23. The transcription factor X binds a 10 base pair DNA stretch. In the DNA of an organism, X was found to bind at 20 distinct sites. An analysis of these 20 binding sites showed the following distribution:

What is the consensus sequence for the binding site of X?

• (a) NGTCNNNTNN
• (b) AGTCACNTGC
• (c) CACCTANCTG
• (d) ANNNAACGNGC
  

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  Introduction

  Consensus sequences are widely used in bioinformatics and molecular biology to summarize conserved DNA motifs recognized by proteins such as transcription factors. This solved example explains how to extract a consensus sequence from a binding site table, interpret base frequencies, and analyze multiple-choice answers to select the correct DNA motif.

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  Question Recap

  A transcription factor X binds a 10-bp DNA stretch.
  Twenty binding sites were observed, and base frequencies at each position are given.

  We identify the most frequent nucleotide at every position to derive the consensus.

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  Step-by-Step Consensus Derivation

  Position	A	T	G	C	Consensus
  1	11	3	4	2	A
  2	0	0	20	0	G
  3	2	19	0	1	T
  4	0	0	0	20	C
  5	16	1	2	1	A
  6	2	3	4	11	C
  7	4	4	6	6 (tie)	Ambiguous (N or M)
  8	0	20	0	0	T
  9	4	2	12	2	G
  10	3	4	2	11	C

  At position 7, no base decisively dominates
  (C=6, G=6, A=4, T=4).
  That leads to ambiguity.
  Most exams assign N where no nucleotide clearly dominates.

  Final Consensus

  AGTCA C N T G C

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  Correct Answer

  ✔ (b) AGTCACNTGC

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  Option-by-Option Analysis

  (a) NGTCNNNTNN

  ❌ Incorrect

  • First base should be A, not N

  • Too many Ns inserted—data show clear single-base majorities at most positions

  (b) AGTCACNTGC

  ✔ Correct

  • Matches the majority base at 9 positions

  • Uses N at position 7 where no base strongly dominates

  • Exactly reflects the binding frequency table

  (c) CACCTANCTG

  ❌ Incorrect

  • Position 1 starts with C instead of A

  • Several other mismatches show it doesn’t follow the frequency distribution

  (d) ANNNACGNGC

  ❌ Incorrect

  • Replaces many clearly dominant positions with N

  • Data support strong consensus at most positions; only one should be ambiguous

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  Conclusion

  Interpreting nucleotide frequency tables is a fundamental bioinformatics skill. By selecting the most frequent base at each position and using N only for ambiguous positions, we derive the correct consensus sequence:

  ⭐ AGTCACNTGC

  This approach helps identify regulatory motifs in DNA, predict transcription factor binding sites, and analyze genetic control networks.