Systematic investigation of sequence requirements for DNA
i-motif formation

J 2019

Systematic investigation of sequence requirements for DNA i-motif formation

SKOLAKOVA, P., D. RENCIUK, J. PALACKY, Daniel KRAFČÍK, Z. DVORAKOVA et. al.

Basic information

Original name

Systematic investigation of sequence requirements for DNA i-motif formation

Authors

SKOLAKOVA, P. (203 Czech Republic), D. RENCIUK (203 Czech Republic), J. PALACKY (203 Czech Republic), Daniel KRAFČÍK (703 Slovakia, guarantor, belonging to the institution), Z. DVORAKOVA (203 Czech Republic), I. KEJNOVSKA (203 Czech Republic), K. BEDNAROVA (203 Czech Republic) and M. VORLICKOVA (203 Czech Republic)

Edition

Nucleic acids research, Oxford, Oxford University Press, 2019, 0305-1048

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10608 Biochemistry and molecular biology

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 11.502

RIV identification code

RIV/00216224:14740/19:00108184

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1093/nar/gkz046

UT WoS

000467963700010

Keywords in English

GENE-EXPRESSION; RATIONAL DESIGN; G-QUADRUPLEX; LOOP LENGTH; STABILITY; THERMODYNAMICS; KINETICS

Abstract

V originále

The formation of intercalated motifs (iMs) secondary DNA structures based on hemiprotonated C.C+ pairs in suitable cytosine-rich DNA sequences, is reflected by typical changes in CD and UV absorption spectra. By means of spectroscopic methods, electrophoresis, chemical modifications and other procedures, we characterized iM formation and stability in sequences with different cytosine block lengths interrupted by various numbers and types of nucleotides. Particular attention was paid to the formation of iMs at pH conditions close to neutral. We identified the optimal conditions and minimal requirements for iM formation in DNA sequences, and addressed gaps and inaccurate data interpretations in existing studies to specify principles of iM formation and modes of their folding.

Links

GA17-12075S, research and development project

Name: Polymorfní G-quadruplexy v promotorových oblastech genů

Investor: Czech Science Foundation

Citovat

SKOLAKOVA, P., D. RENCIUK, J. PALACKY, Daniel KRAFČÍK, Z. DVORAKOVA, I. KEJNOVSKA, K. BEDNAROVA and M. VORLICKOVA. Systematic investigation of sequence requirements for DNA i-motif formation. Nucleic acids research. Oxford: Oxford University Press, 2019, vol. 47, No 5, p. 2177-2189. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkz046.

@article{1635177,
   author = {Skolakova, P. and Renciuk, D. and Palacky, J. and Krafčík, Daniel and Dvorakova, Z. and Kejnovska, I. and Bednarova, K. and Vorlickova, M.},
   article_location = {Oxford},
   article_number = {5},
   doi = {http://dx.doi.org/10.1093/nar/gkz046},
   keywords = {GENE-EXPRESSION; RATIONAL DESIGN; G-QUADRUPLEX; LOOP LENGTH; STABILITY; THERMODYNAMICS; KINETICS},
   language = {eng},
   issn = {0305-1048},
   journal = {Nucleic acids research},
   title = {Systematic investigation of sequence requirements for DNA i-motif formation},
   url = {https://academic.oup.com/nar/article/47/5/2177/5305265},
   volume = {47},
   year = {2019}
}

TY  - JOUR
ID  - 1635177
AU  - Skolakova, P. - Renciuk, D. - Palacky, J. - Krafčík, Daniel - Dvorakova, Z. - Kejnovska, I. - Bednarova, K. - Vorlickova, M.
PY  - 2019
TI  - Systematic investigation of sequence requirements for DNA i-motif formation
JF  - Nucleic acids research
VL  - 47
IS  - 5
SP  - 2177-2189
EP  - 2177-2189
PB  - Oxford University Press
SN  - 03051048
KW  - GENE-EXPRESSION
KW  - RATIONAL DESIGN
KW  - G-QUADRUPLEX
KW  - LOOP LENGTH
KW  - STABILITY
KW  - THERMODYNAMICS
KW  - KINETICS
UR  - https://academic.oup.com/nar/article/47/5/2177/5305265
L2  - https://academic.oup.com/nar/article/47/5/2177/5305265
N2  - The formation of intercalated motifs (iMs) secondary DNA structures based on hemiprotonated C.C+ pairs in suitable cytosine-rich DNA sequences, is reflected by typical changes in CD and UV absorption spectra. By means of spectroscopic methods, electrophoresis, chemical modifications and other procedures, we characterized iM formation and stability in sequences with different cytosine block lengths interrupted by various numbers and types of nucleotides. Particular attention was paid to the formation of iMs at pH conditions close to neutral. We identified the optimal conditions and minimal requirements for iM formation in DNA sequences, and addressed gaps and inaccurate data interpretations in existing studies to specify principles of iM formation and modes of their folding.
ER  -

SKOLAKOVA, P., D. RENCIUK, J. PALACKY, Daniel KRAFČÍK, Z. DVORAKOVA, I. KEJNOVSKA, K. BEDNAROVA and M. VORLICKOVA. Systematic investigation of sequence requirements for DNA i-motif formation. \textit{Nucleic acids research}. Oxford: Oxford University Press, 2019, vol.~47, No~5, p.~2177-2189. ISSN~0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkz046.

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