Revealing structural peculiarities of homopurine GA repetition
stuck by i-motif clip

J 2021

Revealing structural peculiarities of homopurine GA repetition stuck by i-motif clip

NOVOTNÝ, Aleš, Jan NOVOTNÝ, Iva KEJNOVSKÁ, Michaela VORLÍČKOVÁ, Radovan FIALA et. al.

Základní údaje

Originální název

Revealing structural peculiarities of homopurine GA repetition stuck by i-motif clip

Autoři

NOVOTNÝ, Aleš (203 Česká republika, domácí), Jan NOVOTNÝ (203 Česká republika, domácí), Iva KEJNOVSKÁ (203 Česká republika), Michaela VORLÍČKOVÁ (203 Česká republika), Radovan FIALA (203 Česká republika, domácí) a Radek MAREK (203 Česká republika, garant, domácí)

Vydání

Nucleic Acids Research, Oxford, Oxford University Press, 2021, 0305-1048

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10608 Biochemistry and molecular biology

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

DOI: 10.1093/nar/gkab915

Impakt faktor

Impact factor: 19.160

Kód RIV

RIV/00216224:14740/21:00122684

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1093/nar/gkab915

UT WoS

000728384400008

Klíčová slova anglicky

DNA; i-motif; duplex; NMR spectroscopy; CD; molecular dynamics

Štítky

CF NMR, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 30. 10. 2024 14:17, Ing. Martina Blahová

Anotace

V originále

Non-canonical forms of nucleic acids represent challenging objects for both structure-determination and investigation of their potential role in living systems. In this work, we uncover a structure adopted by GA repetition locked in a parallel homoduplex by an i-motif. A series of DNA oligonucleotides comprising GAGA segment and C3 clip is analyzed by NMR and CD spectroscopies to understand the sequence–structure–stability relationships. We demonstrate how the relative position of the homopurine GAGA segment and the C3 clip as well as single-base mutations (guanine deamination and cytosine methylation) affect base pairing arrangement of purines, i-motif topology and overall stability. We focus on oligonucleotides C3GAGA and methylated GAGAC3 exhibiting the highest stability and structural uniformity which allowed determination of high-resolution structures further analyzed by unbiased molecular dynamics simulation. We describe sequence-specific supramolecular interactions on the junction between homoduplex and i-motif blocks that contribute to the overall stability of the structures. The results show that the distinct structural motifs can not only coexist in the tight neighborhood within the same molecule but even mutually support their formation. Our findings are expected to have general validity and could serve as guides in future structure and stability investigations of nucleic acids.

Návaznosti

EF16_013/0001776, projekt VaV

Název: Česká infrastruktura pro integrativní strukturní biologii pro lidské zdraví

LM2018140, projekt VaV

Název: e-Infrastruktura CZ (Akronym: e-INFRA CZ)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, e-Infrastruktura CZ

90127, velká výzkumná infrastruktura

Název: CIISB II

Citovat

NOVOTNÝ, Aleš, Jan NOVOTNÝ, Iva KEJNOVSKÁ, Michaela VORLÍČKOVÁ, Radovan FIALA a Radek MAREK. Revealing structural peculiarities of homopurine GA repetition stuck by i-motif clip. Nucleic Acids Research. Oxford: Oxford University Press, 2021, roč. 49, č. 20, s. 11425-11437. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkab915.

@article{1800082,
   author = {Novotný, Aleš and Novotný, Jan and Kejnovská, Iva and Vorlíčková, Michaela and Fiala, Radovan and Marek, Radek},
   article_location = {Oxford},
   article_number = {20},
   doi = {http://dx.doi.org/10.1093/nar/gkab915},
   keywords = {DNA; i-motif; duplex; NMR spectroscopy; CD; molecular dynamics},
   language = {eng},
   issn = {0305-1048},
   journal = {Nucleic Acids Research},
   title = {Revealing structural peculiarities of homopurine GA repetition stuck by i-motif clip},
   url = {http://dx.doi.org/10.1093/nar/gkab915},
   volume = {49},
   year = {2021}
}

TY  - JOUR
ID  - 1800082
AU  - Novotný, Aleš - Novotný, Jan - Kejnovská, Iva - Vorlíčková, Michaela - Fiala, Radovan - Marek, Radek
PY  - 2021
TI  - Revealing structural peculiarities of homopurine GA repetition stuck by i-motif clip
JF  - Nucleic Acids Research
VL  - 49
IS  - 20
SP  - 11425-11437
EP  - 11425-11437
PB  - Oxford University Press
SN  - 03051048
KW  - DNA
KW  - i-motif
KW  - duplex
KW  - NMR spectroscopy
KW  - CD
KW  - molecular dynamics
UR  - http://dx.doi.org/10.1093/nar/gkab915
N2  - Non-canonical forms of nucleic acids represent challenging objects for both structure-determination and investigation of their potential role in living systems. In this work, we uncover a structure adopted by GA repetition locked in a parallel homoduplex by an i-motif. A series of DNA oligonucleotides comprising GAGA segment and C3 clip is analyzed by NMR and CD spectroscopies to understand the sequence–structure–stability relationships. We demonstrate how the relative position of the homopurine GAGA segment and the C3 clip as well as single-base mutations (guanine deamination and cytosine methylation) affect base pairing arrangement of purines, i-motif topology and overall stability. We focus on oligonucleotides C3GAGA and methylated GAGAC3 exhibiting the highest stability and structural uniformity which allowed determination of high-resolution structures further analyzed by unbiased molecular dynamics simulation. We describe sequence-specific supramolecular interactions on the junction between homoduplex and i-motif blocks that contribute to the overall stability of the structures. The results show that the distinct structural motifs can not only coexist in the tight neighborhood within the same molecule but even mutually support their formation. Our findings are expected to have general validity and could serve as guides in future structure and stability investigations of nucleic acids.
ER  -

NOVOTNÝ, Aleš, Jan NOVOTNÝ, Iva KEJNOVSKÁ, Michaela VORLÍČKOVÁ, Radovan FIALA a Radek MAREK. Revealing structural peculiarities of homopurine GA repetition stuck by i-motif clip. \textit{Nucleic Acids Research}. Oxford: Oxford University Press, 2021, roč.~49, č.~20, s.~11425-11437. ISSN~0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkab915.

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