Consecutive GC base pairs determine the energy barrier of DNA duplex formation under molecularly crowded conditions

Abstract

The kinetics of DNA duplex formation was affected by the addition of PEGs with different masses (MW = 200–8000) to an aqueous solution; for each condition, two duplexes (5′-TAGGTTATAA-3′/5′-TTATAACCTA-3′ and 5′-CAGGTCACAG-3′/5′-CTGTGACCTG-3′) with different stabilities were formed after overcoming the same association activation energy barrier, suggesting that the formation of consecutive GC base pairs in the helices rather than the helix terminus is the initiation nucleus for DNA duplex formation not only in the absence, but also in the presence of PEGs.