Scientific journals on nucleic acids

In my knowledge, Nucleic Acids Research (NAR) is a highly respected scientific journal with a broad impact in the field of nucleic acids. Over the years, I have been browsing NAR webpage on a regular basis to keep myself up to date to the latest development in this area. It is thus no surprise that the initial 3DNA paper was submitted to and published in NAR in 2003. Among the 500+ citations to that 3DNA paper, over 1/5 (100+) articles are from NAR itself (as an example, please see my January 22, 2011 blog post titled "Three structural biology papers in the latest issue of NAR cite 3DNA"). My latest contribution to NAR is the GpU story, which was actually selected as a featured article.

Another related journal I am quite familiar with is RNA, a publication of the RNA society. As the "About" section of its webpage succinctly summarizes,

RNA serves as an international forum for publishing original reports on RNA research in the broadest sense. The journal aims to unify this field by cutting across established disciplinary lines and focusing on "RNA-centered" science.

RNA currently has an impact factor (IF) of 5.198 (2009), slightly lower than NAR's 7.479. It is, nevertheless, a very decent journal in RNA-related research, and I frequently visit its website. As a side note, the GpU paper was initially submitted to RNA for its RNA-specific content and as a way to diversify my publication spectrum (as mentioned above, 3DNA was initially published in NAR). Unfortunately, the GpU paper was rejected by the RNA journal after two rounds of review, spanning over 6 months.

Another journal closely related to RNA (name wise) is called RNA Biology, which even has a slightly higher IF of 5.56. Admittedly, I was not familiar with this journal at all. Browsing through its website, I am interested in seeing the journal's explicit policy to reconsider papers "rejected by high impact journals [CNS] for reasons of novelty and impact, rather than the importance of the study or the integrity of the data." By enclosing "the reviewers’ and/or editorial comments" from these high impact journals, "it is possible the article might be accepted [by RNA Biology] based on its previous review. This will allow the urgent and competitive research to be published on the day of submission."

I became aware of the journal DNA Research quite recently through an email. From its website, "DNA Research is an internationally peer-reviewed journal which aims at publishing papers of highest quality in broad aspects of DNA and genome-related research." The journal currently has an IF of 4.917. Browsing a couple of its online issues, I sense that the journal is more on genome- than structure-related research.

While following up 3DNA citations recently, I noticed the paper titled "Insights into the Structures of DNA Damaged by Hydroxyl Radical: Crystal Structures of DNA Duplexes Containing 5-Formyluracil" by Tsunoda and Taknaka. It was published in the Journal of Nucleic Acids, which I have never (but probably should have) heard of before. From its website, "Journal of Nucleic Acids is a peer-reviewed, open access journal that publishes original research articles as well as review articles in all areas of nucleic acids." By virtue of this structure paper and its citation to 3DNA, I think the journal is surely of personal interest, and I have added it into my watch-list.

To sum up, there are currently four scientific journals (I know of) that are devoted to nucleic acids:

• Nucleic Acids Research
• RNA
• RNA Biology
• DNA Research
• Journal of Nucleic Acids

Do I still miss something? Please make your suggestion in the comment area.

[revised on May 17, 2011 by adding RNA Biology]

Ebook "Gregory Petsko in Genome Biology: The first 10 years"

Over the years, I have read some of Gregory Petsko's monthly columns in Genome Biology while browsing the journal online, and I like his sensible and entertaining columns quite a bit. Recently, I became aware of the ebook from BioMed Central, "Gregory Petsko in Genome Biology: The first 10 years":

Structural biologist Gregory Petsko has contributed a thought-provoking and entertaining monthly column to the scientific journal Genome Biology every month since its launch in 2000. To mark the 10th anniversary of Genome Biology this eBook brings together 10 years of Petsko's columns.

I downloaded the epub version of the book, and googled around, trying to find a corresponding ebook reader for my MacBook Pro (Snow Leopard) – even though I have some ebooks in the generic PDF format, I am not that familiar with epub or mobi. I finally settled with NOOK for Mac from B&N. It turns out reading ebooks with specifically-desinged apps such as NOOK is quite a different, yet more enjoyable, experience than through a PDF reader.

