The 3'-terminal nucleotide sequences of lambda DNA

DNA sequence analysis: a general, simple and rapid method for sequencing large oligodeoxyribonucleotide fragments by mapping

Several electrophoretic and chromatographic systems have been investigated and compared for sequence analysis of oligodeoxyribonucleotides. Three systems were found to be useful for the separation of a series of sequential degradation products resulting from a labeled oligonucleotide: (I) 2-D electrophoresisdagger; (II) 2-D PEI-cellulose; and (III) 2-D homochromatography. System (III) proved generally most informative regardless of base composition and sequence. Furthermore, only in this system will the omission of an oligonucleotide in a series of oligonucleotides be self-evident from the two-dimensional map. The sequence of up to fifteen nucleotides can be determined solely by the characteristic mobility shifts of its sequential degradation products distributed on the two-dimensional map. With this method, ten nucleotides from the double-stranded region adjacent to the left-hand 3'-terminus and seven from the right-hand 3'-terminus of bacteriophage lambda DNA have been sequenced. Similarly, nine nucleotides from the double-stranded region adjacent to the left-hand 3'-terminus and five nucleotides from the right-hand terminus of bacteriophage phi80 DNA have also been sequenced. The advantages and disadvantages of each separation system with respect to sequence analysis are discussed.

Alignment of two DNA helices: a model for recognition of DNA base sequences by the termini-generating enzymes of phage lambda, 186, and P2

Based on the 3'- and 5'-terminal sequences of DNA of phage lambda, P2, and 186, a model is proposed for recognition of DNA sequences by enzymes responsible for generation of cohesive ends. Two copies of the cohered ends, either on separate molecules or on a concatemer, are aligned with their helical axes parallel but running in opposite directions. The nicking system is dimeric, with each of the two monomers carrying identical sequence-recognition sites. Two pairs of nicks are introduced into the two aligned DNA molecules by the nicking system. The applicability of this model to other biological processes, such as integration of a viral genome into a host genome and the cutting of concatemeric T7 DNA, is discussed.

The 3'-terminal nucleotide sequences of bacteriophage lambda DNA

Analyses of radioactive oligonucleotides in endonuclease digests of 3'-terminally labeled lambda DNA revealed the 3' terminal sequence -GTTACG for the l strand and -ACCCGCG for the r strand. These sequences, together with those previously known for the 5' cohesive ends, provide a total of 25 known base-pairs in the vicinity of the termini. When the cohesive ends are paired, the sequence between the nicks can be bisected by a 2-fold rotational axis of symmetry. Five of the first eight base-pairs, on either side of the axis, are rotationally symmetric. This symmetry may be involved in the recognition of the site by an enzyme responsible for formation of the cohesive ends.