Figure 3

RAM reaction process in detail. A) Three early steps in a RAM reaction. An elongating primary transcript (pt) is shown with forward-primer sub-sequences indicated by left-pointing arrows. Reverse primers (right-pointing arrows) are numbered in their binding order. Primer extension is shown as a broken line. A slanted broken line indicates displacement of an extended primer. The letter "i" indicates an "inert" product; inert products are not shown beyond the step in which they are created. B) Fates of reverse primers 2 and 3. The circular template and primary transcript are omitted for clarity. An asterisk at reverse primer 2 product, step 6, marks a structure similar to the reverse 3 primer structure marked with an asterisk in step 10. C) Accumulation of inert RAM reaction products. The initiating reverse primer of the indicated inert dsDNA product is numbered (left column). Inert products are represented by a bar; a triangle to the bar's left indicates a product initiated by a reverse primer; a triangle to the right indicates initiation by a forward primer. The step (Figure 3, A and B) at which the product was produced is shown by a parenthesized number to the right of the reverse primer 1-3 products. Columns to the right tally the RAM reaction products by reaction step and size. Reaction products are represented by dots in length-ordered columns. For each reaction step the sum of the products produced at the current and preceding step is shown to the right of a sigma summation symbol..