Probing Sequence-Specific DNA Flexibility in A-Tracts and Pyrimidine-Purine Steps by Nuclear Magnetic Resonance ¹³C Relaxation and Molecular Dynamics Simulations

Abstract

Sequence-specific DNA flexibility plays a key role in a variety of cellular interactions that are critical for gene packaging, expression, and regulation. Yet, few studies have experimentally explored the sequence dependence of DNA dynamics that occur on biologically relevant timescales. Here, we use nuclear magnetic resonance (NMR) carbon spin relaxation combined with molecular dynamics (MD) simulations to examine the picosecond to nanosecond dynamics in a variety of dinucleotide steps as well as in varying length homopolymeric An•Tn repeats (An-tracts, n = 2, 4 and 6) that exhibit unusual structural and mechanical properties. We extend the NMR spin relaxation timescale sensitivity deeper into the nanosecond regime by using glycerol and a longer DNA duplex to slow down overall tumbling. Our studies reveal a structurally unique A-tract core (for n > 3) that is uniformly rigid, flanked by junction steps that show increasing sugar flexibility with A-tract length. High sugar mobility is observed at pyrimidine residues at the A-tract junctions, which is encoded at the dinucleotide level (CA, TG and CG steps) and increases with A-tract length. The MD simulations reproduce many of these trends, particularly the overall rigidity of A-tract base and sugar sites, and suggest that the sugar-backbone dynamics could involve transitions in sugar pucker and phosphate backbone BI↔BII equilibria. Our results reinforce an emerging view that sequence-specific DNA flexibility can be imprinted in dynamics occurring deep within the nanosecond time regime that is difficult to characterize experimentally at the atomic level. Such large amplitude sequence-dependent backbone fluctuations might flag the genome for specific DNA recognition.

On the Possibility of Facilitated Diffusion of Dendrimers Along DNA

“…Our findings in the area of bond motion via S 2 could be readily verifiable by NMR liquid state experiments, 67,87 in which one can label the nitrogens with 15 N isotopes, and can reveal binding dynamics through the measurement of order parameters.…”

Lessons learned in atomistic simulation of double-stranded DNA: Solvation and salt concerns [Article v1.0]

“…The dynamic nature of terminal base pair fraying makes it difficult to study experimentally. Spin relaxation measurements on DNA with G:C terminal pairs report motions in the picosecond to nanosecond time scale [58,59]. As a way to assess these events, we measured the distance between the C1' atoms of pairing bases.…”

Local DNA Sequence Controls Asymmetry of DNA Unwrapping from Nucleosome Core Particles

“…In addition, DNA sequences encode mechanical features to facilitate its packaging and to control nucleotide access. For example, the CG content of a sequence correlates with an increase in short-range ($3 bases) bending and a decrease in longer-range bending ($10 bases) (15), and poly-A stretches contribute to especially rigid conformations (16). Finally, dinucleotide pyrimidine-purine steps (YR, such as CA, CG, TA, and TG) are known to be the most conformationally flexible (17).…”