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. 2011 Feb 8;39(11):4818–4826. doi: 10.1093/nar/gkr071

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© The Author(s) 2011. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 2. — MALDI-MS spectra of RNase digests of tRNA 1, 5 and 6. (a) RNase A digest of tRNA 1 (cmnm⁵s²U-tRNA^Glu). (b) RNase T1 digest of tRNA 1. (c) Expanded section of (b) showing the anticodon–stem loop fragment of tRNA 1. Extra peaks are assigned as follows. a: 3165.5, Fragment A [AAUCCCCUAGcp (cp = cyclic phosphate)]; b: 3182.9, Fragment B (AAUCCCCUAGp); c: 3203.7, Fragment A – H + K and Fragment B – H + Na; d: 3221.3, Fragment B – H + K; e: 3235.6, Fragment C (CCCUcmnm⁵s²UUCm²ACGcp); f: 3242.4, Fragment A – 2H + 2K; g: 3258.4, Fragment B – 2H + 2K; h: 3274.4, Fragment C – H + K and Fragment D (CCCUcmnm⁵s²UUCm²ACGp) – H + Na; i: 3290.9, Fragment D – H + K; j: 3296.0, Fragment B – 3H + 3K. (d) Section of a RNase T1 digest of tRNA 5 (nm⁵s²U-tRNA^Glu) showing the nm⁵s²U-containing fragment. Extra peaks are assigned as follows. a: 3165.3, Fragment A (AAUCCCCUAGcp); b: 3177.8, Fragment E (CCCUnm⁵s²UUCm²ACGcp), c: 3182.9, Fragment B (AAUCCCCUAGp); d: 3204.2, Fragment B – H + Na; e: 3215.8, Fragment E – H + K; f: 3221.2, Fragment B – H + K; g: 3233.5, Fragment F (CCCUnm⁵s²UUCm²ACGp) – H + K; h: 3243.3, Fragment B – 2H + Na + K; i: 3258.5, Fragment B – 2H + 2K; j: 3270.1, Fragment F – 2H + 2K; k: 3296.1, Fragment B – 3H + 3K; l: 3307.8, Fragment F – 3H + 3K. (e) Section of an RNase T1 digest of tRNA 6 (mnm⁵s²U-tRNA^Glu) showing the mnm⁵s²U-containing fragment. Extra peaks are assigned as follows. a: 3165.4, Fragment A (AAUCCCCUAGcp); b: 3182.9, Fragment B (AAUCCCCUAGp); c: 3191.0, Fragment G (CCCUmnm⁵s²UUCm²ACGcp); d: 3204.9, Fragment B – H + Na; e: 3221.0, Fragment B – H + K; f: 3229.3, Fragment G – H + K; g: 3246.4, Fragment H (CCCUmnm⁵s²UUCm²ACGp) – H + K; h: 3258.9, Fragment B – 2H + 2K; i: 3267.3, Fragment G – 2H + 2K; j: 3283.9, Fragment H – 2H + 2K; k: 3296.5, Fragment B – 3H + 3K; l: 3306.7, Fragment A – 3H + 3K; m: 3322.0, Fragment H – 3H + 3K; n: Fragment B – 4H + 4K. The tRNA fragments analysed in (a) and (b) are labelled with mass and sequence on each spectrum, and coloured in red on each corresponding tRNA diagram. The data in (c)–(e) are calibrated to the constant fragment B (AAUCCCCUAGp, 3182.9) to allow accurate determination of the variable anticodon fragment.