Now the ebook has become the top one in casual reading list. I am reading it from the very beginning, one column at a time, to have a historical perspective. So far I found the columns indeed very "thought-provoking and entertaining".

Tips and tricks from "The Geek Stuff"

As a devoted command line user, I am always interested in learning new tricks to make my life more enjoyable. Recently, I came across Ramesh Natarajan’s blog “The Geek Stuff” which is full of “instruction guides, how-to, troubleshooting tips and tricks on Linux, database, hardware, security and web” to help solve practical problems.

For example, in the section “Best of the Blog”, I recently benefitted quite a bit by reading the following posts:

• 15 Awesome Google Search Tips and Tricks
• 6 Awesome Linux cd command Hacks
• wget Tutorial: 15 Awesome Examples to Download Files from Internet

There are many other helpful tips/tricks as well; since I have bookmarked the site, I will surely come back!

Scripting in Ruby is fun

Over the years, I have played around with various scripting languages, including awk, bash, Perl, Python and Ruby. By far, I have enjoyed Ruby the most; nowadays, I write scripts nearly exclusively in Ruby.

Created by Yukihiro "Matz" Matsumoto in Japan during the mid-1990s, Ruby became popular worldwide in mid-2000s, with the Rails web application framework. Indeed, I first dug into Ruby through Rails, and by reading David Black's book "Ruby for Rails; Ruby techniques for Rails developers". As an exercise, I implemented the current 3DNA v2.0 website with Rails v1.x. Then I quickly realized that the rapidly evolving Rails framework was beyond my time and interest to follow. However, I did begin to appreciate Ruby's simplicity, consistency and expressiveness. Over the past few years, I have collected over a dozen Ruby-related (e)books, including "The Well-Grounded Rubyist" (David Black, covering v1.9), "The Ruby Programming Language" (David Flanagan and Yukihiro Matsumoto), and "Metaprogramming Ruby: Program Like the Ruby Pros" (Paolo Perrotta). Just as my experience with (ANSI) C, I feel Ruby "wears well as one's experience with it grows" (K&R, in the preface of "The C Programming Language"). The better I know Ruby, the more I enjoy using it.

I recently wrote two Ruby scripts for the analysis of molecular dynamics (MD) simulation trajectories using 3DNA. Honestly, I would not have bothered with Perl for the task (otherwise, it would have been done long time ago), given the sideline nature of my support of 3DNA. Yet, writing and refining the Ruby scripts (with help of git and rake) have turned out to be a pleasant experience. Another reason why scripting in Ruby is fun is due to its large, active and friendly user community; there are many user-contributed libraries (gems) that serve well of common programming needs. As an example, in the 3DNA-MD scripts, I took advantage of the elegant Trollop commandline option parser by William Morgan. I picked Trollop among many other choices because it is self-contained in a single file, simple to use, and "gets out of your way".

In the Ruby community, exciting new developments are happening all the time. Recently, I was drawn to thor, "a simple and efficient tool for building self-documenting command line utilities". Over the past couple of years, I have browsed Sinatra and Sequel – they also look brilliant! Of course, for bioinformatics, there is the BioRuby project.

Overall, in my experience, scripting in Ruby is fun and exciting. Are you a Rubist yet?

DNA fiber models ABC

Among the 55 fiber models available in 3DNA, the A-, B- and C-DNA types are the most generic – they can be built with bases A, C, G and T in any combination (see table below). Moreover, in addition to the well-known Arnott fiber models (#1, #4 and #7, all from calf thymus), there are newer variants from van Dam & Levitt (#46 and #47) and Premilat & Albiser (#53 to #55).

 1   32.7   2.548  A-DNA (calf thymus)
 4   36.0   3.375  B-DNA (calf thymus)
 7   38.6   3.310  C-DNA (calf thymus)
46   36.0   3.38   B-DNA (BI-type nucleotides)
47   40.0   3.32   C-DNA (BII-type nucleotides)
53  -38.7   3.29   C-DNA (depreciated)
54   32.73  2.56   A-DNA [cf. #1]
55   36.0   3.39   B-DNA [cf. #4]

As shown in Figure 9 of the 3DNA 2003 NAR paper (linked below), the A-, B- and C-DNA fiber models are all right-handed regular straight helices, yet each has distinguished features.

