Saturday, March 5, 2011

Retraction of scientific publications

Once in a while, I come across retraction notices of scientific publications in leading journals/magazines. Even for cases not directly related to my research areas, I normally browse through them.

In the March 3, 2011 issue of Nature, there is a retraction of the Letter "Mediation of pathogen resistance by exudation of antimicrobials from roots" [Nature 434, 217–221 (2005)]. I am intrigued by the first sentence of the note:
The authors wish to retract this Letter after a key reference by Walker et al. (ref. 9 in this Letter) was retracted from the scientific literature.

It turns out that the 2003 Walter et al. J. Agric. Food Chem. paper (withdrawn in October 2009) and the 2005 Nature Letter were from the same group. Overall, it took ~6 years each for the two papers to be retracted. As of today, they have been cited 76 and 84 times respectively accordingly to Google scholar.

Sunday, February 27, 2011

Evidences for transient Hoogsteen base pairs in canonical DNA duplex

In the February 24, 2011 issue of Nature, there is an interesting article by Nikolova et al., titled "Transient Hoogsteen base pairs in canonical duplex DNA". Its main discovery is succinctly summarized in the abstract:
By using nuclear magnetic resonance relaxation dispersion spectroscopy in concert with steered molecular dynamics simulations, we have observed transient sequence-specific excursions away from Watson–Crick base-pairing at CA and TA steps inside canonical duplex DNA towards low-populated and short-lived A•T and G•C Hoogsteen base pairs. The observation of Hoogsteen base pairs in DNA duplexes specifically bound to transcription factors and in damaged DNA sites implies that the DNA double helix intrinsically codes for excited state Hoogsteen base pairs as a means of expanding its structural complexity beyond that which can be achieved based on Watson–Crick base-pairing.
Geometrically, the Hoogsteen base pair is related to the Watson-Crick base pair by a 180-degree rotation about the glycosidic bond (N9–C1'). While the A•T Hoogsteen base pair is classic, the similar G•C+ Hoogsteen pair (with protonation of cytosine N3) is equally possible. The A•T and G•C Hoogsteen base pairs have two perfect H-bonds, so they are energetically stable. As for their existence in DNA duplex, the most direct evidence comes from the "trap" experiments (see Fig.3 of the paper). In the News & Views section, Honig and Rohs provide a nice recap of the main point and implications of this work.

As also observed in another recent publication, "Replication infidelity via a mismatch with Watson–Crick geometry", the base sequence has a subtle role in influencing the base-pairing schemes, three-dimensional structures and biological functions of DNA. However, we should not forget that only the Watson-Crick base pairs, and to a less extent, the G-U wobble pair, have the correct symmetry to ensure a "regular" double helical structure.