Reversible bending and helix geometry in a B-DNA dodecamer: CGCGAATTBrCGCG.

Fratini, Albert; Kopka, Mary L.; Drew, Horace R.; Dickerson, Richard E.

doi:10.1016/s0021-9258(18)33335-0

Cited by 622 publications

(215 citation statements)

References 51 publications

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“…This at first surprising finding is in fact quite consistent with the 'polar-on-polarizable' stacking observed in crystals of nucleic acid constituents [22], hydrophobic interiors of proteins [23,24], aromatic molecules in general [25] and oligonucleotides [26]. 4. Because the minor groove runs at roughly a 40° angle to the DNA helix axis, the ring-upon-amide stacking just mentioned ensures that two drug rings sit next to one another at approximately the level of each base pair.…”

Section: Introductionsupporting

confidence: 78%

“…Secondly, because an AT base pair has only two hydrogen bonds, it can twist or propeller more than a GC pair with three such bonds. Propeller twisting narrows the groove by shifting the positions of C1′ atoms (see Figure 9 of [4]), producing a narrow groove that is hospitable to a planar drug molecule. Thirdly, the absence of an N2 amine group on adenine makes the groove deeper; conversely, the guanine amine tends to push the drug away.…”

Section: Introductionmentioning

confidence: 99%

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Defining GC-specificity in the minor groove: side-by-side binding of the di-imidazole lexitropsin to C-A-T-G-G-C-C-A-T-G

et al. 1997

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Im and Py rings distinguish AT from GC base pairs because of steric factors involving the bulk of the guanine amine, and the ability of Im to form a hydrogen bond with the amine. Side-by-side Im and Py rings differentiate GC from CG base pairs because of tight steric contacts and sp2 hybridization at the amine nitrogen atom, with the favored conformations being G/Im,Py/C and C/Py,Im/G. Discrimination between AT and TA base pairs may be possible using bulkier rings, such as thiazole to select the A end of the base pair.

show abstract

Section: Introductionsupporting

confidence: 78%

Section: Introductionmentioning

confidence: 99%

Defining GC-specificity in the minor groove: side-by-side binding of the di-imidazole lexitropsin to C-A-T-G-G-C-C-A-T-G

et al. 1997

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“…The hybrid duplex adopts a standard A-form conformation (Figure 2) with all the helical parameters resembling those of A-DNA or A-RNA. Helical parameters were calculated using the program NEWHEL92 [24]. As indicated in Table 1, the helical parameters manifest a highly regular A-form duplex.…”

Section: Helical Parameters and Backbone Conformationmentioning

confidence: 99%

Crystal structure and conformation of a DNA–RNA hybrid duplex with a polypurine RNA strand: d(TTCTTBr5CTTC)–r(GAAGAAGAA)

Xiong

Sundaralingam

1998

Structure

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“…Polyamines bind to DNA and neutralize these charges (11), although hydrogen bonding, hydrophobic interactions and possible site-specificity have also been invoked in the binding of these compounds to DNA (for review see 2). X-ray crystallographic data and studies based on energy minimization calculations, indicate that spermine is localized along the edge of the major groove ofDNA (12)(13)(14)(15)(16). Polyamine binding has profoundeffects on DNA structure causing transitions from B to both A and Z forms (17-20) and at higher concentrations condensation of either naked DNA (21)(22)(23)(24)(25)(26) or chromatin (27,28).…”

Section: Introductionmentioning

confidence: 99%

Polyamines alter sequence-specific DNA-protein interactions

Panagiotidis

Artandi

Calame

et al. 1995

Nucleic Acids Research

111

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The polyamines are abundant biogenic cations implicated in many biological processes. Despite a plethora of evidence on polyamine-induced DNA conformational changes, no thorough study of their effects on the activities of sequence-specific DNA binding proteins has been performed. We describe the in vitro effects of polyamines on the activities of purified, representative DNA-binding proteins, and on complex protein mixtures. Polyamines at physiological concentrations enhance the binding of several proteins to DNA (e.g. USF, TFE3, Ig/EBP, NF-IL6, YY1 and ICP-4, a herpes simplex virus gene regulator), but inhibit others (e.g. Oct-1). The degree of enhancement correlates with cationic charge; divalent putrescine is ineffective whereas tetravalent spermine is more potent than trivalent spermidine. Polyamine effects on USF and ICP-4 result from increased rate of complex formation rather than a decreased rate of dissociation. DNAse I footprint analysis indicated that polyamines do not alter DNA-protein contacts. Polyamines also facilitate formation of complexes involving binding of more than one protein on a DNA fragment.

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Reversible bending and helix geometry in a B-DNA dodecamer: CGCGAATTBrCGCG.

Cited by 622 publications

References 51 publications

Defining GC-specificity in the minor groove: side-by-side binding of the di-imidazole lexitropsin to C-A-T-G-G-C-C-A-T-G

Defining GC-specificity in the minor groove: side-by-side binding of the di-imidazole lexitropsin to C-A-T-G-G-C-C-A-T-G

Crystal structure and conformation of a DNA–RNA hybrid duplex with a polypurine RNA strand: d(TTCTTBr5CTTC)–r(GAAGAAGAA)

Polyamines alter sequence-specific DNA-protein interactions

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