User talk:Sean T. Smith/DNA/Questioned
Reference Check
If a reference checks out, add the relevant quote, so that your checking can be verified later. If you have access to journals which require a subscription, please prioritise those marked "not checked - no access".
- 1ab, 2 not checked - no access
- 3 ERROR - based on abstract: source gives 22-26 angstrom (2.2 - 2.6 nm) width
- 4 not checked - no access
- 5ab checked OK
- a quote="The novel feature of the structure is the manner in which the two cheins are held together by the purine and pyrimidine beses. The planes of the bases are perpendicular to the fiber axis. They are joined together in pairs, a single base from one chain being hydrogen-bonded to a single base from the other chain"
- b quote not applicable
- 6 not checked - no access
- 7ab ERROR
- 7a ERROR - does not seem a suitable source: supporting information may or may not be inferred but suggest replacement with a source that provides it explicitly
- 7b ERROR - does not provide structural information of nucleotides not explicitly state that A+G are purines while C+T are pyramidines
- 8ab not checked - no access
- 9 not checked - no access
- 10, 11 in progress
- 12 not checked - no access
- 13 ERROR - based on pubmed abstract: quote="Cro, repressor, and CAP use alpha-helices for many of the contacts between side chains and bases in the major groove" - suggest this is insufficient to make the assertion that "proteins like transcription factors that can bind to specific sequences in double-stranded DNA usually make contacts to the sides of the bases exposed in the major groove" - suggest further scrutiny of entire text (no access).
- 14 checked ok - quote="The situation in nucleic acid systems is somewhat different: from our present model, the analysis of the different contributions seen in Table 2 shows that the components base stacking, hydrogen bonding, and van der Waals terms are the major partners; the relative contributions are 33.4% base stacking, 30.3% van der Waaks, 18.2% hydrogen bonding, 12.1% hydrophobic, and 6.1% electrostatic"
- 15 in progress
- 16 skipped - too complex
- 17, 18, 19, 20 not checked - no access
- 21 checked and corrected ok - see Table 1
- 22ab checked ok
- 22a - quote="...these short overlapping sequences may be involved in expression regulatory mechanisms"
- 22b - quote="...approximately a third of all genes in the [microbial] genomes are overlapping..."
- 23, 24 not checked - no access
- 25 checked ok - quote="As a linear, single-stranded DNA, the parvovirus genome represents a relatively unusual structure in terms of DNA replication."
Reference Check Discussion
Should we just correct the article re: Ref 3, and then pass it? I don't have access to the full article but the abstract was in direct contravention of what it says in the article. --Sean T. Smith 07:01, 17 May 2007 (CDT)
I'll get going on finding the references you want to check when i have a bit of free time. Probably will work in spurts. Chris Day (talk) 12:20, 18 May 2007 (CDT)
Images
I am working on importing the images - currently delayed due to a technical problem. Please bear with me. --Sean T. Smith 15:06, 17 May 2007 (CDT)
Proposed Sentence Cut
Re: sentence: A considerable number of DNA sequences in prokaryotes and eukaryotes, and more in plasmids and viruses, have overlapping genes which may both occur in the same direction, on the same strand (parallel) or in opposite directions, on opposite strands (antiparallel), thus bluring the distinction made above between sense and antisense strands.
I would argue that overlap does not blur the distinction between sense and antisense, since the sense and antisense are only applicable to a particular gene - the antisense strand for one gene can be the sense strand for another gene and this distinction isn't blurred (I don't think) by the genes overlapping. Would anyone object to me scrapping "thus bluring the distinction made above between sense and antisense strands"? --Sean T. Smith 19:01, 18 May 2007 (CDT)