Detecting variable (V), diversity (D) and joining (J) gene segment recombination using a two-colour fluorescence system

Table 1 Diversity at coding joint sequences

RSS23 coding end sequence	Nucleotides lost	Nucleotides added	Nucleotides lost	RSS12 coding end sequence
ATTACGCGC*				*GGTACCGTC
Deletion substrate:
ATTACGCG	-C	+GC	-G	GTACCGTC
ATTACG	-CGC		-GG	TACCGTC
ATTACGC	-GC		-GGTAC	CGTC
ATTACGCG	-C	+GG	-GGTA	CCGTC
ATTACGCG	-C		-GG	TACCGTC
ATTACGCG	-C	+GCG	-GGTA	CCGTC
ATTACG	-CGC		-G	GTACCGTC
ATTACGCG	-C		-G	GTACCGTC
ATTACGCG	-C		-G	GTACCGTC
Inversion substrate:
ATTACGCGC	-C	+G	-GGTA	CCGTC
ATTACG	-CGC		-GG	TACCGCG
ATTACGCG	-C	+GC	-GGT	ACCGTC
ATTACGCG	-C			GGTACCGTC
ATTACGCG	-C	+GC	-GGT	ACCGTC
ATTACGCG	-C	+GC	-GGT	ACCGTC
ATTACG	-CGC		-GG	TACCGTC
ATTACGC	-GC		-GGTAC	CGTC
ATTACGCG	-C	+GC	-G	GTACCGTC
ATTACGCG	-C		-G	GTACCGTC

DNA is cleaved at the boundary of the recombination signal sequence (RSS) motifs and the ends are joined. Joining involves the trimming of nucleotides and the addition of bases via terminal deoxynucleotide transferase (TdT), resulting in diversity at the coding joint.
*The sequences marked indicate the predicted sequence if recombination involved no nucleotide loss or addition. The actual sequences obtained for the deletion and inversion substrate are shown, with nucleotides loss and gained indicated.

ISSN: 1759-8753