Structure of oligonucleotides with either a strand break or a bulged nucleotide

Roll, Claus; Ketterlé, Christophe; Boulard, Yves; Fazakerley, G. Victor

doi:10.1016/s0300-9084(97)82008-1

Cited by 2 publications

(4 citation statements)

References 29 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In contrast to the imino proton signal of terminal base pairs that disappears at 16 °C, the imino protons of gap-flanking dG·dC pairs are quite visible at this temperature . Similar observations have been done for the case of a gap-containing duplex with an orphan adenosine 10b , , indicating that base pairs flanking the gap are more stable and ordered than the duplex ends. However, this is not the case of duplexes 11a , b , mimicking the damage caused by the bleomycin antibiotic family .…”

Section: 12 Effect Of Nicks and Gaps On Duplex Structuresupporting

confidence: 74%

“…In addition, phosphorylation at the 5‘-side of the nick does not affect its structure considerably, causing only small distance variations, estimated by the authors not to exceed more than 1 Å, between the aromatic protons of nick-flanking residues . The NMR spectra of all nick mimics studied to date exhibit slightly broadened and moderately upfield-shifted imino proton signals for the nick-flanking base pairs, demonstrating partial fraying of the duplex at the nick site. ,− However, the temperature dependence of exchangeable proton spectra shows that imino proton signals of nick-flanking and internal base pairs disappear simultaneously, indicating that these dumbbells melt cooperatively.…”

Section: 12 Effect Of Nicks and Gaps On Duplex Structurementioning

confidence: 96%

“…41 The NMR spectra of all nick mimics studied to date exhibit slightly broadened and moderately upfield-shifted imino proton signals for the nick-flanking base pairs, demonstrating partial fraying of the duplex at the nick site. 42,[44][45][46] However, the temperature dependence of exchangeable proton spectra shows that imino proton signals of nick-flanking and internal base pairs disappear simultaneously, indicating that these dumbbells melt cooperatively.…”

Section: Effect Of Nicks and Gaps On Duplex Structurementioning

confidence: 99%

See 2 more Smart Citations

NMR Structures of Damaged DNA

2006

View full text Add to dashboard Cite

Section: 12 Effect Of Nicks and Gaps On Duplex Structuresupporting

confidence: 74%

Section: 12 Effect Of Nicks and Gaps On Duplex Structurementioning

confidence: 96%

Section: Effect Of Nicks and Gaps On Duplex Structurementioning

confidence: 99%

See 1 more Smart Citation

NMR Structures of Damaged DNA

2006

View full text Add to dashboard Cite

“…Because of the redundancy of many of these distances (intrasugar) and others with any structural information (H5–H6, H8–H2, …) we kept just 128 of them as constraints for the model construction as well as for the MD runs. The torsion angle constraints were determined as described previously [27,29]. Comparing the relative intensities of the H6/H8–H2′ and H6/H8–H3′ NOE cross peaks in a NOESY spectrum recorded with 60 ms mixing time gave us the sugar conformation which was confirmed in a DQF‐COSY spectrum.…”

Section: Methodsmentioning

confidence: 99%

Solution structures of a duplex containing an adenine opposite a gap (absence of one nucleotide)

Roll

Ketterlé

Fazakerley

et al. 1999

European Journal of Biochemistry

View full text Add to dashboard Cite

We investigated the behaviour of a 15mer DNA duplex, [5 H d(CAGAGTCACTGGCTC)3 H ].[5 H d(GAGCCAG)3 H + 5 H d(GACTCTG)3 H ] which contained an adenine opposite the gap. Analysis of the NMR data showed the existence of one major species, which was in equilibrium with two minor species. Their relative concentrations varied as a function of pH with a pK a of <4.5. For the major species, the duplex was globally in B conformation with the central adenine stacked in the helix. The two G´C base pairs adjacent to the central adenine were well formed and a gap was present in front of this adenine. For the minor species, major structural perturbations occurred in the centre of the duplex. At neutral pH, the central adenine was involved in a G´A mismatch with G23 adjacent to the gap. Cytosine C7 was then extrahelical and no gap was observed. Under these conditions, the major neutral species corresponded to 70% of the total and the minor species to 30%. At acidic pH, the central adenine of the minor species was protonated and was involved in a G(syn)´A + (anti) mismatch. The difference is that C9 is now extrahelical and G22 is implicated in the mispair. Three-dimensional models were built to initiate molecular dynamic simulations, which were in good agreement with the NMR data. Their structural stability in terms of hydrogen bonding and their flexibility are discussed and the biological significance for the interaction with DNA polymerase is evoked.Keywords: DNA; gap; molecular dynamics; NMR; repair.DNA duplexes containing gaps of one nucleotide may occur as a result of damaging processes, but also as an intermediate during a DNA repair mechanism. The damage product is the result of an oxidative attack on DNA, which has two main origins: normal aerobic cellular metabolism and ionizing radiation [1]. Oxidative damage to DNA is a frequent event: it occurs up to 150 000 times per day per cell (105 times per min per cell; [2]). In aerobic metabolism and after ionizing radiation, the hydroxyl radical is the most important species to reacts with and modify the DNA structure [3,4]. The nature of the damage product depends on the reaction site of the hydroxyl radical on the DNA [5,6]. Hydroxyl attack on the sugars at the C1 H atom leads to base release (abasic sites); attack at the C4 H atom or on the phosphate backbone may lead to single-strand breaks (nicks) or loss of a single nucleotide (gap). Finally, hydroxyl attack on the bases leads to base damage or, ultimately, base release. In these different cases, O-H, phosphate groups or modified sugars are adjacent to the gap The proteins or protein±DNA complexes involved in this mechanism have been the subject of several recent structural or biochemical reports [16±18]. These reports showed that a particular structure of the DNA duplex during the complexation with DNA polymerase b is required for nucleotide insertion. The base facing the gap must be stacked over its neighbouring base in the 5 H direction. This position of DNA in the active site of DNA polymerase is necessary for plac...

show abstract

Structure of oligonucleotides with either a strand break or a bulged nucleotide

Cited by 2 publications

References 29 publications

NMR Structures of Damaged DNA

NMR Structures of Damaged DNA

Solution structures of a duplex containing an adenine opposite a gap (absence of one nucleotide)

Contact Info

Product

Resources

About