{"_id":"qjFssJbvGxFdRTjqP","bibbaseid":"kendrick-akiyama-hecht-hurley-theimotifinthebcl2p1promoterformsanunexpectedlystablestructurewithaunique857loopfoldingpattern-2009","author_short":["Kendrick, S.","Akiyama, Y.","Hecht, S. M","Hurley, L. H"],"bibdata":{"bibtype":"article","type":"article","title":"The i-Motif in the bcl-2 P1 promoter forms an unexpectedly stable structure with a unique 8:5:7 loop folding pattern","volume":"131","issn":"0002-7863","url":"http://dx.doi.org/10.1021/ja9076292","doi":"10.1021/ja9076292","abstract":"Transcriptional regulation of the bcl-2 proto-oncogene is highly complex, with the majority of transcription driven by the P1 promoter site and the interaction of multiple regulatory proteins. A guanine- and cytosine-rich (GC-rich) region directly upstream of the P1 site has been shown to be integral to bcl-2 promoter activity, as deletion or mutation of this region significantly increases transcription. This GC-rich element consists of six contiguous runs of guanines and cytosines that have the potential to adopt DNA secondary structures, the G-quadruplex and i-motif, respectively. Our laboratory has previously demonstrated that the polypurine-rich strand of the bcl-2 promoter can form a mixture of three different G-quadruplex structures. In this current study, we demonstrate that the complementary polypyrimidine-rich strand is capable of forming one major intramolecular i-motif DNA secondary structure with a transition pH of 6.6. Characterization of the i-motif folding pattern using mutational studies coupled with circular dichroic spectra and thermal stability analyses revealed an 8:5:7 loop conformation as the predominant structure at pH 6.1. The folding pattern was further supported by chemical footprinting with bromine. In addition, a novel assay involving the sequential incorporation of a fluorescent thymine analog at each thymine position provided evidence of a capping structure within the top loop region of the i-motif. The potential of the GC-rich element within the bcl-2 promoter region to form DNA secondary structures suggests that the transition from the B-DNA to non-B-DNA conformation may play an important role in bcl-2 transcriptional regulation. Furthermore, the two adjacent large lateral loops in the i-motif structure provide an unexpected opportunity for protein and small molecule recognition.","number":"48","journal":"Journal of the American Chemical Society","author":[{"propositions":[],"lastnames":["Kendrick"],"firstnames":["Samantha"],"suffixes":[]},{"propositions":[],"lastnames":["Akiyama"],"firstnames":["Yoshitsugu"],"suffixes":[]},{"propositions":[],"lastnames":["Hecht"],"firstnames":["Sidney","M"],"suffixes":[]},{"propositions":[],"lastnames":["Hurley"],"firstnames":["Laurence","H"],"suffixes":[]}],"year":"2009","keywords":"#nosource","pages":"17667–17676 ST – The i–Motif in the bcl–2 P1 Prom","bibtex":"@article{Kendrick2009,\n\ttitle = {The i-{Motif} in the bcl-2 {P1} promoter forms an unexpectedly stable structure with a unique 8:5:7 loop folding pattern},\n\tvolume = {131},\n\tissn = {0002-7863},\n\turl = {http://dx.doi.org/10.1021/ja9076292},\n\tdoi = {10.1021/ja9076292},\n\tabstract = {Transcriptional regulation of the bcl-2 proto-oncogene is highly complex, with the majority of transcription driven by the P1 promoter site and the interaction of multiple regulatory proteins. A guanine- and cytosine-rich (GC-rich) region directly upstream of the P1 site has been shown to be integral to bcl-2 promoter activity, as deletion or mutation of this region significantly increases transcription. This GC-rich element consists of six contiguous runs of guanines and cytosines that have the potential to adopt DNA secondary structures, the G-quadruplex and i-motif, respectively. Our laboratory has previously demonstrated that the polypurine-rich strand of the bcl-2 promoter can form a mixture of three different G-quadruplex structures. In this current study, we demonstrate that the complementary polypyrimidine-rich strand is capable of forming one major intramolecular i-motif DNA secondary structure with a transition pH of 6.6. Characterization of the i-motif folding pattern using mutational studies coupled with circular dichroic spectra and thermal stability analyses revealed an 8:5:7 loop conformation as the predominant structure at pH 6.1. The folding pattern was further supported by chemical footprinting with bromine. In addition, a novel assay involving the sequential incorporation of a fluorescent thymine analog at each thymine position provided evidence of a capping structure within the top loop region of the i-motif. The potential of the GC-rich element within the bcl-2 promoter region to form DNA secondary structures suggests that the transition from the B-DNA to non-B-DNA conformation may play an important role in bcl-2 transcriptional regulation. Furthermore, the two adjacent large lateral loops in the i-motif structure provide an unexpected opportunity for protein and small molecule recognition.},\n\tnumber = {48},\n\tjournal = {Journal of the American Chemical Society},\n\tauthor = {Kendrick, Samantha and Akiyama, Yoshitsugu and Hecht, Sidney M and Hurley, Laurence H},\n\tyear = {2009},\n\tkeywords = {\\#nosource},\n\tpages = {17667--17676 ST -- The i--Motif in the bcl--2 P1 Prom},\n}\n\n","author_short":["Kendrick, S.","Akiyama, Y.","Hecht, S. M","Hurley, L. H"],"key":"Kendrick2009","id":"Kendrick2009","bibbaseid":"kendrick-akiyama-hecht-hurley-theimotifinthebcl2p1promoterformsanunexpectedlystablestructurewithaunique857loopfoldingpattern-2009","role":"author","urls":{"Paper":"http://dx.doi.org/10.1021/ja9076292"},"keyword":["#nosource"],"metadata":{"authorlinks":{}},"html":""},"bibtype":"article","biburl":"https://bibbase.org/zotero/eric.larG4","dataSources":["4i5C7S78DvJNsaHyg","5L2zM5wNE5CBYNuea"],"keywords":["#nosource"],"search_terms":["motif","bcl","promoter","forms","unexpectedly","stable","structure","unique","loop","folding","pattern","kendrick","akiyama","hecht","hurley"],"title":"The i-Motif in the bcl-2 P1 promoter forms an unexpectedly stable structure with a unique 8:5:7 loop folding pattern","year":2009}