Badania strukturalne kompleksów Z-DNA oraz hybrydy RNA:DNA z kationami organicznymi i nieorganicznymi
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Date
2014-02-20
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Structural studies of Z-DNA complexes and RNA:DNA hybrid with organic and inorganic cations
Abstract
Zarejestrowano wysokorozdzielcze dane i rozwiązano struktury kryształów nie opisywanych dotychczas w literaturze kompleksów d(CGCGCG)2–Spm4+–Mn2+, d(CGCGCG)2–Spm4+–Zn2+, d(CGCGCG)2–Put2+–K+ i d(CGCGCG)2–Cr3+ oraz RNA:DNA–Mg2+. Za wyjątkiem kompleksu z Mn2+, w pozostałych strukturach z Z-DNA łańcuch kwasu nukleinowego wykazuje nieuporządkowanie (podwójne konformacje), którego stopień można uszeregować w następującej kolejności d(CGCGCG)2–Cr3+ > d(CGCGCG)2–Put2+–K+ > d(CGCGCG)2–Spm4+–Zn2+ > d(CGCGCG)2–Spm4+–Mn2+. Uzyskane w niniejszej pracy rezultaty świadczą o wysokim stopniu labilności konformacyjnej helisy d(CGCGCG)2. Uzyskane rezultaty dla RNA:DNA–Mg2+ dotyczące konformacji i parametrów helikalnych porównano z wartościami charakteryzującymi dwa, jak dotąd, opisane dupleksy RNA:DNA z sekwencją analogiczną do PPT. Analiza porównawcza wykazała różnice w konformacji cukrów, stopniu nieuporządkowania nici RNA, oddziaływaniach warstwowych w regionie a5-g6-a7 i w trajektorii osi helisy. Przekształcenia strukturalne zaobserwowane dla kompleksu RNA:DNA–Mg2+ występują w wielu miejscach łańcucha RNA z sekwencją PPT, co sugeruje, że są jednym z warunków wstępnych w efektywnej syntezie retrowirusowego DNA przez RT/HIV-1. Uzyskane wyniki wzbogacają wiedzę o procesie odwrotnej transkrypcji w retrowirusach oraz o stabilności kwasu nukleinowego w formie Z-DNA.
High-resolution data were recorded and structures were solved of crystals of d(CGCGCG)2–Spm4+–Mn2+, d(CGCGCG)2–Spm4+–Zn2+, d(CGCGCG)2–Put2+–K+, d(CGCGCG)2–Cr3+ and RNA:DNA–Mg2+ complexes that have not yet been reported in the literature. With the exception of the complex with Mn2+, the nucleic acid chain shows a disorder (alternate conformations) in the remaining structures with Z-DNA. The degree of this disorder is as follows: d(CGCGCG)2–Cr3+ > d(CGCGCG)2–Put2+–K+ > d(CGCGCG)2–Spm4+–Zn2+ > d(CGCGCG)2–Spm4+–Mn2+. The results obtained in the present study of new Z-DNA complexes indicate a high degree of conformational lability for the d(CGCGCG)2 helix. The results concerning the conformation and helical parameters obtained for the RNA:DNA–Mg2+ complex were compared with the values characterizing two RNA:DNA duplexes with the PPT sequence of the HIV-1 virus, described to date. A comparative analysis has shown differences in sugar pucker, the degree of disorder of the RNA strand, stacking interactions in the a5-g6-a7 region and trajectory of the helix axis between the dodecamer and decamer of RNA:DNA with PPT sequence. Structural transformations observed in the RNA:DNA–Mg2+ complex occur in many sites of the RNA chain with PPT sequence, which suggests that they are one of preconditions in the effective synthesis of retroviral DNA by RT/HIV-1. The data obtained as a result of the studies correspond to reverse transcription processes in retroviruses and are associated with possibilities of nucleic acid stabilization in Z-DNA form.
High-resolution data were recorded and structures were solved of crystals of d(CGCGCG)2–Spm4+–Mn2+, d(CGCGCG)2–Spm4+–Zn2+, d(CGCGCG)2–Put2+–K+, d(CGCGCG)2–Cr3+ and RNA:DNA–Mg2+ complexes that have not yet been reported in the literature. With the exception of the complex with Mn2+, the nucleic acid chain shows a disorder (alternate conformations) in the remaining structures with Z-DNA. The degree of this disorder is as follows: d(CGCGCG)2–Cr3+ > d(CGCGCG)2–Put2+–K+ > d(CGCGCG)2–Spm4+–Zn2+ > d(CGCGCG)2–Spm4+–Mn2+. The results obtained in the present study of new Z-DNA complexes indicate a high degree of conformational lability for the d(CGCGCG)2 helix. The results concerning the conformation and helical parameters obtained for the RNA:DNA–Mg2+ complex were compared with the values characterizing two RNA:DNA duplexes with the PPT sequence of the HIV-1 virus, described to date. A comparative analysis has shown differences in sugar pucker, the degree of disorder of the RNA strand, stacking interactions in the a5-g6-a7 region and trajectory of the helix axis between the dodecamer and decamer of RNA:DNA with PPT sequence. Structural transformations observed in the RNA:DNA–Mg2+ complex occur in many sites of the RNA chain with PPT sequence, which suggests that they are one of preconditions in the effective synthesis of retroviral DNA by RT/HIV-1. The data obtained as a result of the studies correspond to reverse transcription processes in retroviruses and are associated with possibilities of nucleic acid stabilization in Z-DNA form.
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Wydział Chemii: Zakład Chemii Koordynacyjnej
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Keywords
kwasy nukleinowe, nucleic acids, struktura krystalograficzna, crystal structure, kationy metali, metal cations, poliaminy biogenne, biogenic polyamines, oddziaływania, Non-covalent interaction