Slow Freeze-Thaw Cycles Enhanced Hybridization of Kilobase DNA with Long Complementary Sticky Ends

Abstract

The creation of large information molecules may have played an essential role in the origins of life. In this study, we conducted slow freeze-thaw (F/T) experiments to test the possibility of enhanced hybridization between the complementary sticky ends attached to kilobase-sized DNA fragments at sub-nanomolar concentrations. DNA fragments of 2- and 3-kilobase pairs (kbp) with 50-base complementary sticky ends that can form 5 kbp-sized hybridization products were mixed. While simple incubation provided little hybridization product, significantly effective hybridization was observed after freezing and thawing at a controlled time rate (<0.3 K min⁻¹), even with small DNA concentrations (<1 nM). Furthermore, slow thawing had a more effect on hybridization than slow freezing. The reaction efficiency was reduced by rapid thawing instead of slow thawing, suggesting that the eutectic phase concentration played an important role in hybridization. A slow F/T cycle was effective even for the hybridization reaction between two 10 kbp DNA fragments, which yielded a 20 kbp product at sub-nanomolar concentrations. Repeating the slow F/T cycle significantly improved the reaction efficiency. The possible role of the F/T cycles in early Earth environments is discussed here.