Structure of an alternating-B DNA helix and its relationship to A-tract DNA.

Yoon, Chun; Privé, G.G.; Goodsell, David S.; Dickerson, Richard E.

doi:10.1073/pnas.85.17.6332

Cited by 252 publications

(233 citation statements)

References 34 publications

Supporting

Mentioning

215

Contrasting

Unclassified

Order By: Relevance

“…Characteristic shifts in position, lineshape, and intensity also occur for each of the other peaks. Calculated SXD patterns of B-form duplex models built by using d(A) 20 and d(AT) 10 sequences are almost identical (data not shown), indicating that characteristic B-and BЈ-form SXD patterns arise from conformational differences and not sequence differences.…”

Section: Resultsmentioning

confidence: 84%

“…Fig. 2A shows experimental SXD patterns measured for d(AT) 10 , d(A) 20 , and d(A) 10 duplexes from top to bottom, respectively, each recorded in 100 mM NaCl solution at two temperatures, room temperature and 3°C. The detection of diffraction peaks for solution-state DNA is significant because it provides a direct measure of in situ structure and configurational dispersion.…”

Section: Resultsmentioning

confidence: 99%

“…Experimental SXD patterns are quantitatively compared with those calculated from coordinate models and MD simulations for three AT-rich duplex DNA sequences, d(A) 10 , d(A) 20 , and d(AT) 10 . SXD experiments show that the alternating poly(deoxyadenosine-deoxythymidine)-poly(deoxyadenosine-deoxythymidine) duplex [poly(AT)] and homopolyer poly(deoxyadenosine)-poly(deoxythymidine) duplex [poly(A)-poly(T)] sequences differ in solution-state conformation and adopt conformations close to canonical B-form and BЈ-form conformations (18)(19)(20)(21), respectively. In contrast, MD simulations for a variety of AT-rich sequences were found to be biased toward similar B-form conformations, and clear discrepancies are resolved between experimentally observed and simulated ensembles.…”

mentioning

confidence: 99%

See 2 more Smart Citations

X-ray diffraction “fingerprinting” of DNA structure in solution for quantitative evaluation of molecular dynamics simulation

Zuo

Cui

Merz

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

109

137

View full text Add to dashboard Cite

Solution state x-ray diffraction fingerprinting is demonstrated as a method for experimentally assessing the accuracy of molecular dynamics (MD) simulations. Fourier transforms of coordinate data from MD simulations are used to produce reciprocal space ''fingerprints'' of atomic pair distance correlations that are characteristic of the ensemble and are the direct numerical analogues of experimental solution x-ray diffraction (SXD). SXD experiments and MD simulations were carried out to test the ability of experiment and simulation to resolve sequence-dependent modifications in helix conformation for B-form DNA. SXD experiments demonstrated that solution-state poly(AT) and poly(A)-poly(T) duplex DNA sequences exist in ensembles close to canonical B-form and B -form structures, respectively. In contrast, MD simulations analyzed in terms of SXD fingerprints are shown to deviate from experiment, most significantly for poly(A)-poly(T) duplex DNA. Compared with experiment, MD simulation shortcomings were found to include both mismatches in simulated conformer structures and number population within the ensembles. This work demonstrates an experimental approach for quantitatively evaluating MD simulations and other coordinate models to simulate biopolymer structure in solution and suggests opportunities to use solution diffraction data as experimental benchmarks for developing supramolecular force fields optimized for a range of in situ applications. solution x-ray scattering ͉ wide-angle x-ray scattering ͉ A-tract DNA ͉ structural landscape C haracterization of the structure and dynamics of biological macromolecules in liquids and other physiologically relevant noncrystalline media is critical for achieving a full understanding of chemical and biological function at the molecular level (1, 2). Molecular dynamics (MD) simulations based on molecular mechanical force fields and Ewald-type treatments for the long-range electrostatic interactions have been remarkably successful in simulating the general features of DNA sequence-dependent conformations, conformational transitions, and nucleic acid-drug interactions (3-5). However, variances in the details of simulated DNA structure based on choice of force fields and simulation conditions (4, 6) suggest levels of uncertainty in the prediction of DNA structure that are likely to undermine attempts to understand function at the atomic scale.A general problem for the evaluation of MD simulation is the lack of a sufficient experimental database on solution-state DNA structure. Crystal-packing distortions of DNA and the intrinsic lack of long-range structural data from NMR measurements restricts the reliable database on DNA structure to local structural parameters (7,8). It is an open question whether force fields focused primarily on local structure parameters are sufficient to accurately model the full range of DNA conformational landscapes in solution.Recently, a number of reports have shown that wide-angle x-ray scattering provides a direct measure of macromolecular conforma...

