Genomic sequences susceptible to form G-quadruplexes (G4s) are always flanked by other nucleotides, but G4 formation in vitro is generally studied with short synthetic DNA or RNA oligonucleotides, for which bases adjacent to the G4 core are often omitted. Herein, we systematically studied the effects of flanking nucleotides on structural polymorphism of 371 different oligodeoxynucleotides that adopt intramolecular G4 structures. We found out that the addition of nucleotides favors the formation of a parallel fold, defined as the 'flanking effect' in this work. This 'flanking effect' was more pronounced when nucleotides were added at the 5'-end, and depended on loop arrangement. NMR experiments and molecular dynamics simulations revealed that flanking sequences at the 5'-end abolish a strong syn-specific hydrogen bond commonly found in non-parallel conformations, thus favoring a parallel topology. These analyses pave a new way for more accurate prediction of DNA G4 folding in a physiological context.
- MeSH
- cirkulární dichroismus MeSH
- DNA genetika ultrastruktura MeSH
- G-kvadruplexy * MeSH
- konformace nukleové kyseliny MeSH
- nukleotidy chemie genetika MeSH
- oligonukleotidy chemie genetika MeSH
- polymorfismus genetický genetika MeSH
- RNA genetika ultrastruktura MeSH
- simulace molekulární dynamiky MeSH
- vodíková vazba MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Electron microscopy in situ hybridization (EM-ISH) represents a powerful method that enables the localization of specific sequences of nucleic acids at high resolution. We provide here an overview of three different nonisotopic EM-ISH approaches that allow the visualization of nucleic acid sequences in cells. A comparison of various methods with respect to their sensitivity and the structural preservation of the sample is presented, with the aim of helping the reader to choose a convenient hybridization procedure. The post-embedding EM-ISH protocol that currently represents the most widely used technique is described in detail, with a special emphasis on the organization of the cell nucleus.
- MeSH
- Cercopithecus aethiops MeSH
- COS buňky MeSH
- denaturace nukleových kyselin MeSH
- deoxyribonukleasa I MeSH
- DNA genetika ultrastruktura MeSH
- elektronová kryomikroskopie metody MeSH
- elektronová mikroskopie metody MeSH
- endopeptidasa K MeSH
- financování organizované MeSH
- fixativa MeSH
- geny rRNA MeSH
- HeLa buňky MeSH
- HIV-1 genetika MeSH
- hybridizace in situ metody MeSH
- lidé MeSH
- mikrotomie metody MeSH
- molekulární sondy MeSH
- pankreatická ribonukleasa MeSH
- RNA virová genetika ultrastruktura MeSH
- RNA genetika ultrastruktura MeSH
- zalévání tkání plastickou hmotou MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- srovnávací studie MeSH
- MeSH
- finanční podpora výzkumu jako téma MeSH
- poruchy vyvolané tepelným stresem genetika klasifikace metabolismus MeSH
- potkani Long-Evans genetika psychologie MeSH
- potkani Sprague-Dawley genetika psychologie MeSH
- RNA metabolismus ultrastruktura MeSH
- systém hypofýza - nadledviny metabolismus sekrece MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- srovnávací studie MeSH
- MeSH
- autoradiografie MeSH
- chromatin klasifikace ultrastruktura MeSH
- elektronová mikroskopie MeSH
- histocytochemie MeSH
- lidé MeSH
- mikrotomie MeSH
- puffy klasifikace ultrastruktura MeSH
- ribonukleoproteiny malé jadérkové * biosyntéza klasifikace ultrastruktura MeSH
- ribonukleoproteiny * biosyntéza klasifikace ultrastruktura MeSH
- RNA ultrastruktura MeSH
- struktury buněčného jádra * ultrastruktura MeSH
- struktury chromozomu MeSH
- Check Tag
- lidé MeSH
