# Color-Coded Hand and Finger and other tricks

I’m starting to play with ways to make the relationships between the nucleotides more apparent in the switch labs.

Here is an image with the two shapes for one submission:

And again with related NTs circled with the same color:

With all related groups colored it becomes hard to read. With just a couple of groups, it is easier to follow. For example, here is an image with just the dependencies related to NTs 18-22 colored in:

Another way to denote dependencies is to use lists of paired nodes. For example:

A!44+U!27+A58+U67+G18+C52

This means:
position 44 is fixed at A (pairs with 27),
position 27 is fixed at U (pairs with 44 and 58),
position 58 is assigned A (pairs with 27 and 67),
position 67 is assigned U (pairs with 58 and 18),
position 18 is assigned G (pairs with 67 and 52),
position 52 is assigned C (pairs with 18).

With this notation we can see possibilities for changes:

58 could possibly become G, forming two GU bonds instead of AU bonds;
if it did, 67 could possibly become C forming two GC bonds.
52 could possibly become U forming a GU bond;
if it did, 18 could possibly become A, forming two AU bonds.

Sometimes (especially at loop openings) it is important to note that pairs do NOT form as in:

A!26-C59+G66+C19+G51

Here we specify that the fixed A26 should *not* bond with the NT at 59. In this case we used C, but it might be possible to use G instead and invert the rest of the chain, giving:

A!26-G59+C66+G19+C51

And, when tested, that also works! So by using an appropriate notation, not only can we see how things are related, but what some other possibilities might be.

2 Likes

looks good

A more complete example of the notation:

• means the adjacent NTs should bond
• means the adjacent NTs should NOT bond
! means the NT is fixed
. means the NT is fixed by pairing (e.g. A!+U., C!+G.)

G6+C75+G10+U71-U14+A55+U30+A41
U7+A74+U11+A70
A8+U73+A12-A69
A9+U72+A13-A56+U29+A42
G15+C54+G31+C40+G!45
U16+G53-A32+U.39+A!46
A!44+U!27+A58+U67+G18+C52-A17-G53
A!26-C59+G66+C19+G51
A35-A50+U20+G65+C60
A!21+U.64
G!22+C63
C43+G28+C57+G68-A17
U33-U.38+A!47
C36+G!49
C37+G!48

(I THINK that captures all of the main dependencies in the foregoing example.)

Suggestions for “mutating” the sequence:

A can often be replaced by G; G can sometimes be replaced by A.
C can often be replaced by U; U can sometimes be replaced by C.
A sequence of A+U+… can often be inverted to U+A+…
A sequence of G+C+… can often be inverted to C+G+…
A sequence of A+U+G+C+… can sometimes be inverted to C+G+U+A+…

Like the approach very much. Working on an easier way to visually/graphically identify what I term ‘chains’ in [Switch] puzzles (what you call 'dependencies related to NT 18-22 'in your example above).

Interesting notation.

Nice suggestion - a bit too overwhelmingly colored en masse, but useful for short groups (as you already state)