Nanomechanics of Diaminopurine-Substituted DNA

Abstract

2,6-diaminopurine (DAP) is a nucleobase analog of adenine. When incorporated into double-stranded DNA (dsDNA), it forms three hydrogen bonds with thymine. Rare in nature, DAP substitution alters the physical characteristics of a DNA molecule without sacrificing sequence specificity. Here, we show that in addition to stabilizing double-strand hybridization, DAP substitution also changes the mechanical and conformational properties of dsDNA. Thermal melting experiments reveal that DAP substitution raises melting temperatures without diminishing sequence-dependent effects. Using a combination of atomic force microscopy (AFM), magnetic tweezer (MT) nanomechanical assays, and circular dichroism spectroscopy, we demonstrate that DAP substitution increases the flexural rigidity of dsDNA yet also facilitates conformational shifts, which manifest as changes in molecule length. DAP substitution increases both the static and dynamic persistence length of DNA (measured by AFM and MT, respectively). In the static case (AFM), in which tension is not applied to the molecule, the contour length of DAP-DNA appears shorter than wild-type (WT)-DNA; under tension (MT), they have similar dynamic contour lengths. At tensions above 60 pN, WT-DNA undergoes characteristic overstretching because of strand separation (tension-induced melting) and spontaneous adoption of a conformation termed S-DNA. Cyclic overstretching and relaxation of WT-DNA at near-zero loading rates typically yields hysteresis, indicative of tension-induced melting; conversely, cyclic stretching of DAP-DNA showed little or no hysteresis, consistent with the adoption of the S-form, similar to what has been reported for GC-rich sequences. However, DAP-DNA overstretching is distinct from GC-rich overstretching in that it happens at a significantly lower tension. In physiological salt conditions, evenly mixed AT/GC DNA typically overstretches around 60 pN. GC-rich sequences overstretch at similar if not slightly higher tensions. Here, we show that DAP-DNA overstretches at 52 pN. In summary, DAP substitution decreases the overall stability of the B-form double helix, biasing toward non-B-form DNA helix conformations at zero tension and facilitating the B-to-S transition at high tension.

Nanomechanics of negatively supercoiled diaminopurine-substituted DNA

“…Accordingly, the dashed lines in Figure 2 show the slopes calculated following the model in ref. (34), assuming a best fit value of persistence length Lp=80 obtained from MT measurements has been already reported in literature (5,9) and is compatible with our best fit values.…”

“…WT and DAP DNA were prepared as previously described (9). Briefly, for the MT experiments T7 DNA ligase was used to ligate a ∼1.0 kbp, multiply digoxigenin-labeled (dig-tail) DNA fragment at one end of a 4642 bp (main) DNA fragment and a ∼0.9 kbp, multiply biotin-labeled (bio-tail) DNA fragment to the other end.…”

“…Other data regarding the cyclization of DAP-substituted DNA (DAP-DNA) fragments or binding and obligate tight curling around histone octamers to form nucleosomes indicates that DAP-DNA is flexurally stiffer than unmodified DNA (10,11,12). This is substantiated by increased stiffness exhibited by DAP-DNA molecules a few hundred-to kilo-bases in length deposited on surfaces for atomic force microscopy (9,11,12) and the increased persistence lengths determined using optical or magnetic tweezers to stretch single molecules of DAP-DNA (9,12). Overtwisting DAP-DNA under slight tension also exhibits increased flexural stiffness associated with creating plectonemic coils (5).…”

“…Substitution of DAP for adenine is known to increase the melting temperature of the B-form (1,6,7). Sequence-specific effects persist and the Santa Lucia model for calculating the melting temperature (8) can be adjusted by uniformly scaling the dinucleotide enthalpies (9). Other data regarding the cyclization of DAP-substituted DNA (DAP-DNA) fragments or binding and obligate tight curling around histone octamers to form nucleosomes indicates that DAP-DNA is flexurally stiffer than unmodified DNA (10,11,12).…”

“…Overtwisting DAP-DNA under slight tension also exhibits increased flexural stiffness associated with creating plectonemic coils (5). While the persistence length of DAP-DNA reflects increased rigidity, the overstretching transition of this DNA occurs at a lower tension (9). Thus, DAP-DNA is more rigid and also more susceptible to mechanically induced, structural, phase changes.…”