Molecular crowding creates an essential environment for the formation of stable G-quadruplexes in long double-stranded DNA

• Published in: Nucleic acids research 2010-01, Vol.38 (1), p.327-338
• Main Authors: Zheng, Ke-wei, Chen, Zhao, Hao, Yu-hua, Tan, Zheng
• Format: Article
• Language: English
• Subjects: DNA - chemistry; DNA Footprinting; Electrophoresis, Polyacrylamide Gel; G-Quadruplexes; Humans; Polyethylene Glycols - chemistry; Potassium - chemistry; Structural Biology; Sulfuric Acid Esters
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkp898

Large numbers of guanine-rich sequences with potential to form G-quadruplexes have been identified in genomes of various organisms. Such sequences are constrained at both ends by long DNA duplex with a complementary strand in close proximity to compete for duplex formation. G-quadruplex/duplex competition in long double-stranded DNA has rarely been studied. In this work, we used DMS footprinting and gel electrophoresis to study G-quadruplex formation in long double-stranded DNA derived from human genome under both dilute and molecular crowding condition created by PEG. G-quadruplex formation was observed in the process of RNA transcription and after heat denaturation/renaturation under molecular crowding condition. Our results showed that the heat denaturation/renaturation treatment followed by gel electrophoresis could provide a simple method to quantitatively access the ability of G-quadruplex formation in long double-stranded DNA. The effect of K⁺ and PEG concentration was investigated and we found that stable G-quadruplexes could only form under the crowding condition with PEG at concentrations near the physiological concentration of biomass in living cells. This observation reveals a physical basis for the formation of stable G-quadruplexes in genome and supports its presence under the in vivo molecular crowding condition.