TABLE 3.

Substrate library

Assay and substrate name	Length (nt)	RNA or DNA	Fluorophore	Sequencea
Deaminase assays for substrate length
JBs01b	40	DNA	5'-6-FAM	AATGAAAGATATAAGACTCAAATTGAAATAGTTAAGATTA
JBs02	16	DNA	5'-6-FAM	TAAGAATCAAATTGAT
JBs03	10	DNA	5'-6-FAM	AGACTCAAAT
Competition binding fluorescence polarization experiments
JBs13	60	DNA		TATAATGAAAAATGAAAGATATAAGACTCAAATTGAAATAGTTAAGATTAAATAGATTAA
JBs12	50	DNA		TGAAAAATGAAAGATATAAGACTCAAATTGAAATAGTTAAGATTAAATAG
JBs05	40	DNA		AATGAAAGATATAAGACTCAAATTGAAATAGTTAAGATTA
JBs06	30	DNA		AAGATATAAGACTCAAATTGAAATAGTTAA
JBs07	25	DNA		ATATAAGACTCAAATTGAAATAGTT
JBs08	16	DNA		TAAGACTCAAATTGAA
JBs09	10	DNA		AGACTCAAAT
Heteroduplex deaminase assays and fluorescence polarization
JBs27	40	RNA		UAAUCUUAACUAUUUCAAUUUGAGUCUUAUAUCUUUCAUU
JBs28	40	RNA		UAAUCUUAACUAUUUCAAUUUAUUUCUUAUAUCUUUCAUU
JBs29	40	RNA		UAAUCUUAUACAUUUCAAUUUGAGUCUUAUAUCUUUCAUU
JBs30	17	RNA		GUCUUAUAUCUUUCAUU
JBs31	20	RNA		UAAUCUUAACUAUUUCAAUU
JBs32	40	DNA		TAATCTTAACTATTTCAATTTGAGTCTTATATCTTTCATT
JBs33	42	DNA	5'-6-FAM	TGAATGAAAGATATAAGACTCAAATTGAAATAGTTAAGATTA
JBs34	18	RNA		UCUUAUAUCUUUCAUUCA
JBs35	17	RNA		CUUAUAUCUUUCAUUCA
JBs36	40	RNA	5'-6-FAM	AAUGAAAGAUAUAAGACUCAAAUUGAAAUAGUUAAGAUUA
Deaminase assays for sequence specificity
JBs37	16	DNA	5'-6-FAM	TAAGAATCTAATTGAT
JBs38	16	DNA	5'-6-FAM	TAAGAATCGAATTGAT
JBs39	16	DNA	5'-6-FAM	TAAGAATCCAATTGAT
JBs40	16	DNA	5'-6-FAM	TAAGATTCAAATTGAT
JBs41	16	DNA	5'-6-FAM	TAAGAGTCAAATTGAT
JBs42	16	DNA	5'-6-FAM	TAAGACTCAAATTGAT
JBs43	40	DNA	5'-6-FAM	AATGAAAGATATAAGACTUAAATTGAAATAGTTAAGATTA

^aThe TC dinucleotide motif and −2, −1, 0, or +1 nucleotides are shown in boldface type and underlined.

^bJBs01 is the main substrate used in deaminase assays and fluorescence polarization experiments with huA3H and pgtA3Hα mutants.