Adjacent G:A mismatch base pairs contain BII phosphodiesters in solution

Chou, Seemay; Cheng, Jya Wei; Fedorov, O.; Chuprina, V. P.; Reid, Brian R.

doi:10.1021/ja00034a055

Cited by 52 publications

(38 citation statements)

References 0 publications

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“…These changes, to a B11 phosphate geometry from a B1 type, have been documented previously, particularly in the native crystal structure (26) (at residues C-10 and C-22), in several decamers (27), including an A-G mismatch structure (28), and in several recent NMR studies of purine-purine mismatches (15,29,30).…”

Section: (Anti)supporting

confidence: 70%

Crystal structure of an oligonucleotide duplex containing G.G base pairs: influence of mispairing on DNA backbone conformation.

Skelly

Edwards

Jenkins

et al. 1993

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

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The structure of the G-G mispaired dodecanucleotide d(CGCGAATTGGCG)2 has been solved by x-ray crystallography and refined to an R factor of 18.8% at 2.2 A resolution for 3513 reflections. The dodecamer crystallizes as a B-type DNA double helix. It contains two G(and){G(syn) base pairs-i.e., G-4/G-16(antd)G-21/G-9(syn). The Hoogsteen base pairing involves atoms 0-6 and N-7 of the guanne in the syn conformation with atoms N-1 and N-2 of the anti-paired purine. One G-G base pair has a bifurcated hydrogen bond between G-4(N-1).G-21(N-7) and G-4(N-1)-G-21(O-6). There is little overall structural distortion of the double helix induced as a consequence of the mispiring. The helical width is significantly increased by comparison with the structure of the native duplex, and the minor groove width in the 5'-AATT region is decreased. The GIG base pairing induces high-BIu phosphate conformations at residues G-9 and T-20 in addition to more normal Be conformations at G-10 and G-22. It is suggested that these backbone aberrations provide signals for the facile repairability of GIG mispairs in DNA.DNA base mispairings or mismatches occur as a consequence of errors in genetic recombination and/or replication (1-3). These errors are corrected by a repair system that recognizes the lesion, unwinds the duplex, and excises the newly synthesized strand. Purine-containing mispairs occur more frequently than pyrimidine-pyrimidine pairs, with the ARC and G-G mispairings being the most efficiently repaired. G-G base pairing plays a major role in stabilizing telomere structure (4-9) and is important in purine-purine DNA triplexes (10) and in various RNA stem bulges (11).Several models for G-G-mispaired structures have been proposed (see, for example, refs. 6, 8, 12, and 13). A G(anti)-G(syn) base arrangement has been suggested for the GIG pairing in a DNA duplex, while NMR data and molecular models suggest that the guanines are hydrogen-bonded in a cyclic fashion for the four-stranded quartet structure in telomeric DNA. NMR solution data for the d(GAGGAGGACG)-d(CGTGCGTCCTC) duplex, containing a central G-G mispair (14), suggest that the bases adopt a symmetrical anti-syn arrangement and are stacked into the helical axis. The hydrogen-bonding pattern preferred by these authors involves symmetric hydrogen bonding between the N-1 imino protons and the 0-6 carbonyl oxygen atom. A recent solution NMR analysis of the d(CGCGAATTGGCG)2 duplex indicates that the G(anti)-G(anti) conformation is favored at low temperatures and under high-salt conditions, with the structure characterized by non-hydrogen-bonded G&G base pairs. This conformation is, however, unstable at higher temperatures, as judged by spectral heterogeneity, with the mispairing bases providing a focus for localized melting. Localized DNA bulges were considered to result from unusual phosphate backbone torsion angles in the vicinity of the G-G sites (15). In contrast, the recently reported crystal structure and NMR analysis of the four-stranded d(G4T4G4)2 sequence from the 3'...

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Section: (Anti)supporting

confidence: 70%

Crystal structure of an oligonucleotide duplex containing G.G base pairs: influence of mispairing on DNA backbone conformation.

