( ( For example ) ( , ( ( one ( of ( the ( ( more common ) methods ) ) ) ) ( ( ( ( ( ( ( ( ( involves ( digestion ( of ( the ( DNA template ) ) ) ) ) ( using ( ( RNase-free DNase ) I ) ) ) , ) ( ( followed ( by ( gel filtration ) ) ) ( to ( remove ( unincorporated nucleotides ) ) ) ) ) , ) and ) then ) ( ( phenol extraction ) ( to ( ( remove ( proteins ( and ( ethanol precipitation ) ) ) ) ( to ( concentrate ( the RNA ) ) ) ) ) ) ) . ) ) ) )
(ROOT (S (PP (IN For) (NP (NN example))) (, ,) (NP (NP (CD one)) (PP (IN of) (NP (DT the) (ADJP (RBR more) (JJ common)) (NNS methods)))) (VP (VP (VBZ involves) (NP (NP (NN digestion)) (PP (IN of) (NP (DT the) (NNP DNA) (NN template)))) (S (VP (VBG using) (S (NP (NNP RNase-free) (NNP DNase)) (NP (PRP I)))))) (, ,) (VP (VBD followed) (PP (IN by) (NP (NN gel) (NN filtration))) (S (VP (TO to) (VP (VB remove) (NP (JJ unincorporated) (NNS nucleotides)))))) (, ,) (CC and) (RB then) (VP (NP (JJ phenol) (NN extraction)) (S (VP (TO to) (VP (VB remove) (NP (NNS proteins) (CC and) (NN ethanol) (NN precipitation)) (S (VP (TO to) (VP (VB concentrate) (NP (DT the) (NNP RNA)))))))))) (. .)))
For example, one of the more common methods involves digestion of the DNA template using RNase-free DNase I, followed by gel filtration to remove unincorporated nucleotides, and then phenol extraction to remove proteins and ethanol precipitation to concentrate the RNA.
(ROOT (S (ADVP (RB Deletions)) (VP (VB remove) (NP (NP (QP (CD one) (CC or) (JJR more)) (NNS nucleotides)) (PP (IN from) (NP (DT the) (NN dna)))))))