The detailed conformational dynamics of the melted region in double stranded DNA has been studied using ensemble and single molecule FRET measurements. We have observed the millisecond time scale fluctuation kinetics of the two stands that varies with the size of the bubble. The individual strands at the melting bubble believed to behave as single stranded DNA and hence fluctuate dynamically to attain energetically favoured configurations. The rate of fluctuation increases with increase in the bubble size. However, irrespective of the number of base pair mismatches present in different short DNAs under investigation, they were never found to form a knot to cross each other. Rather, the two strands prefer staying away from each other, as the size of the bubble increases and follow exactly an opposite trend for bubbles with smaller size. From the measured FRET values, the range within which the bubble strands fluctuate are accurately monitored in nanometre resolution. The shape of the bubble, which plays a crucial role in determining the activity of that DNA has been speculated. The results shall be useful in quantifying chemical processes within DNA, as well as to develop a deeper understanding of the activity of the DNA due to induced mismatches.

Direct observation of breathing dynamics at the mismatch induced DNA bubble by smFRET measurement

253rd National Meeting (2017)

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