Do single nucleotides spontaneously bind to ss DNA? AT. GC. I realize the rhibisome is usually needed for making a strand, but what about randomly hbonded base pairs? Does this occur?

  • $\begingroup$ note that a binding might be thermally unstable; e.g.: assume 1-2 nucleotides in various approximations for annealing temperature of oligo-nucleotides such as jeltsch.org/annealing_temperature and note that annealing temperature would be very low, and potentially at a temperature where water is frozen $\endgroup$
    – tsttst
    Commented Nov 19, 2017 at 4:45
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    $\begingroup$ “I realize the rhibisome is usually needed for making a strand”. If this is indicative of your knowledge I suggest you do some homework by reading a book on molecular biology before asking questions of this type. An introductory section on basic chemistry would also not come amiss. $\endgroup$
    – David
    Commented Nov 19, 2017 at 21:41
  • $\begingroup$ Potentially, transiently. There’s an entropic penalty for a single nucleotide to bind a DNA strand which would not be offset by any enthalpic gain (if there is any). I’ve no idea where that equilibrium lies, but it’s probably far away from base pairing. $\endgroup$
    – canadianer
    Commented Nov 24, 2017 at 3:33

1 Answer 1


I am no expert on the topic, but single stranded DNA is commonly found during DNA replication, when DNA helicase splits apart the DNA strands so that the DNA can be replicated. When this occurs, the two DNA strands naturally have a high affinity for each other, bearing complementary base pair sequences, and another molecule must be present in order to prevent the two DNA strands from re-binding. These are single-stranded binding proteins, and they bind to ssDNA to prevent re-binding from occurring. As this prevents the DNA from binding to the antiparallel strand, I would imagine it has a role in preventing single DNA nucleotides from binding to the DNA strand as well.

  • $\begingroup$ Please reference your response! $\endgroup$ Commented Nov 24, 2017 at 8:02

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