Non-Watson-Crick base associations in DNA and RNA revealed by single crystal x-ray diffraction methods: Mismatches, modified bases, and nonduplex DNA

Brown, Tom; Hunter, William N.

doi:10.1002/(sici)1097-0282(1997)44:1<91::aid-bip6>3.0.co;2-v

Cited by 23 publications

(14 citation statements)

References 61 publications

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“…3e). This minor groovespecific interaction is unlike other G-A interactions described previously [23][24][25][26][27] . The junction between A24 and A25 is stabilized by a 2.82 Å hydrogen bond between the 2'-OH of A24 and the O4' of A25 (not shown).…”

Section: An Extended Minor-groove Rna Triplexcontrasting

confidence: 48%

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et al. 1999

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Many viruses regulate translation of polycistronic mRNA using a -1 ribosomal frameshift induced by an RNA pseudoknot. A pseudoknot has two stems that form a quasi-continuous helix and two connecting loops. A 1.6 A crystal structure of the beet western yellow virus (BWYV) pseudoknot reveals rotation and a bend at the junction of the two stems. A loop base is inserted in the major groove of one stem with quadruple-base interactions. The second loop forms a new minor-groove triplex motif with the other stem, involving 2'-OH and triple-base interactions, as well as sodium ion coordination. Overall, the number of hydrogen bonds stabilizing the tertiary interactions exceeds the number involved in Watson-Crick base pairs. This structure will aid mechanistic analyses of ribosomal frameshifting.

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Section: An Extended Minor-groove Rna Triplexcontrasting

confidence: 48%

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et al. 1999

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“…These are (i) N (1) (40). If extended beyond the dimer level, iii results in a polymeric ribbon structure, as does a combination of i and iv (41).…”

Section: Discussionmentioning

confidence: 99%

Canonical and unconventional pairing schemes between bis(nucleobase) complexes oftrans-a₂Pt^II: Artificial nucleobase quartets and C—H…N bonds

Freisinger

Rother

Lüth

et al. 2003

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

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If two nucleobases are crosslinked by trans-a2Pt II , self-association via H bonding may take place either through individual bases or jointly through both bases. Due to the blockage of an acceptor site by the metal, the number of feasible pairing patterns can be reduced, and the preferred ones altered. If the metalated base pair as a whole undergoes association, base quartets can form. Various scenarios resulting from the application of guanine, hypoxanthine, and cytosine model nucleobases are discussed. Unconventional COH. . .N hydrogen bonding has been observed in several instances.H bonding ͉ platinum T he existence of cyclic guanine (G) quartets and the association of poly(G) and poly(I) into four-stranded structures have been known for quite some time (1, 2). Proof of the formation of G quartets in telomere sequences (3) and their existence in human cells (4), new insights on the structure of human telomeric DNA (5, 6), and, above all, implications that G quartets are potential drug targets for the chemotherapy of cancer, on the one hand, and can play a dysfunctional role, on the other (7), have made the field of DNA quadruplex structures a booming area. From an inorganic chemistry point of view, the involvement of metal ions in the formation and stabilization of G 4 structural elements is of particular interest. That these cations, K ϩ and Na ϩ under physiological conditions and many other cations under nonphysiological conditions, are absolutely essential for maintaining the G 4 structure elements has been recognized at an early stage. Moreover, it is now clear that a stem of G 4 quartets stabilizes other quartet structures, including those between dimers of Watson-Crick pairs, e.g., [GC] 2 (C, cytosine) (8).Small molecules that bind specifically to quadruplex DNA, thereby interfering with the enzyme telomerase or inhibiting expression of a crucial gene, are believed to be useful for chemotherapeutic applications. Among these, cationic porphyrins such as tetra-(N-methyl-4-pyridyl)porphine are particularly promising (4, 9, 10). Our interest in this area stems from our experience with metal-nucleobase complexes representing artificial base quartets that are cationic and flat and that have dimensions compatible with the natural base quartets. Because of their shape and charge, these compounds can be expected to have a natural affinity for tetra-stranded DNA in general and telomere sequences in particular. The use of metal ions (M) displaying linear coordination geometries and the fact that purine nucleobases, on simultaneous metal binding to N1 and N7, provide 90°angles between their M-N vectors and hence represent angular building blocks of squares and rectangles have enabled the construction of a variety of artificial M-base quartets (11-16). Examples are given in Scheme 1. Depending on the metal ions applied and the degree of crosslinking, these quartets can be kinetically labile or robust, also occasionally assembled by remarkably strong H bonds, even in solution. It will be our ultimate goal to probe t...

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“…Interestingly, the mismatch repair system does not repair all types of mismatches with equal efficiency, 3–5,18–23 suggesting that the differences in the intrinsic properties of DNA owing to different mismatches may play a role. Several biophysical, 24–26 biochemical, 27 and molecular biology experiments 18–21 have been carried out to characterize the mismatch efficiencies for different mismatch types. It was found that the probability of repair is correlated with both the mismatch and the neighboring nucleotide sequence.…”

Section: Introductionmentioning

confidence: 99%

DNA Bending Propensity in the Presence of Base Mismatches: Implications for DNA Repair

et al. 2013

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DNA bending is believed to facilitate the initial recognition of the mismatched base for repair. The repair efficiencies are dependent on both the mismatch type and neighboring nucleotide sequence. We have studied bending of several DNA duplexes containing canonical matches: A:T, G:C, various mismatches: A:A, A:C, G:A, G:G, G:T, C:C, C:T, T:T, and a bis-abasic site: X:X. Free energy profiles were generated for DNA bending using umbrella sampling. The highest energetic cost associated with DNA bending is observed for canonical matches while bending free energies are lower in the presence of mismatches, with the lowest value for the abasic site. In all of the sequences, DNA duplexes bend towards the major groove with widening of the minor groove. For homoduplexes, DNA bending is observed to occur via smooth deformations, whereas for heteroduplexes, kinks are observed at the mismatch site during strong bending. In general, pyrimidine:pyrimidine mismatches are the most destabilizing, while purine:purine mismatches lead to intermediate destabilization and purine:pyrimidine mismatches are the least destabilizing. The ease of bending is partially correlated with the binding affinity of MutS to the mismatch pairs and subsequent repair efficiencies, indicating that intrinsic DNA bending propensities are a key factor of mismatch recognition.

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Non-Watson-Crick base associations in DNA and RNA revealed by single crystal x-ray diffraction methods: Mismatches, modified bases, and nonduplex DNA

Cited by 23 publications

References 61 publications

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Canonical and unconventional pairing schemes between bis(nucleobase) complexes oftrans-a₂Pt^II: Artificial nucleobase quartets and C—H…N bonds

DNA Bending Propensity in the Presence of Base Mismatches: Implications for DNA Repair

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Non-Watson-Crick base associations in DNA and RNA revealed by single crystal x-ray diffraction methods: Mismatches, modified bases, and nonduplex DNA

Cited by 23 publications

References 61 publications

Untitled

Untitled

Canonical and unconventional pairing schemes between bis(nucleobase) complexes oftrans-a2PtII: Artificial nucleobase quartets and C—H…N bonds

DNA Bending Propensity in the Presence of Base Mismatches: Implications for DNA Repair

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Canonical and unconventional pairing schemes between bis(nucleobase) complexes oftrans-a₂Pt^II: Artificial nucleobase quartets and C—H…N bonds