title: Intramolecular folding in human ILPR fragment with three C-rich repeats.
abstract: Enrichment of four tandem repeats of guanine (G) rich and cytosine (C) rich sequences in functionally important regions of human genome forebodes the biological implications of four-stranded DNA structures, such as G-quadruplex and i-motif, that can form in these sequences. However, there have been few reports on the intramolecular formation of non-B DNA structures in less than four tandem repeats of G or C rich sequences. Here, using mechanical unfolding at the single-molecule level, electrophoretic mobility shift assay (EMSA), circular dichroism (CD), and ultraviolet (UV) spectroscopy, we report an intramolecularly folded non-B DNA structure in three tandem cytosine rich repeats, 5'-TGTC4ACAC4TGTC4ACA (ILPR-I3), in the human insulin linked polymorphic region (ILPR). The thermal denaturation analyses of the sequences with systematic C to T mutations have suggested that the structure is linchpinned by a stack of hemiprotonated cytosine pairs between two terminal C4 tracts. Mechanical unfolding and Br(2) footprinting experiments on a mixture of the ILPR-I3 and a 5'-C4TGT fragment have further indicated that the structure serves as a building block for intermolecular i-motif formation. The existence of such a conformation under acidic or neutral pH complies with the strand-by-strand folding pathway of ILPR i-motif structures.
authors: Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio, United States of America.
authors: Soma
authors: S
authors: Dhakal
authors: Javonne L
authors: JL
authors: Lafontaine
authors: Zhongbo
authors: Z
authors: Yu
authors: Deepak
authors: D
authors: Koirala
authors: Hanbin
authors: H
authors: Mao
mesh_terms: D002942:Circular Dichroism; D003596:Cytosine; D024202:Electrophoretic Mobility Shift Assay; D006801:Humans; D007328:Insulin / Q000235:genetics*; D009154:Mutation; D056951:Photoelectron Spectroscopy; D011110:Polymorphism, Genetic; D020080:Tandem Repeat Sequences
chemical_list: D007328:Insulin; D003596:Cytosine