Matematicheskaya Biologiya i Bioinformatika
RUS  ENG    JOURNALS   PEOPLE   ORGANISATIONS   CONFERENCES   SEMINARS   VIDEO LIBRARY   PACKAGE AMSBIB  
General information
Latest issue
Archive
Impact factor

Search papers
Search references

RSS
Latest issue
Current issues
Archive issues
What is RSS



Mat. Biolog. Bioinform.:
Year:
Volume:
Issue:
Page:
Find






Personal entry:
Login:
Password:
Save password
Enter
Forgotten password?
Register


Matematicheskaya Biologiya i Bioinformatika, 2013, Volume 8, Issue 2, Pages 553–664 (Mi mbb162)  

This article is cited in 14 scientific papers (total in 14 papers)

Review Articles

Theoretical and Experimental Investigations of DNA Open States

A. S. Shigaev, O. A. Ponomarev, V. D. Lakhno

Institute of Mathematical Problems of Biology, Russian Academy of Sciences, 142290, Pushchino, Moscow Region, Russia
References:
Abstract: This research is a review and assay of literature data on the properties of DNA open states. The states result from large fluctuations of a duplex and have a great influence on a wide range of biochemical processes, including electric charge transfer in DNA. A comparative analysis of kinetic and thermodynamic experimental data on DNA open states has been performed for a wide temperature range. Apparent contradictions between the data of different experiments have been explained. Based on differences in thermodynamic properties and other characteristics three different types of DNA open states have been identified; a modern definition of the term "open state" has been given. A brief review of simple mathematical models of DNA has been presented; in most of the models the state of every base pair is defined by one or two variables. The central problems of investigation of heterogeneous DNA within the approaches of the level considered are examined. The roles of every model group in experimental data interpretation are discussed. Special emphasis is placed on the study of transfer and localization of base pair vibration energy in mechanical models. These processes have been shown to play a key role in heterogeneous duplex dynamics, and their theoretical treatment is critically important for the development of modern molecular biology and biophysics. The key features of theoretical approaches, that enabled description of various experimental data, have been considered. The future development of the models has been desribed, some particular details of their optimization have been suggested; probable ways of improving some experimental techniques have been proposed.
Key words: DNA models, DNA dynamics, energy transfer, energy localization, DNA open state, denaturation bubble, base pair flip-out.
Received 22.10.2013, Published 11.12.2013
Document Type: Article
UDC: 538.9:577.31
Language: Russian
Citation: A. S. Shigaev, O. A. Ponomarev, V. D. Lakhno, “Theoretical and Experimental Investigations of DNA Open States”, Mat. Biolog. Bioinform., 8:2 (2013), 553–664
Citation in format AMSBIB
\Bibitem{ShiPonLak13}
\by A.~S.~Shigaev, O.~A.~Ponomarev, V.~D.~Lakhno
\paper Theoretical and Experimental Investigations of DNA Open States
\jour Mat. Biolog. Bioinform.
\yr 2013
\vol 8
\issue 2
\pages 553--664
\mathnet{http://mi.mathnet.ru/mbb162}
Linking options:
  • https://www.mathnet.ru/eng/mbb162
  • https://www.mathnet.ru/eng/mbb/v8/i2/p553
    Translation
    This publication is cited in the following 14 articles:
    Citing articles in Google Scholar: Russian citations, English citations
    Related articles in Google Scholar: Russian articles, English articles
     
      Contact us:
     Terms of Use  Registration to the website  Logotypes © Steklov Mathematical Institute RAS, 2024