While I could easily envisioned possible applications of the fiber models, especially in connection with analysis and rebuilding routines in 3DNA, it was still a nice surprise to see a recent article by Gossett and Harvey, titled "Computational Screening and Design of DNA-Linked Molecular Nanowires" [Nano Lett., 2011, 11 (2), pp 604–608]. The abstract is quoted below:

DNA can be used as a structural component in the process of making conductive polymers called nanowires. Accurate molecular models could lead to a better understanding of how to prepare these types of materials. Here we present a computational tool that allows potential DNA-linked polymer designs to be screened and evaluated. The approach involves an iterative procedure that adjusts the positions of DNA-linked monomers in order to obtain reasonable molecular geometry compatible with normal DNA conformations and with the properties of the polymer being formed. This procedure has been used to evaluate designs already reported experimentally, as well as to suggest a new design based on pyrrylene vinylene (PV) monomers.

In the article, 3DNA (the web interface version w3DNA) was cited as follows:

The selection of DNA structures is important because the DNA remains fixed throughout the procedure. To reduce the risk of an incorrect result, one should choose a subset of DNA structures that are in some sense representative of DNA conformational space. The DNA structures (A-, B-, and C-form DNA) were obtained using the Web 3DNA web server. We used a poly(dG)-poly(dC) sequence with ideal geometry for each DNA structure. A-DNA was constructed with rise = 2.548 Å and twist = 32.7˚ , B-DNA was constructed with rise = 3.375 Å and twist = 36.0 ˚, and C-DNA was constructed with rise = 3.310 Å and twist = 38.6 ˚.

Indeed, this is a novel application of fiber DNA ABC models!

3DNA citations reach over 500

On Friday, June 5, 2009, I blogged on the topic titled "3DNA citations reach over 300". At that time, I wrote (towards the end):

I still remember that the number of citations to 3DNA was less than 150 nearly two years ago [~ summer 2007], when I started to wrote the first draft of our 2008 Nature Protocols paper. Now it is more than doubled! I would blog on this topic again when the number reaches 500.

When I checked Google scholar for 3DNA citations right now, the citation number is already over 500 for the initial 2003 3DNA NAR paper alone. Combined with the two direct follow-ups – the 2008 Nature Protocols paper and the 2009 NAR web server paper – the three 3DNA publications have been cited a total of 550 times.

Again, as noted in that blog post,

In my opinion, some of 3DNA features are still (heavily) underused. Now that we have a sizable user community, 3DNA could only become better and would be more widely used. I have every reason to believe that in the not-so-distant-future, the citations to 3DNA would reach over 1000.

A decade after its initial humber release, 3DNA has been successfully applied to many real-world problems. As spare time permits, I have actively maintained and continuously refined 3DNA based largely on users' feedbacks. Over the time, I also see clearly that 3DNA can be moved to the next level both in functionality and usability to enjoy an even larger/broader impact.

Now more than half-way through, it won't be long when citations to 3DNA reach 1000, and then beyond.

Review article on NMR analysis of protein–DNA interactions by Milon et al

Through Google scholar, I became aware of a recent review article by Milon et al., titled "Nuclear magnetic resonance analysis of protein–DNA interactions" in the journal J. R. Soc. Interface:

This review focuses on the experimental strategies currently employed to solve structures of protein–DNA complexes and to analyse their dynamics. It highlights how these approaches can help in understanding detailed molecular mechanisms of target recognition.

I browsed through the text to get myself more familiar with NMR the methodology and its applications in protein-DNA recognition. I was surprised that 3DNA was cited in the article, especially with respect to its unique analyze/rebuild complementarity:

In addition, several software programs have been developed to model DNA bending such as the 3DNA program, which allows analysis of DNA structural parameters and enables it to be rebuilt with customized DNA models [76]. Several Web servers have been created recently and provide interesting tools to analyse and rebuild DNA models [77,78].

I am only wishing that 3DNA's neat features could be more widely recognized; hopefully I'd have the opportunity to further refine 3DNA and move it to the next level.

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.

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.