Molecular Basis for Sequence‐Dependent Induced DNA Bending

Abstract

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

Structure‐Dependent Binding of Arylimidamides to the DNA Minor Groove

“…Replication of the circular, interlocked kinetoplast DNA appears to be particularly sensitive to the diamidines, perhaps due to compound-induced conformational changes that disrupt the kinetoplast structure. [22][23][24] There are no known DNA structures in humans that are equivalent to the kinetoplast, so targeting the kinetoplast offers an excellent route to selective drug action. [11] The diamidines are taken up into T. brucei cells by the P2 membrane transporter, and, because the parasite lives in blood in all initial stages of infection, uptake is quite effective.…”

First Structure of a Designed Minor Groove Binding Heterocyclic Cation that Specifically Recognizes Mixed DNA Base Pair Sequences

“…The rmsd value for DB2277-DNA is in good agreement with the values obtained from previous DNA minor groove complex studies. [16,31] The average structure from the 2 ns rMD is used as a reference for rmsd fitting. Snapshots were obtained every 10 ps for the last 100 ps of rMD calculations for both free DNA and the DB2277-DNA complex.…”

“…These protona ssignments were further confirmed and supported by employing 2D TOCSY, 31 P-correlated 2D spectra (HPCOR) and 13 C-1 HH SQC experiments (see details in the Supporting Information). Ap roton-decoupled 31 Ps pectrum with phosphorus assignments for free DNA is shown in Figure S3A and chemical shifts of a 31 P( d P in ppm) signalf or both free DNA andD B2277-DNAc omplex are plottedi nF igure S3B.…”

“…This sequence has been used in the high-resolution NMR investigations of the DB2277-AAGATAc omplex structure reported here. Both 1D and 2D 1 Ha nd 31 Ps pectra were collected in H 2 Oa nd D 2 O( buffer solution).T he NMR results were used in restrained molecular dynamics (rMD) calculations to determine the structure of the DB2277c omplex. Examination of the structure indicates that the aza BI group forms two strong H-bonds with the G·C bp.…”

Fluorescent Methods to Study Transcription Initiation and Transition into Elongation

“…DNA conformational changes like bending can be detected using structural methods such as X-ray crystallography [31-33], nuclear magnetic resonance [34], electron microscopy [35], atomic force microscopy [36, 37], electrophoretic mobility assays like circular permutation assay [38–40] and helical phasing assay [39, 41, 40], ring closure methods [39, 42, 40], and fluorescence methods including Förster resonance energy transfer (FRET). FRET methods are increasingly used in transcription for monitoring DNA bending changes and for monitoring movements of the RNAP relative to the DNA [19, 43, 30, 22, 44].…”