Special Properties of Modification of SsDNA Target by Alkylating Derivatives of Oligonucleotides in Tandem Complexes

Pyshnyi, D. V.; Lokhov, S. G.; Иванова, Е. М.; Зарытова, В. Ф.

doi:10.1080/07328319808004758

Cited by 2 publications

(3 citation statements)

References 4 publications

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“…This section will review the structural traits of the DNA–complex which can increase the selectivity of the enzymatic reaction. One of the simplest ways to increase enzymatic ligation effectiveness is to use a method based on “modified” probes, which consist of tandems of short oligonucleotides [83–85]. The presence among the ligated components of mini–probes of penta– and even tetra–nucleotides makes these composite complexes less effective as substrates, and their enzymatic selectivity appears to be high [83, 85].…”

Section: Effect Of Structural Disruptions Of the Dna Substrate On Thementioning

confidence: 99%

“…One of the simplest ways to increase enzymatic ligation effectiveness is to use a method based on “modified” probes, which consist of tandems of short oligonucleotides [83–85]. The presence among the ligated components of mini–probes of penta– and even tetra–nucleotides makes these composite complexes less effective as substrates, and their enzymatic selectivity appears to be high [83, 85]. If a tetranucleotide is used as the central part of a three–part tandem, the discrimination factor for any type of mismatch in the region of the substrate complex is more than 300 when using the mesophilic Т 4 DNA–ligase [85].…”

Section: Effect Of Structural Disruptions Of the Dna Substrate On Thementioning

confidence: 99%

“…The presence among the ligated components of mini–probes of penta– and even tetra–nucleotides makes these composite complexes less effective as substrates, and their enzymatic selectivity appears to be high [83, 85]. If a tetranucleotide is used as the central part of a three–part tandem, the discrimination factor for any type of mismatch in the region of the substrate complex is more than 300 when using the mesophilic Т 4 DNA–ligase [85]. Such high selectivity of the enzyme is unattainable if the DNA–duplex is formed by oligonucleotides, which are long enough to provide optimal conditions for enzyme binding on the molecule (see [37] for an instance).…”

Section: Effect Of Structural Disruptions Of the Dna Substrate On Thementioning

confidence: 99%

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Selectivity of Enzymatic Conversion of Oligonucleotide Probes during Nucleotide Polymorphism Analysis of DN

Vinogradova

Пышный

2010

Acta Naturae

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The analysis of DNA nucleotide polymorphisms is one of the main goals of DNA diagnostics. DNA–dependent enzymes (DNA polymerases and DNA ligases) are widely used to enhance the sensitivity and reliability of systems intended for the detection of point mutations in genetic material. In this article, we have summarized the data on the selectiveness of DNA–dependent enzymes and on the structural factors in enzymes and DNA which influence the effectiveness of mismatch discrimination during enzymatic conversion of oligonucleotide probes on a DNA template. The data presented characterize the sensitivity of a series of DNA–dependent enzymes that are widely used in the detection of noncomplementary base pairs in nucleic acid substrate complexes. We have analyzed the spatial properties of the enzyme–substrate complexes. These properties are vital for the enzymatic reaction and the recognition of perfect DNA–substrates. We also discuss relevant approaches to increasing the selectivity of enzyme–dependent reactions. These approaches involve the use of modified oligonucleotide probes which “disturb” the native structure of the DNA–substrate complexes.

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Section: Effect Of Structural Disruptions Of the Dna Substrate On Thementioning

confidence: 99%

Section: Effect Of Structural Disruptions Of the Dna Substrate On Thementioning

confidence: 99%

Section: Effect Of Structural Disruptions Of the Dna Substrate On Thementioning

confidence: 99%

See 1 more Smart Citation

Selectivity of Enzymatic Conversion of Oligonucleotide Probes during Nucleotide Polymorphism Analysis of DN

Vinogradova

Пышный

2010

Acta Naturae

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Thermodynamic Analysis of Stacking Hybridization of Oligonucleotides with DNA Template

Pyshnyi

Pyshnaya

Левина

et al. 2001

Journal of Biomolecular Structure and Dynamics

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Contiguous stacking hybridization of oligodeoxyribonucleotides with DNA as template was investigated using three types of complexes: oligonucleotide contiguously stacked with the stem of the preformed minihairpin (complexes I), oligonucleotide tandems containing two (complexes II) or three (complexes III) short oligomers with a common DNA template. Enthalpy Delta H degrees and entropy Delta S degrees of the coaxial stacking of adjacent duplexes were determined for GC/G*pC, GT/A*pC, AC/G*pT, AT/A*pT, CT/A*pG, AG/C*pT, AA/T*pT and TT/A*pA nicked (*) dinucleotide base pairs. The maximal efficiency of co-operative interaction was found for the GC/G*pC interface (Delta G degrees(NN/N*pN)=-2.7 kcal/mol) and the minimal one for the AA/T*pT interface (Delta G degrees(NN/N*pN)=-1.2 kcal/mol) at 37 degrees C. As a whole, the efficiency of the base pairs interaction Delta G degrees(NN/N*pN) in the nick is not lower than that within the intact DNA helix (Delta G degrees(NN/NN)). These observed Delta G degrees(NN/N*pN) values are proposed may include the effect of the partial removal of fraying at the adjacent helix ends additionally to the effect of the direct stacking of the terminal base pairs in the duplex junction (Delta G degrees(NN/NN). The thermodynamic parameters have been found to describe adequately the formation of all tandem complexes of the II and III types with oligonucleotides of various length and hybridization properties. The performed thermodynamic analysis reveals features of stacking oligonucleotide hybridization which allow one to predict the temperature dependence of association of oligonucleotides and the DNA template within tandem complexes as well as to determine optimal concentration for formation of these complexes characterized by high co-operativity level.

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Special Properties of Modification of SsDNA Target by Alkylating Derivatives of Oligonucleotides in Tandem Complexes

Cited by 2 publications

References 4 publications

Selectivity of Enzymatic Conversion of Oligonucleotide Probes during Nucleotide Polymorphism Analysis of DN

Selectivity of Enzymatic Conversion of Oligonucleotide Probes during Nucleotide Polymorphism Analysis of DN

Thermodynamic Analysis of Stacking Hybridization of Oligonucleotides with DNA Template

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