG(GT)(4)G-3' (hp-GT), had been shown to form a novel parallel-stranded (ps) double helix with G.G and T.T base pairs (hp-GT ps-DNA) [A. K. Shchyolkina et al. J. Biomol. Struct. Dyn. 18, 493-503 (2001)]. In the present study the intercalator ethidium bromide (Et) was used for probing the two structures. The mode of Et binding and its effect on thermostability of qGT and hp-GT were compared. The quantum yield (q) and the fluorescence lifetime (tau) of Et:qGT (q = 0.15 +/- 0.01 and tau = 24 +/- 1 ns) and Et:hp-GT (q = 0.10 +/- 0.01 and tau = 16.5 +/- 1 ns) indicative of intercalation mode of Et binding were determined. Et binding to qGT was found to be cooperative with corresponding coefficient omega = 3.9 +/- 0.1 and the binding constant Kappa = (6.4 +/- 0.1).10(4) M(-1). The maximum number of Et molecules intercalating into GT-quadruplex is as high as twice the number of innerspaces between G-quartets (eight in our case). The data conform to the model of Et association with GT-quadruplex suggested earlier [O. F. Borisova et al. Mol. Biol. (Russ) 35, 732-739 (2001)]. The anticooperative type of Et binding was observed in case of hp-GT ps-DNA, with the maximum number of bound Et molecules, N = 4 / 5, and the association constant Kappa = (1.5 +/- 0.1).10(5) M(-1). Thermodynamic parameters of formation of Et:qGT and EtBr:hp-GT complexes were calculated from UV thermal denaturation profiles.},\n pmid = {12744708},\n keywords = {\\#nosource,Animals,Base Sequence,DNA,DNA: chemistry,DNA: metabolism,Ethidium,Ethidium: metabolism,Fluorescent Dyes,Fluorescent Dyes: metabolism,G-Quadruplexes,Guanine,Guanine: chemistry,Molecular Sequence Data,Oligonucleotides,Oligonucleotides: metabolism,Spectrophotometry,Telomere,Telomere: chemistry,Temperature,Thermodynamics,Thymine,Thymine: chemistry,Ultraviolet}\n}\n\n","author_short":["a Beschetnova, I.","Kaluzhny, D. N","a Livshits, M.","Shchyolkina, A. K","Borisova, O. F"],"key":"Beschetnova2003","id":"Beschetnova2003","bibbaseid":"abeschetnova-kaluzhny-alivshits-shchyolkina-borisova-ethidiumprobingoftheparalleldoubleandfourstrandedstructuresformedbythetelomericdnasequencesdggt4ganddgt5-2003","role":"author","urls":{},"keyword":["#nosource","Animals","Base Sequence","DNA","DNA: chemistry","DNA: metabolism","Ethidium","Ethidium: metabolism","Fluorescent Dyes","Fluorescent Dyes: metabolism","G-Quadruplexes","Guanine","Guanine: chemistry","Molecular Sequence Data","Oligonucleotides","Oligonucleotides: metabolism","Spectrophotometry","Telomere","Telomere: chemistry","Temperature","Thermodynamics","Thymine","Thymine: chemistry","Ultraviolet"],"metadata":{"authorlinks":{}},"html":""},"bibtype":"generic","biburl":"https://bibbase.org/f/F7MP3WMbDyMbtFCC8/My Library.bib","dataSources":["4i5C7S78DvJNsaHyg"],"keywords":["#nosource","animals","base sequence","dna","dna: chemistry","dna: metabolism","ethidium","ethidium: metabolism","fluorescent dyes","fluorescent dyes: metabolism","g-quadruplexes","guanine","guanine: chemistry","molecular sequence data","oligonucleotides","oligonucleotides: metabolism","spectrophotometry","telomere","telomere: chemistry","temperature","thermodynamics","thymine","thymine: chemistry","ultraviolet"],"search_terms":["ethidium","probing","parallel","double","four","stranded","structures","formed","telomeric","dna","sequences","a beschetnova","kaluzhny","a livshits","shchyolkina","borisova"],"title":"Ethidium Probing of the Parallel Double- and Four-Stranded Structures Formed by the Telomeric DNA Sequences dG(GT)4G and d(GT)5.","year":2003}