19 KB440 KB16 KB199820252011Johnson, Mark R.Merzel, Francištevilka:3letnik:58str. 442-447ISSN:1318-0207COBISSID:4786458URN:URN:NBN:SI:doc-IJLVMX5LenSlovenian Chemical SocietySlovensko kemijsko društvoActa chimica slovenicabase-pair openingB-DNADNKkemijska strukturakvaziharmonska analizamolecular dynamics simulationsquasiharmonic analysistališčevibrational density of statesLow-frequency vibrations of DNA and base pair opening|DNA melts at temperatures around 70 °C (~340 K) depending on the base-pair composition, level of hydration, type of counterions and excess salt concentration. Vibrational modes, which increase the separation between base molecules, i.e. perform the base pair opening, are thought to play an important role in DNA-bubble formation but these are typically assigned frequencies around 90 cm-1 (120 K). Understanding DNA melting and related biological processes requires this apparent energy gap of more than 200 K to be understood. We have performed atomistic molecular simulations which enable us to reconcile this energy difference between cause and effect. Using quasi-harmonic analysis we have analyzed the way in which vibrational modes of DNA change with the temperatureMolekula DNK ima tališče okrog 70 °C (~340 K) odvisno od zaporedja baznih parov, stopnje hidracije, tipa protiionov in presežne koncentracije soli. Nihajnim načinom DNK, pri katerih se spreminja razmik med baznimi molekulami in ki imajo pomembno vlogo pri nastanku mehurčkov v dvojni vijačnici, ustrezajo frekvence okrog 90 cm-1 (120 K). Za zvezo med nihajnimi načini, ki razpirajo bazne pare in taljenjem DNK je torej potrebno razumeti obstoj energijske reže velikosti ~200 K. V ta namen smo izvedli atomistične simulacije, ki nam pojasnijo energijsko razliko v luči povezave med vzrokom in učinkom. Z uporabo kvaziharmonske analize smo analizirali tudi temperaturno odvisnost narave nihajnih načinov DNKTEXTznanstveno časopisjejournalsSlovenian National E-content AggregatorNational and University Library of SloveniaSlovensko kemijsko društvo