Microscopic Rearrangement of Bound Minor Groove Binders Detected by NMR

High-resolution crystal structures of the DNA duplex sequence d(CGCGAATTCGCG)2 complexed with three minor-groove ligands, are reported. A highly-conserved cluster, of eleven linked water molecules, has been found in the native and all three ligand-bound structures, positioned at the boundary of the A/T and G/C regions where the minor groove widens. This cluster appears to play a key structural role in stabilizing non-covalently-binding small molecules in the AT region of the B-DNA minor groove. The cluster extends from the backbone phosphate groups along the mouth of the groove and links to DNA and ligands by a network of hydrogen bonds that help to maintain the ligands in position. This arrangement of water molecules is distinct from, but linked by hydrogen-bonding to the well-established spine of hydration, which is displaced by bound ligands. Features of the water cluster and observed differences in binding modes help to explain the measured binding affinities and thermodynamic characteristics of these ligands on binding to AT sites in DNA.

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“…This suggests that DB1055 may be present in two orientations as found in solution for several other minor-groove ligands. 29 …”

Section: Resultsmentioning

confidence: 99%

Small-molecule Binding to the DNA Minor Groove Is Mediated by a Conserved Water Cluster

Wei¹,

Wilson

Neidle³

2013

J. Am. Chem. Soc.

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“…However, in addition to the slow exchange between free and bound DNA, netropsin similar to other minor groove binding ligands, exhibits microscopic rearrangements on the millisecond time scale. [30] In order to minimize this process we reduced the salt concentration to 20mM NaCl and temperature to 278K. Under these conditions, exchange cross peaks visible in NOESY and ROESY experiments between symmetry related protons (i.e.…”

Section: Resultsmentioning

confidence: 99%

“…[10,29,30,39] Briefly, continuous base-to-sugar NOESY networks between neighboring residues were used for the sequential assignment of both the free DNA (Supplementary Material, SM Figure 1) and netropsin complex (Figure 3A). In addition, DQF-COSY spectra were used to support the assignment of intraresidue sugar protons.…”

Section: Resultsmentioning

confidence: 99%

“…[12] X-ray and NMR structures of DNA duplexes with A-tracts have narrow minor grooves while alternating AT structures have been observed with both narrow and wide minor grooves and a variety of polymorphic structures. [25–30] …”

Section: Introductionmentioning

confidence: 99%

“…We have previously shown that minor groove binding ligands exhibit microscopic rearrangements on the millisecond time scale without dissociating off the DNA into the bulk solution. [30] This rearrangement results in chemical exchange processes and NMR signals that greatly complicate structure determination. It is therefore necessary to explore solution conditions and minor groove binding ligands where exchange process are minimal.…”

Section: Introductionmentioning

confidence: 99%

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Molecular Basis for Sequence‐Dependent Induced DNA Bending

et al. 2013

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With a growing understanding of the microstructural variations of DNA it has become apparent that subtle conformational features are essential for specific DNA molecular recognition and function. DNA containing an A-tract has a narrow minor groove and a globally bent conformation but the structural features of alternating AT DNA is less understood. Several studies indicate that alternating AT sequences are polymorphic with different global and local properties than A-tracts. The mobility of alternating AT DNA in gel electrophoresis is extensively reduced upon binding with minor groove binding agents such as netropsin. Although this suggests that such complexes are bent, similarly as A-tract DNA, direct evidence and structural information on AT DNA and the induced conformational change is lacking. We have used NMR and residual dipolar coupling together with restrained molecular dynamics simulations to determine the solution structures of an alternating AT DNA segment, with and without netropsin, in order to evaluate the molecular basis of the binding induced effects. Complex formation causes a significant narrowing of the minor groove and a pronounced change in bending, from a slight bend towards the major groove for the free DNA to a pronounced minor groove bend in the complex. This observation demonstrates that conformational features and the inherent malleability of AT sequences are essential for specific molecular recognition and function. These results take the field of DNA structures into new areas while opening up avenues to target novel DNA sequences

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Using capillary electrophoresis to characterize the hydrodynamic and electrostatic properties of DNA in solutions containing various monovalent cations

Stellwagen

2021

Electrophoresis

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Using capillary electrophoresis to characterize the hydrodynamic and electrostatic properties of DNA in solutions containing various monovalent cationsThis review describes the results obtained by using free-solution capillary electrophoresis to probe the electrostatic and hydrodynamic properties of DNA in solutions containing various monovalent cations. In brief, we found that the mobilities of double-stranded DNAs (dsDNAs) increase with increasing molecular weight before leveling off and becoming constant at molecular weights ≥400 bp. The mobilities of single-stranded DNAs (ssDNAs) go through a maximum at ∼10-20 nucleotides before decreasing and becoming constant for oligomers larger than ∼30-50 bases. The mobilities of both ss-and dsDNAs increase linearly with the logarithm of increasing charge per unit length and decrease linearly with the logarithm of increasing ionic strength. Surprisingly, ss-and dsDNA mobilities level off and become nearly constant at ionic strengths ≥0.6 M. The thermal stabilities of dsDNAs decrease linearly with increasing solution viscosity. The diffusion coefficients of dsDNA are modulated by the diffusion coefficients of their counterions because of electrostatic DNA-cation coupling interactions. Finally, the anomalously slow mobilities observed for A-tract-containing DNAs can be attributed both to differences in shape and to the preferential localization of small cations in the A-tract minor groove. Since many of these results are mirrored in other polyion-counterion systems, free-solution electrophoresis can be viewed as a reporter of the electrostatics and hydrodynamics of highly charged polyions. New results describing the mobilities of dsDNA analogues of a microRNA-messenger RNA complex are also presented.

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Microscopic Rearrangement of Bound Minor Groove Binders Detected by NMR

Cited by 12 publications

References 43 publications

Small-molecule Binding to the DNA Minor Groove Is Mediated by a Conserved Water Cluster

Small-molecule Binding to the DNA Minor Groove Is Mediated by a Conserved Water Cluster

Molecular Basis for Sequence‐Dependent Induced DNA Bending

Using capillary electrophoresis to characterize the hydrodynamic and electrostatic properties of DNA in solutions containing various monovalent cations

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