کد مقاله | کد نشریه | سال انتشار | مقاله انگلیسی | نسخه تمام متن |
---|---|---|---|---|
10546956 | 964485 | 2005 | 13 صفحه PDF | دانلود رایگان |
عنوان انگلیسی مقاله ISI
Investigation of the Initial Fragmentation of Oligodeoxynucleotides in a Quadrupole Ion Trap: Charge Level-Related Base Loss
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موضوعات مرتبط
مهندسی و علوم پایه
شیمی
شیمی آنالیزی یا شیمی تجزیه
پیش نمایش صفحه اول مقاله
![عکس صفحه اول مقاله: Investigation of the Initial Fragmentation of Oligodeoxynucleotides in a Quadrupole Ion Trap: Charge Level-Related Base Loss Investigation of the Initial Fragmentation of Oligodeoxynucleotides in a Quadrupole Ion Trap: Charge Level-Related Base Loss](/preview/png/10546956.png)
چکیده انگلیسی
The charge state distribution and CID fragmentation of two series of deprotonated oligodeoxynucleotide (ODN) 9-mers (5â²-GGTTXTTGG-3â² and 5â²-CCAAYAACC-3â², X/Y = G, C, A, or T) have been studied in detail in an ion trap in an effort to understand the intrinsic properties of DNA in vacuo. The distribution of charge states (â2 to â6) is similar for both the X- and Y-series, with the most abundant being the â4 charge state. The T-rich X-series prefers higher charge states (â6 and â5) than does the Y-series. Calculations show that phosphate groups located nearest a thymine are more acidic than those near an adenine, cytosine, or guanine, thus explaining why the X-series prefers higher charge states. We use the term “charge level” to define the ratio of the charge state to the total number of phosphate groups present in the ODN. We find, consistent with previous studies, that the initial step of fragmentation is loss of nucleobase either as an anion or as a neutral. We observe the former for ODNs with charge levels greater than 50% and the latter for ODNs with charge levels below 50%. The overall anionic base loss follows the trend Aâ â« Gâ â Tâ > Câ; electrostatic potential calculations indicate that this trend follows delocalization of electron density for each anion, with Aâ being the most stabilized through delocalization. For neutral base loss, thymine (TH) is rarely cleaved, while the preferences for AH, GH, and CH loss vary. Proton affinity (PA) calculations show that a nearby negatively charged phosphate enhances the PA of proximally located nucleobases; this PA enhancement probably plays a role in promoting neutral base loss. The trends differ by charge level. At a charge level of 37.5% (â3 charge state), AH loss is preferred over CH and GH loss, regardless of sequence. However, at a charge level of 25% (â2 charge state), the terminal bases are preferentially lost over the internal bases, regardless of identity. By reconstructing the ODN sequences from structurally informative (a-BH) and w ions, we are able to identify the charge locations for the â3 and â2 charge states. For the â3 charge state, one charge resides on each “most terminal” phosphate, with the third being in the middle. For the â2 charge state, each charge resides on the penultimate phosphate groups. We compare our data to earlier experiments in an effort to generalize trends.
ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Journal of the American Society for Mass Spectrometry - Volume 16, Issue 11, November 2005, Pages 1853-1865
Journal: Journal of the American Society for Mass Spectrometry - Volume 16, Issue 11, November 2005, Pages 1853-1865
نویسندگان
Su Pan, Kathryn Verhoeven, Jeehiun K. Lee,