Document Detail

Self-Assembly of Polydeoxyadenylic Acid Studied at the Single-Molecule Level.
MedLine Citation:
PMID:  22085264     Owner:  NLM     Status:  Publisher    
The investigation on the self-assembly of polydeoxyadenylic acid (poly(dA)) is of high importance to fully understand its biological function and for the nano-machine application. Using the fluorescence resonance energy transfer (FRET) technique, we report investigations for the self-assembly of adenine oligomers induced by pH and coralyne binding at the single-molecule level and in the bulk phase. Results presented here show that <b>A-motif 1</b> (Alexa488-5'-(dA)<sub>20</sub>-3'-Cy5-5'-(dA))<sub>20</sub>-3'-Alexa488) forms the wire-type duplex at acidic pH, whereas the same conformation of <b>A-motif 2</b> (Alexa488-5'-(dA))<sub>20</sub>-3'-Cy5-3'-(dA))<sub>20</sub>-5'-Alexa488) is induced by coralyne binding at neutral pH. These results indicate that poly(dA) at acidic pH forms a right-handed helical duplex with parallel-mannered chains whereas the coralyne-poly(dA) binding induces a stable anti-parallel duplex. Furthermore, we found that the anti-parallel duplex of poly(dA) formed by coralyne binding has a rather extended and less twisted structure compared to the parallel duplex of poly(dA) formed at acidic pH. On the other hand, from dilution experiments, we found that the parallel duplex formed at acidic pH is converted to "S-form", which has the single-stranded structure with short intramolecular double-stranded regions formed by intramolecular A:A base pairing, while the A-motif-coralyne assembly is dissociated into single strands under a certain concentration. The formation of S-form with a short intramolecular double-stranded region formed at acidic pH and very low concentration is confirmed by the quantitative analysis of FCS curve to measure the hydrodynamic radius of a molecule.
Sooyeon Kim; Jungkweon Choi; Tetsuro Majima
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Publication Detail:
Type:  JOURNAL ARTICLE     Date:  2011-11-15
Journal Detail:
Title:  The journal of physical chemistry. B     Volume:  -     ISSN:  1520-5207     ISO Abbreviation:  -     Publication Date:  2011 Nov 
Date Detail:
Created Date:  2011-11-16     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  101157530     Medline TA:  J Phys Chem B     Country:  -    
Other Details:
Languages:  ENG     Pagination:  -     Citation Subset:  -    
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