Molecular dynamics of DNA quadruplex molecules containing
inosine, 6-thioguanine and 6-thiopurine

J 2001

Molecular dynamics of DNA quadruplex molecules containing inosine, 6-thioguanine and 6-thiopurine

ŠTEFL, Richard; Naděžda ŠPAČKOVÁ; Imre BERGER; Jaroslav KOČA; Jiří ŠPONER et al.

Základní údaje

Originální název

Molecular dynamics of DNA quadruplex molecules containing inosine, 6-thioguanine and 6-thiopurine

Autoři

ŠTEFL, Richard; Naděžda ŠPAČKOVÁ; Imre BERGER; Jaroslav KOČA a Jiří ŠPONER

Vydání

Biophysical Journal, Bethesda, USA, Biophysical Society, 2001, 0006-3495

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: 4.636

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14310/01:00005556

Organizační jednotka

Přírodovědecká fakulta

UT WoS

000166647700038

Klíčová slova anglicky

STRANDED GUANINE TETRAPLEX; OXYTRICHA TELOMERIC DNA; MESH EWALD METHOD; G-C REPEATS; CRYSTAL-STRUCTURE; FORCE-FIELD; BASE-PAIRS; AB-INITIO; G-QUARTET; STABLE TRAJECTORIES

Štítky

AB-INITIO, BASE-PAIRS, CRYSTAL-STRUCTURE, FORCE-FIELD, G-C REPEATS, G-QUARTET, MESH EWALD METHOD, OXYTRICHA TELOMERIC DNA, STABLE TRAJECTORIES, STRANDED GUANINE TETRAPLEX

Změněno: 26. 1. 2007 17:16, prof. Mgr. Richard Štefl, Ph.D.

Anotace

V originále

The ability of the four-stranded guanine (G)-DNA motif to incorporate nonstandard guanine analogue bases 6-oxopurine (inosine, I), 6-thioguanine (tG), and 8-thiopurine (tl) has been investigated using large-scale molecular dynamics simulations. The simulations suggest that a G-DNA stem can incorporate inosines without any marked effect on its structure and dynamics. In the simulations, the incorporation of 6-thioguanine and 6-thiopurine sharply destabilizes four-stranded G-DNA structures, in close agreement with experimental data. The main reason is the size of the thiogroup leading to considerable steric conflicts and expelling the cations out of the channel of the quadruplex stem. The G-DNA stem can accommodate a single thioguanine base with minor perturbations. Incorporation of a thioguanine quartet layer is associated with a large destabilization of the G-DNA stem whereas the all-thioguanine quadruplex immediately collapses.

Návaznosti

GA203/00/0633, projekt VaV

Název: Struktura, dynamika a funkce DNA

IAA4040903, projekt VaV

Název: Interakce kovových iontů s nukleovými kyselinami a jejich fragmenty. Ab initio kvantově-chemická studie

VS96095, projekt VaV

Název: Laboratoř struktury a dynamiky biomolekul

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Laboratoř struktury a dynamiky biomolekul

Citovat

ŠTEFL, Richard; Naděžda ŠPAČKOVÁ; Imre BERGER; Jaroslav KOČA a Jiří ŠPONER. Molecular dynamics of DNA quadruplex molecules containing inosine, 6-thioguanine and 6-thiopurine. Biophysical Journal. Bethesda, USA: Biophysical Society, 2001, roč. 80, č. 1, s. 455-468. ISSN 0006-3495.

@article{399772,
   author = {Štefl, Richard and Špačková, Naděžda and Berger, Imre and Koča, Jaroslav and Šponer, Jiří},
   article_location = {Bethesda, USA},
   article_number = {1},
   keywords = {STRANDED GUANINE TETRAPLEX; OXYTRICHA TELOMERIC DNA; MESH EWALD METHOD; G-C REPEATS; CRYSTAL-STRUCTURE; FORCE-FIELD; BASE-PAIRS; AB-INITIO; G-QUARTET; STABLE TRAJECTORIES},
   language = {eng},
   issn = {0006-3495},
   journal = {Biophysical Journal},
   title = {Molecular dynamics of DNA quadruplex molecules containing inosine, 6-thioguanine and 6-thiopurine},
   volume = {80},
   year = {2001}
}

TY  - JOUR
ID  - 399772
AU  - Štefl, Richard - Špačková, Naděžda - Berger, Imre - Koča, Jaroslav - Šponer, Jiří
PY  - 2001
TI  - Molecular dynamics of DNA quadruplex molecules containing inosine, 6-thioguanine and 6-thiopurine
JF  - Biophysical Journal
VL  - 80
IS  - 1
SP  - 455
EP  - 455
PB  - Biophysical Society
SN  - 00063495
KW  - STRANDED GUANINE TETRAPLEX
KW  - OXYTRICHA TELOMERIC DNA
KW  - MESH EWALD METHOD
KW  - G-C REPEATS
KW  - CRYSTAL-STRUCTURE
KW  - FORCE-FIELD
KW  - BASE-PAIRS
KW  - AB-INITIO
KW  - G-QUARTET
KW  - STABLE TRAJECTORIES
N2  - The ability of the four-stranded guanine (G)-DNA motif to incorporate nonstandard guanine analogue bases 6-oxopurine (inosine, I), 6-thioguanine (tG), and 8-thiopurine (tl) has been investigated using large-scale molecular dynamics simulations. The simulations suggest that a G-DNA stem can incorporate inosines without any marked effect on its structure and dynamics. In the simulations, the incorporation of 6-thioguanine and 6-thiopurine sharply destabilizes four-stranded G-DNA structures, in close agreement with experimental data. The main reason is the size of the thiogroup leading to considerable steric conflicts and expelling the cations out of the channel of the quadruplex stem. The G-DNA stem can accommodate a single thioguanine base with minor perturbations. Incorporation of a thioguanine quartet layer is associated with a large destabilization of the G-DNA stem whereas the all-thioguanine quadruplex immediately collapses.
ER  -

ŠTEFL, Richard; Naděžda ŠPAČKOVÁ; Imre BERGER; Jaroslav KOČA a Jiří ŠPONER. Molecular dynamics of DNA quadruplex molecules containing inosine, 6-thioguanine and 6-thiopurine. \textit{Biophysical Journal}. Bethesda, USA: Biophysical Society, 2001, roč.~80, č.~1, s.~455-468. ISSN~0006-3495.

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