title: Formation of i-motif structure at neutral and slightly alkaline pH.
abstract: It is well known that oligonucleotides containing tracts cytosines can form i-motif structures under acidic conditions (pH < 7). However, whether i-motif can be formed under normal physiological cellular conditions (pH 7.0-7.5) is yet no conclusive proof. In the present work, using circular dichroism (CD), UV absorption spectroscopies and native polyacrylamide gel electrophoresis (PAGE), we provided the compelling evidence for the formation of i-motif structures by four cytosine clusters, [C(3)TA(2)](3)C(3) (HT), [C(4)G](3)C(4)TA (RET), C(2)T(3)C(2)T(4)C(2)T(3)C(2) (CTC) and GC(2)GC(3)A(4)C(6)G (Rb), at neutral and slightly alkaline pH at 4 degrees C. Furthermore, for HT, we also supplied the evidence for the formation of i-motif structure by fluorescence resonance energy transfer (FRET) and investigated its folding kinetics. The formation time constants obtained by CD and fluorescence experiments are 214 and 493 s, respectively, indicating that HT can slowly form i-motif structure at pH 7.0 and 4 degrees C. This work implies that i-motif structures may possible form in vivo.
authors.affiliation: State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Zhou
authors.forename: Chunying
authors.initials: C
authors.lastname: Wei
authors.forename: Guoqing
authors.initials: G
authors.lastname: Jia
authors.forename: Xiuli
authors.initials: X
authors.lastname: Wang
authors.forename: Zhaochi
authors.initials: Z
authors.lastname: Feng
authors.forename: Can
authors.initials: C
authors.lastname: Li
mesh_terms: D002942:Circular Dichroism; D003596:Cytosine / Q000378:metabolism; D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D031541:Fluorescence Resonance Energy Transfer; D006801:Humans; D006863:Hydrogen-Ion Concentration; D007700:Kinetics; D009690:Nucleic Acid Conformation; D016615:Telomere / Q000737:chemistry / Q000235:genetics / Q000378:metabolism
chemical_list: D003596:Cytosine; D004247:DNA