A-like Guanine-Guanine Stacking in the Aqueous DNA

J 2001

A-like Guanine-Guanine Stacking in the Aqueous DNA

ŠTEFL, Richard; Lukáš TRANTÍREK; Michaela VORLÍČKOVÁ; Jaroslav KOČA; Vladimír SKLENÁŘ et al.

Základní údaje

Originální název

A-like Guanine-Guanine Stacking in the Aqueous DNA

Autoři

ŠTEFL, Richard; Lukáš TRANTÍREK; Michaela VORLÍČKOVÁ; Jaroslav KOČA; Vladimír SKLENÁŘ a Jaroslav KYPR

Vydání

Journal of Molecular Biology, USA, Academic Press, 2001, 0022-2836

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10600 1.6 Biological sciences

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Impakt faktor

Impact factor: 5.826

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14310/01:00003142

Organizační jednotka

Přírodovědecká fakulta

Klíčová slova anglicky

A-like guanine stacking; B/A intermediate structure;heteronomous duplex

Štítky

A-like guanine stacking, B/A intermediate structure, heteronomous duplex

Změněno: 26. 1. 2007 17:15, prof. Mgr. Richard Štefl, Ph.D.

Anotace

V originále

We have used CD spectroscopy, NMR spectroscopy and unrestrained molecular dynamics to study conformational properties of a DNA duplex formed by the self-complementary octamer d(GGGGCCCC). Its unusual CD spectrum contains features indicating A-like stacking of half of the bases, whereas the other half stack in a B-like fashion. Unrestrained mol- ecular dynamics simulations converged to a stable B-like double-helix of d(GGGGCCCC). However, the double-helix contained a central hole whose size was half of that occurring in structure A. In the canonical structure B, the hole does not exist at all because the base-pairs cross the double-helix centre. The cytosine bases were stacked in the duplex of d(GGGGCCCC) as in structure B, while stacking of the guanine bases displayed features characteristic for structure A. NMR spectroscopy revealed that the A-like guanine-guanine stacking was accompanied by an increased tendency of the deoxyribose rings attached to the guanine bases to be puckered in an A-like fashion. Otherwise, the duplex of d(GGGGCCCC) showed no clash, no bend and no other signiŽcant devi- ation from structure B. The present analysis demonstrates a remarkable propensity of the guanine runs to stack in an A-like fashion even within the B-DNA framework. This property explains why the oligo(dG). oligo(dC) tracts switch into structure A so easily. Secondly, this property may inŻuence replication, because structure A is replicated more faith- fully than structure B. Thirdly, the oligo(dG) runs might have played an important role in early evolution, when DNA took on functions that orig- inally evolved on RNA. Fourthly, the present study extends the vocabu- lary of DNA secondary structures by the heteronomous duplex of d(GGGGCCCC) in which the B-like strand of oligo(dC) is bound to the A-like strand of oligo(dG).

Návaznosti

LN00A016, projekt VaV

Název: BIOMOLEKULÁRNÍ CENTRUM

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

Citovat

ŠTEFL, Richard; Lukáš TRANTÍREK; Michaela VORLÍČKOVÁ; Jaroslav KOČA; Vladimír SKLENÁŘ a Jaroslav KYPR. A-like Guanine-Guanine Stacking in the Aqueous DNA. Journal of Molecular Biology. USA: Academic Press, 2001, roč. 307, č. 1, s. 513-524. ISSN 0022-2836.

@article{359292,
   author = {Štefl, Richard and Trantírek, Lukáš and Vorlíčková, Michaela and Koča, Jaroslav and Sklenář, Vladimír and Kypr, Jaroslav},
   article_location = {USA},
   article_number = {1},
   keywords = {A-like guanine stacking; B/A intermediate structure;heteronomous duplex},
   language = {eng},
   issn = {0022-2836},
   journal = {Journal of Molecular Biology},
   title = {A-like Guanine-Guanine Stacking in the Aqueous DNA},
   volume = {307},
   year = {2001}
}

TY  - JOUR
ID  - 359292
AU  - Štefl, Richard - Trantírek, Lukáš - Vorlíčková, Michaela - Koča, Jaroslav - Sklenář, Vladimír - Kypr, Jaroslav
PY  - 2001
TI  - A-like Guanine-Guanine Stacking in the Aqueous DNA
JF  - Journal of Molecular Biology
VL  - 307
IS  - 1
SP  - 513
EP  - 513
PB  - Academic Press
SN  - 00222836
KW  - A-like guanine stacking
KW  - B/A intermediate structure;heteronomous duplex
N2  - We have used CD spectroscopy, NMR spectroscopy and unrestrained molecular dynamics to study conformational properties of a DNA duplex formed by the self-complementary octamer d(GGGGCCCC). Its unusual CD spectrum contains features indicating A-like stacking of half of the bases, whereas the other half stack in a B-like fashion. Unrestrained mol- ecular dynamics simulations converged to a stable B-like double-helix of d(GGGGCCCC). However, the double-helix contained a central hole whose size was half of that occurring in structure A. In the canonical structure B, the hole does not exist at all because the base-pairs cross the double-helix centre. The cytosine bases were stacked in the duplex of d(GGGGCCCC) as in structure B, while stacking of the guanine bases displayed features characteristic for structure A. NMR spectroscopy revealed that the A-like guanine-guanine stacking was accompanied by an increased tendency of the deoxyribose rings attached to the guanine bases to be puckered in an A-like fashion. Otherwise, the duplex of d(GGGGCCCC) showed no clash, no bend and no other signiŽcant devi- ation from structure B. The present analysis demonstrates a remarkable propensity of the guanine runs to stack in an A-like fashion even within the B-DNA framework. This property explains why the oligo(dG). oligo(dC) tracts switch into structure A so easily. Secondly, this property may inŻuence replication, because structure A is replicated more faith- fully than structure B. Thirdly, the oligo(dG) runs might have played an important role in early evolution, when DNA took on functions that orig- inally evolved on RNA. Fourthly, the present study extends the vocabu- lary of DNA secondary structures by the heteronomous duplex of d(GGGGCCCC) in which the B-like strand of oligo(dC) is bound to the A-like strand of oligo(dG).
ER  -

ŠTEFL, Richard; Lukáš TRANTÍREK; Michaela VORLÍČKOVÁ; Jaroslav KOČA; Vladimír SKLENÁŘ a Jaroslav KYPR. A-like Guanine-Guanine Stacking in the Aqueous DNA. \textit{Journal of Molecular Biology}. USA: Academic Press, 2001, roč.~307, č.~1, s.~513-524. ISSN~0022-2836.

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