show abstract

Section: Resultsmentioning

confidence: 84%

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

See 1 more Smart Citation

X-ray diffraction “fingerprinting” of DNA structure in solution for quantitative evaluation of molecular dynamics simulation

Zuo

Cui

Merz

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

109

137

View full text Add to dashboard Cite

show abstract

“…X-ray crystallographic characterization of relatively short DNA duplexes containing A tracts has shown that the A tract region has a narrowed minor groove and is relatively straight and rigid (4)(5)(6). The large propeller twisting observed for the adenine residues within the A tracts themselves accounts in part for the observed rigidity (7).…”

mentioning

confidence: 99%

“…In the investigation described here, we have examined these structural and energetic features in two DNA dodecamers, which have been characterized by X-ray crystallography (5,6,16). These dodecamers, 5′-CGCAAATTTGCG-3′ and 5′-CGCATATATGCG-3′ [hereafter termed A 3 T 3 and (AT) 3 , respectively], have the same base composition and, at the 5′ and 3′ ends, the same base sequence.…”

mentioning

confidence: 99%

UV Resonance Raman and Circular Dichroism Studies of a DNA Duplex Containing an A₃T₃ Tract: Evidence for a Premelting Transition and Three-Centered H-Bonds

Mukerji

Williams

2001

Biochemistry

View full text Add to dashboard Cite

The presence of A n and A n T n tracts in double-helical sequences perturbs the structural properties of DNA molecules, resulting in the formation of an alternate conformation to standard B-DNA known as B‘-DNA. Evidence for a transition occurring prior to duplex melting in molecules containing A n tracts was previously detected by circular dichroism (CD) and calorimetric studies. This premelting transition was attributed to a conformational change from B‘- to B-DNA. Structural features of A n and A n T n tracts revealed by X-ray crystallography include a large degree of propeller twisting of adenine bases, narrowed minor grooves, and the formation of three-centered H-bonds between dA and dT bases. We report UV resonance Raman (UVRR) and CD spectroscopic studies of two related DNA dodecamer duplexes, d(CGCAAATTTGCG)2 (A3T3) and d(CGCATATATGCG)2 [(AT)3]. These studies address the presence of three-centered H-bonds in the B‘ conformation and gauge the impact of these putative H-bonds on the structural and thermodynamic properties of the A3T3 duplex. UVRR and CD spectra reveal that the premelting transition is only observed for the A3T3 duplex, is primarily localized to the dA and dT bases, and is associated with base stacking interactions. Spectroscopic changes associated with the premelting transition are not readily detectable for the sugar−phosphate backbone or the cytosine and guanosine bases. The temperature-dependent concerted frequency shifts of dA exocyclic NH2 and dT C4O vibrational modes suggest that the A3T3 duplex forms three-centered hydrogen bonds at low temperatures, while the (AT)3 duplex does not. The enthalpy of this H-bond, estimated from the thermally induced frequency shift of the dT C4O vibrational mode, is approximately 1.9 kJ/mol or 0.46 kcal/mol.

show abstract

Theoretical studies of the intercalation of 9-hydroxyellipticine in DNA

1998

View full text Add to dashboard Cite

Structure of an alternating-B DNA helix and its relationship to A-tract DNA.

Abstract: The crystal structure of the synthetic DNA dodecamer CGCATATATGCG has been solved at 2.2-A resolution.

Cited by 252 publications

References 34 publications

X-ray diffraction “fingerprinting” of DNA structure in solution for quantitative evaluation of molecular dynamics simulation

X-ray diffraction “fingerprinting” of DNA structure in solution for quantitative evaluation of molecular dynamics simulation

UV Resonance Raman and Circular Dichroism Studies of a DNA Duplex Containing an A₃T₃ Tract: Evidence for a Premelting Transition and Three-Centered H-Bonds

Theoretical studies of the intercalation of 9-hydroxyellipticine in DNA

Contact Info

Product

Resources

About

Structure of an alternating-B DNA helix and its relationship to A-tract DNA.

Abstract: The crystal structure of the synthetic DNA dodecamer CGCATATATGCG has been solved at 2.2-A resolution.

Cited by 252 publications

References 34 publications

X-ray diffraction “fingerprinting” of DNA structure in solution for quantitative evaluation of molecular dynamics simulation

X-ray diffraction “fingerprinting” of DNA structure in solution for quantitative evaluation of molecular dynamics simulation

UV Resonance Raman and Circular Dichroism Studies of a DNA Duplex Containing an A3T3 Tract: Evidence for a Premelting Transition and Three-Centered H-Bonds

Theoretical studies of the intercalation of 9-hydroxyellipticine in DNA

Contact Info

Product

Resources

About

UV Resonance Raman and Circular Dichroism Studies of a DNA Duplex Containing an A₃T₃ Tract: Evidence for a Premelting Transition and Three-Centered H-Bonds