Structural dynamics and cation interactions of DNA quadruplex
molecules containing mixed guanine/cytosine quartets revealed
by large-scale MD simulations

J 2001

Structural dynamics and cation interactions of DNA quadruplex molecules containing mixed guanine/cytosine quartets revealed by large-scale MD simulations

ŠPAČKOVÁ, Naděžda; Imre BERGER a Jiří ŠPONER

Základní údaje

Originální název

Structural dynamics and cation interactions of DNA quadruplex molecules containing mixed guanine/cytosine quartets revealed by large-scale MD simulations

Autoři

ŠPAČKOVÁ, Naděžda; Imre BERGER a Jiří ŠPONER

Vydání

Journal of the American Chemical Society, Washington, D.C. American Chemical Society, 2001, 0002-7863

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10610 Biophysics

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Impakt faktor

Impact factor: 6.079

Kód RIV

RIV/00216224:14310/01:00005554

Organizační jednotka

Přírodovědecká fakulta

UT WoS

000168078500014

Klíčová slova anglicky

PARTICLE-MESH-EWALD; STRANDED GUANINE TETRAPLEX; OXYTRICHA TELOMERIC DNA; BONDED G-TETRAD; CRYSTAL-STRUCTURE; NUCLEIC-ACIDS; FORCE-FIELD; ANGSTROM RESOLUTION; MINOR-GROOVE; SODIUM-IONS

Štítky

ANGSTROM RESOLUTION, BONDED G-TETRAD, CRYSTAL-STRUCTURE, FORCE-FIELD, MINOR-GROOVE, NUCLEIC-ACIDS, OXYTRICHA TELOMERIC DNA, PARTICLE-MESH-EWALD, SODIUM-IONS, STRANDED GUANINE TETRAPLEX

Změněno: 13. 3. 2002 12:57, Mgr. Naděžda Špačková, Ph.D.

Anotace

V originále

Large-scale molecular dynamics (MD) simulations have been utilized to study G-DNA quadruplex molecules containing mixed GCGC and all-guanine GGGG quartet layers. Incorporation of mixed GCGC quartets into G-DNA stems substantially enhances their sequence variability. The mixed quadruplexes form rigid assemblies that require integral monovalent cations for their stabilization. The interaction of cations with the all-guanine quartets is the leading contribution for the stability of the four-stranded assemblies, while the mixed quartets are rather tolerated within the structure. The simulations predict that two cations are preferred to stabilize a four-layer quadruplex stem composed of two GCGC and two all-guanine quartets. The distribution of cations in the structure is influenced by the position of the GCGC quartets within the quadruplex, the presence and arrangement of thymidine loops connecting the guanine/cytosine stretches forming the stems, and the cation type present (Na+ or K+).

Návaznosti

LN00A016, projekt VaV

Název: BIOMOLEKULÁRNÍ CENTRUM

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Biomolekulární centrum

Citovat

ŠPAČKOVÁ, Naděžda; Imre BERGER a Jiří ŠPONER. Structural dynamics and cation interactions of DNA quadruplex molecules containing mixed guanine/cytosine quartets revealed by large-scale MD simulations. Journal of the American Chemical Society. Washington, D.C.: American Chemical Society, 2001, roč. 123, č. 14, s. 3295-3307. ISSN 0002-7863.

@article{399752,
   author = {Špačková, Naděžda and Berger, Imre and Šponer, Jiří},
   article_location = {Washington, D.C.},
   article_number = {14},
   keywords = {PARTICLE-MESH-EWALD; STRANDED GUANINE TETRAPLEX; OXYTRICHA TELOMERIC DNA; BONDED G-TETRAD; CRYSTAL-STRUCTURE; NUCLEIC-ACIDS; FORCE-FIELD; ANGSTROM RESOLUTION; MINOR-GROOVE; SODIUM-IONS},
   language = {eng},
   issn = {0002-7863},
   journal = {Journal of the American Chemical Society},
   title = {Structural dynamics and cation interactions of DNA quadruplex molecules containing mixed guanine/cytosine quartets revealed by large-scale MD simulations},
   volume = {123},
   year = {2001}
}

TY  - JOUR
ID  - 399752
AU  - Špačková, Naděžda - Berger, Imre - Šponer, Jiří
PY  - 2001
TI  - Structural dynamics and cation interactions of DNA quadruplex molecules containing mixed guanine/cytosine quartets revealed by large-scale MD simulations
JF  - Journal of the American Chemical Society
VL  - 123
IS  - 14
SP  - 3295
EP  - 3295
PB  - American Chemical Society
SN  - 00027863
KW  - PARTICLE-MESH-EWALD
KW  - STRANDED GUANINE TETRAPLEX
KW  - OXYTRICHA TELOMERIC DNA
KW  - BONDED G-TETRAD
KW  - CRYSTAL-STRUCTURE
KW  - NUCLEIC-ACIDS
KW  - FORCE-FIELD
KW  - ANGSTROM RESOLUTION
KW  - MINOR-GROOVE
KW  - SODIUM-IONS
N2  - Large-scale molecular dynamics (MD) simulations have been utilized to study G-DNA quadruplex molecules containing mixed GCGC and all-guanine GGGG quartet layers. Incorporation of mixed GCGC quartets into G-DNA stems substantially enhances their sequence variability. The mixed quadruplexes form rigid assemblies that require integral monovalent cations for their stabilization. The interaction of cations with the all-guanine quartets is the leading contribution for the stability of the four-stranded assemblies, while the mixed quartets are rather tolerated within the structure. The simulations predict that two cations are preferred to stabilize a four-layer quadruplex stem composed of two GCGC and two all-guanine quartets. The distribution of cations in the structure is influenced by the position of the GCGC quartets within the quadruplex, the presence and arrangement of thymidine loops connecting the guanine/cytosine stretches forming the stems, and the cation type present (Na+ or K+).
ER  -

ŠPAČKOVÁ, Naděžda; Imre BERGER a Jiří ŠPONER. Structural dynamics and cation interactions of DNA quadruplex molecules containing mixed guanine/cytosine quartets revealed by large-scale MD simulations. \textit{Journal of the American Chemical Society}. Washington, D.C.: American Chemical Society, 2001, roč.~123, č.~14, s.~3295-3307. ISSN~0002-7863.

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