Skelly

Edwards

Jenkins

et al. 1993

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

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“…144 Structure 8 involves a protonated adenine forming a base pair with an unprotonated adenine, as reported for a DNA duplex. 145,146 Structure 9 involves protonated adenine engaged in Hoogsteen pairing with guanine, as reported for a DNA duplex. 146 backbone, it does offer the possibility for the existence of local regions with enormous negative surface potential.…”

mentioning

confidence: 85%

Catalytic roles for proton transfer and protonation in ribozymes

Bevilacqua

Brown

Nakano³

et al. 2003

Biopolymers

149

185

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Utilization of proton transfer in catalysis, which is well known in the mechanisms of protein enzymes, has been described only relatively recently for RNA enzymes. In this article, we present a current understanding of proton transfer by nucleic acids. Rate enhancement and specificity conferred by general acid-base catalysis are discussed. We also present possibilities for electrostatic catalysis from general acids and bases as well as cationic base pairs. The microenvironments of a large RNA provide the possibility of histidine-like pK(a)s for proton transfer, as well as lysine- and arginine-like pK(a)s for electrostatic catalysis. Discussion on proton transfer focuses on the hepatitis delta virus (HDV) and hairpin ribozymes, with select examples drawn from the protein literature. Discussion on electrostatic catalysis also draws on these two ribozymes, and a postulate for electrostatic catalysis by a cationic base pair in the mechanism of peptidyl transfer in the ribosome is presented. We also provide a perspective on possibilities for phosphoryl transfer mechanisms involving phosphorane intermediates and unusual tautomeric forms of the bases. Lastly, a distinction is made between ground state and "transition state" pK(a)s. We favor a model in which changes in pH lead to changes in the distribution of reactive and nonreactive ionizations of the ribozyme molecules in the ground state, and therefore suggest that "pK(a) changes in the transition state" do not provide an acceptable explanation for observed pH-rate profiles.

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“…A new type of double helix involving sheared or side-by-side tandem G ÁA pairs (A-N 6 H to G-N3 and G-N 2 H to A-N7) was proposed based on G to I substitution (Li et al, 1991a). Extensive studies of tandem GÁA mismatches have since been reported (Chou et al, 1992a(Chou et al, ,b, 1994aCheng et al, 1992;Lane et al, 1992Lane et al, , 1994Katahira et al, 1993;Green et al, 1994). NMR studies revealing several unusual proton NOE proximities have made possible the determination of solution structures of duplexes containing antiparallel GA:GA motifs with quite high precision by distance geometry combined with back-calculation and molecular dynamics re®nement methods (Chou et al, 1994a;Green et al, 1994).…”

Section: The [Py(ga)pu] 2 Motifmentioning

confidence: 99%

“…However, recent experiments have shown that sheared G ÁA base-pairing is an exception to this rule. The special geometry of sheared or side-by-side G Á A pairing has been found to be quite stable and compatible with¯anking WatsonCrick base-paired B-form DNA structure either as tandem base-pairs in (CGAG) 2 or (TGAA) 2 contexts (Li et al, 1991a,b;Chou et al, 1992aChou et al, ,b, 1994aCheng et al, 1992;Lane et al, 1992Lane et al, , 1994Katahira et al, 1993;Green et al, 1994), as base-pairs closing single-residue hairpin loops (Hirao et al, 1994;Zhu et al, 1995aZhu et al, , 1996Chou et al, 1996a,b), as basepairs closing two-residue hairpin loops (Hirao et al, 1989(Hirao et al, , 1990, as base-pairs bracketing unpaired purines (Chou et al, 1994b;Zhu et al, 1995bZhu et al, , 1996, or as base-pairs bracketing a single unpaired purine (our unpublished results). Due to their great potential in important biological functions such as DNA replication and centromere formation, we will describe structural characteristics of this type of basepairing and discuss its occurrence in the chromosomes of several single-stranded DNA viruses and in the centromere of human chromosomes.…”

Section: Introductionmentioning

confidence: 99%