The dependence of fluorescence quantum yield of the tRNA—acriflavine complexes on the conformational changes in tRNA

Borissova, O.F.; Потапов, А. П.; Surovaya, A. N.; Trubitsyn, S.; Volkenstein, M.V.

doi:10.1016/0014-5793(72)80433-2

Cited by 5 publications

(5 citation statements)

References 8 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The measured value of the fluorescence quantum yield (4) of AFoligonucleotide complexes was calculated as described elsewhere [7]. According to [7] it may be expressed by the following equation:…”

Section: Methodsmentioning

confidence: 99%

“…The qAT is the fluorescence quantum yield of AF being intercalated between two AT pairs. The concentration of bound dye was calculated using two independent methods of polarized fluorescence and absorption spectra of AF-oligonucleotide complexes [7,8].…”

Section: Methodsmentioning

confidence: 99%

“…This feature of a parallel helix containing GC pairs may play an important biological role in its interaction with ligands. The fraction of paired bases 8 determined by hyperchromicity at t > 7', , is the total base pairs concentration at 5°C in the 40nucleotide [7].…”

Section: -Nucleotide Duplexesmentioning

confidence: 99%

“…The specialized fluorescent techniques [7,9] permitted us to check the formation of perfect antiparallel I-II and parallel I-III decaduplexes. The following data testify to the I-III parallel decaduplex formation: (i) the number of sites available for intercalation (n = 9) at 3°C was shown to be the same for both antiparallel and parallel duplexes, indicating the absence of unpaired bases in these oligonucleotides; (ii) the measured p values for (I-II) duplex and (I-III) duplex were the same &c = 20 + 1, ns), indicating that the hydrodynamic volumes of the duplexes are equal to each other; (iii) by the 'r-method' the (l-0) value at 5" C was shown to be equal to zero for the antiparallel decaduplex and 0.07 + 0.02 for the parallel decaduplex indicating the presence of one unstable terminal base pair in the latter.…”

Section: 1 Decaduplexesmentioning

confidence: 99%

“…5 = the melting curve of GC pairs calculated by subtraction from the curve (3) of the contribution of melted AT pairs estimated with the help of curve (2). Oligonucleotide concentration was 2.4 x 10e4 M(N); 0.01 M phosphate buffer, pH 7, 0.25 M NaCl; AF concentration was 10m6 M. [AT]/([AT] + [GC]),., = B(q/qAT)"', where [AT] is the AT pair concentration in the 4Onucleotide studied in dependence on temperature, ([AT] + [GC]),., is the total base pairs concentration at 5°C in the 40nucleotide[7].…”

mentioning

confidence: 99%

See 4 more Smart Citations

Relative stability of AT and GC pairs in parallel DNA duplex formed by a natural sequence

et al. 1993

View full text Add to dashboard Cite

The low-cooperative melting of parallel DNA formed by a natural 40 bp long sequence from Drosophila:that possesses a normal nucleotide content was studied by using the special method of measuring the fluorescence of its complex with acriflavine as well as by conventional thermal denaturation. Acriflavine allows discrimination of the melting of AT and GC pairs because its fluorescence is quenched by neighbouring G bases. We have observed that about 40% of AT pairs melt at 14°C while the remainder melt at 42°C. The GC pairs remain stable up to -40°C and melt at 54°C. The higher stability of GC pairs suggests the formation of cis Watson-Crick pairs in parallel DNA.Parallel stranded DNA; Stability of GC pairs

show abstract

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: -Nucleotide Duplexesmentioning

confidence: 99%

Section: 1 Decaduplexesmentioning

confidence: 99%

mentioning

confidence: 99%

See 3 more Smart Citations

Relative stability of AT and GC pairs in parallel DNA duplex formed by a natural sequence

et al. 1993

View full text Add to dashboard Cite

show abstract

The role of carboxymethyl substituents in the interaction of tetracationic porphyrins with DNA

et al. 2012

View full text Add to dashboard Cite

Cationic porphyrin-based compounds capable of interacting with DNA are currently under extensive investigation as prospective anticancer and anti-infective drugs. One of the approaches to enhancing the DNA-binding affinity of these ligands is chemical modification of functional groups of the porphyrin macrocycle. We analyzed the interaction with DNA of novel derivatives containing carboxymethyl and ethoxycarbonylmethyl substituents at quaternary nitrogen atoms of pyridinium groups at the periphery of the porphyrin macrocycle. The parameters of binding of 5,10,15,20-tetrakis(N-carboxymethyl-4-pyridinium)porphyrin (P1) and 5,10,15,20-tetrakis(N-ethoxycarbonylmethyl-4-pyridinium)porphyrin (P2) to double-stranded DNA sequences of different nucleotide content were determined using optical spectroscopy. The association constant of P1 interaction with calf thymus DNA (K = 3.4 × 10(6) M(-1)) was greater than that of P2 (K = 2.8 × 10(5) M(-1)). Preferential binding of P1 to GC- rather than AT-rich oligonucleotides was detected. In contrast, P2 showed no preference for particular nucleotide content. Modes of binding of P1 and P2 to GC and AT duplexes were verified using the induced circular dichroism spectra. Molecular modeling confirmed an intercalative mode of interaction of P1 and P2 with CpG islands. The carboxyl groups of the peripheral substituent in P1 determine the specific interactions with GC-rich DNA regions, whereas ethoxycarbonylmethyl substituents disfavor binding to DNA. This study contributes to the understanding of the impact of peripheral substituents on the DNA-binding affinity of cationic porphyrins, which is important for the design of DNA-targeting drugs.

show abstract

Thermodynamics and Kinetics of Conformational Transitions in Oligonucleotides and tRNA

Riesner

Römer

1973

Structural Studies on Nucleic Acids and Other Biopolymers

View full text Add to dashboard Cite

The dependence of fluorescence quantum yield of the tRNA—acriflavine complexes on the conformational changes in tRNA

Cited by 5 publications

References 8 publications

Relative stability of AT and GC pairs in parallel DNA duplex formed by a natural sequence

Relative stability of AT and GC pairs in parallel DNA duplex formed by a natural sequence

The role of carboxymethyl substituents in the interaction of tetracationic porphyrins with DNA

Thermodynamics and Kinetics of Conformational Transitions in Oligonucleotides and tRNA

Contact Info

Product

Resources

About