This is the molecular weight that is typically observed by electrospray mass spectrometry run in negative ion mode. The protonated molecular weight is also typically equal to the backbone weight plus the total number of phosphates multiplied by 1.01 for each proton (H+). Note that some modifications add additional phosphate groups to the molecular weight calculation, such as a 3’ phosphate modification or 3’ thymidine linked modifications. The weight of each counter ion is generally assumed to 102.2 for Triethylammonium (TEA). This added weight is typically equal to the number of phosphates in the oligo multiplied by the weight of the counter ion. The addition of counter ions is simply the molecular weight backbone plus the total weight of counter ions. MWHAdj = 0, 1, or 2 protons (i.e., 0, 1.01, or 2.02), depending on the presence and structure of 3' and 5' modifications.This is the MW for that portion of a phosphate linkage not already included in MWbase or MWmod. MWPO2 = molecular weight of PO2, i.e., 62.97.nPO2 = total count of internal phosphates, i.e., nbases + nmods - 1. Use of MS instruments is freely available to trained WFU students and faculty members of the Department of Chemistry and their direct collaborators.MWMod = molecular weight of the deprotonated form of each individual modification.MWbase = molecular weight of the deprotonated nucleoside.Molecular weight backbone (g/mol) is calculated using the following formula: MW(backbone) = Σ(nbase * MWbase) + MW Modifications + (nPO2 * MWPO2) + MWHAdj Our Waters SQD is ideal for lower resolution molecular weight measurements on smaller organic and organometallic compounds (Mr typically < 1.5 kDa), and therefore widely used for reaction monitoring and analysing reaction intermediates. These combined words have 17 letters in them and this clue is often given in crossword puzzles. *The extinction coefficient values for all other bases and modifications can be found on under the "Technical Specs" tab available for each oligo modification, or by downloading this PDF. This instrument is equipped with ESI, APCI and APPI techniques and is reserved for walk-up use by arrangement. In chemistry, an instrument used to find mass is a triple-beam balance. All ε260 values are reported in units of M -1.Extinction Coefficient Calculation - The extinction coefficient is calculated with the following method: ε260 = x 0.9, to adjust for hyperchromicity. The instrument is ideal for qualitative sample. The OligoSpec calculator outputs the physical properties for a particular oligo design. The instrument is a benchtop gas chromatograph/ quadrupole mass spectrometer for high precision GC/MS analysis.
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